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From: <si...@us...> - 2011-06-07 15:48:39
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Revision: 4206
http://simupop.svn.sourceforge.net/simupop/?rev=4206&view=rev
Author: simupop
Date: 2011-06-07 15:48:29 +0000 (Tue, 07 Jun 2011)
Log Message:
-----------
Merge from openMP branch
Modified Paths:
--------------
trunk/src/initializer.cpp
trunk/src/mating.h
trunk/src/stator.cpp
trunk/src/utility.cpp
trunk/src/utility.h
trunk/test/performance.csv
trunk/test/performance.log
trunk/test/performance.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/openMP:3999-4176
+ /branches/openMP:3999-4205
Modified: trunk/src/initializer.cpp
===================================================================
--- trunk/src/initializer.cpp 2011-06-07 15:22:29 UTC (rev 4205)
+++ trunk/src/initializer.cpp 2011-06-07 15:48:29 UTC (rev 4206)
@@ -68,9 +68,18 @@
if (!m_sex.empty())
for (; ind.valid(); ++ind, ++idx)
ind->setSex(m_sex[idx % sexSz] == 1 ? MALE : FEMALE);
- else
- for (; ind.valid(); ++ind)
- ind->setSex(ws.draw() == 0 ? MALE : FEMALE);
+ else {
+ if (numThreads() > 1) {
+#pragma omp parallel private(ind)
+ {
+ ind = pop.indIterator(sp->subPop(), omp_get_thread_num());
+ for (; ind.valid(); ++ind)
+ ind->setSex(ws.draw() == 0 ? MALE : FEMALE);
+ }
+ } else
+ for (; ind.valid(); ++ind)
+ ind->setSex(ws.draw() == 0 ? MALE : FEMALE);
+ }
pop.deactivateVirtualSubPop(sp->subPop());
}
return true;
@@ -113,15 +122,31 @@
for (; sp != sp_end; ++sp) {
pop.activateVirtualSubPop(*sp);
- IndIterator ind = pop.indIterator(sp->subPop());
size_t numValues = m_values.size();
- for (; ind.valid(); ++ind, ++idx) {
- for (size_t i = 0; i < infoIdx.size(); ++i) {
- if (values.empty())
- ind->setInfo(m_values.func() (PyObj_As_Double, "()"), infoIdx[i]);
- else
- ind->setInfo(values[idx % numValues], infoIdx[i]);
+ if (numThreads() > 1 && !values.empty()) {
+#ifdef _OPENMP
+# pragma omp parallel firstprivate (idx)
+ {
+ size_t id = omp_get_thread_num();
+ IndIterator ind = pop.indIterator(sp->subPop(), id);
+ idx = idx + id * (pop.subPopSize(sp->subPop()) / numThreads());
+ for (; ind.valid(); ++ind, ++idx)
+ for (size_t i = 0; i < infoIdx.size(); ++i) {
+ ind->setInfo(values[idx % numValues], infoIdx[i]);
+ }
}
+ idx = idx + pop.subPopSize(sp->subPop());
+#endif
+ } else {
+ IndIterator ind = pop.indIterator(sp->subPop());
+ for (; ind.valid(); ++ind, ++idx) {
+ for (size_t i = 0; i < infoIdx.size(); ++i) {
+ if (values.empty())
+ ind->setInfo(m_values.func() (PyObj_As_Double, "()"), infoIdx[i]);
+ else
+ ind->setInfo(values[idx % numValues], infoIdx[i]);
+ }
+ }
}
pop.deactivateVirtualSubPop(sp->subPop());
}
@@ -205,11 +230,24 @@
// will go through virtual subpopulation if sp is virtual
pop.activateVirtualSubPop(*sp);
if (!m_genotype.empty()) {
- IndIterator it = pop.indIterator(sp->subPop());
- for (; it.valid(); ++it)
- for (vectoru::iterator p = ploidy.begin(); p != ploidy.end(); ++p)
- for (vectoru::const_iterator loc = loci.begin(); loc != loci.end(); ++loc, ++idx)
- it->setAllele(ToAllele(m_genotype[idx % sz]), *loc, static_cast<int>(*p));
+#pragma omp parallel firstprivate(idx) if(numThreads() > 1)
+ {
+#ifdef _OPENMP
+ size_t id = omp_get_thread_num();
+ IndIterator it = pop.indIterator(sp->subPop(), id);
+ idx = idx + id * (pop.subPopSize(sp->subPop()) / numThreads()) * (ploidy.end() - ploidy.begin()) * (loci.end() - loci.begin());
+#else
+ IndIterator it = pop.indIterator(sp->subPop());
+#endif
+ for (; it.valid(); ++it)
+ for (vectoru::iterator p = ploidy.begin(); p != ploidy.end(); ++p)
+ for (vectoru::const_iterator loc = loci.begin(); loc != loci.end(); ++loc, ++idx)
+ it->setAllele(ToAllele(m_genotype[idx % sz]), *loc, static_cast<int>(*p));
+
+ }
+#ifdef _OPENMP
+ idx = idx + pop.subPopSize(sp->subPop()) * (ploidy.end() - ploidy.begin()) * (loci.end() - loci.begin());
+#endif
} else if (!m_prop.empty()) {
WeightedSampler ws;
size_t sz = pop.subPopSize(*sp);
@@ -224,33 +262,47 @@
}
} else {
ws.set(m_prop.begin(), m_prop.end(), sz * ploidy.size());
+#pragma omp parallel if(numThreads() > 1)
+ {
+#ifdef _OPENMP
+ IndIterator it = pop.indIterator(sp->subPop(), omp_get_thread_num());
+#else
+ IndIterator it = pop.indIterator(sp->subPop());
+#endif
+ for (; it.valid(); ++it)
+ for (vectoru::iterator p = ploidy.begin(); p != ploidy.end(); ++p) {
+ const vectori & haplotype = m_haplotypes[ws.draw()];
+ size_t hapSz = haplotype.size();
+ size_t j = 0;
+ for (vectoru::const_iterator loc = loci.begin(); loc != loci.end(); ++loc, ++j)
+ it->setAllele(ToAllele(haplotype[j % hapSz]), *loc, static_cast<int>(*p));
+ }
+ }
+ }
+ } else {
+ // m_freq can be empty if ....
+ WeightedSampler ws(m_freq.empty() ? vectorf(m_haplotypes.size(), 1. / m_haplotypes.size()) : m_freq);
+#pragma omp parallel if(numThreads() > 1)
+ {
+#ifdef _OPENMP
+ IndIterator it = pop.indIterator(sp->subPop(), omp_get_thread_num());
+#else
IndIterator it = pop.indIterator(sp->subPop());
+#endif
for (; it.valid(); ++it)
for (vectoru::iterator p = ploidy.begin(); p != ploidy.end(); ++p) {
- const vectori & haplotype = m_haplotypes[ws.draw()];
- size_t hapSz = haplotype.size();
- size_t j = 0;
- for (vectoru::const_iterator loc = loci.begin(); loc != loci.end(); ++loc, ++j)
- it->setAllele(ToAllele(haplotype[j % hapSz]), *loc, static_cast<int>(*p));
+ if (m_haplotypes.empty()) {
+ for (vectoru::const_iterator loc = loci.begin(); loc != loci.end(); ++loc)
+ it->setAllele(ToAllele(ws.draw()), *loc, static_cast<int>(*p));
+ } else {
+ const vectori & haplotype = m_haplotypes[ws.draw()];
+ size_t hapSz = haplotype.size();
+ size_t j = 0;
+ for (vectoru::const_iterator loc = loci.begin(); loc != loci.end(); ++loc, ++j)
+ it->setAllele(ToAllele(haplotype[j % hapSz]), *loc, static_cast<int>(*p));
+ }
}
}
- } else {
- // m_freq can be empty if ....
- WeightedSampler ws(m_freq.empty() ? vectorf(m_haplotypes.size(), 1. / m_haplotypes.size()) : m_freq);
- IndIterator it = pop.indIterator(sp->subPop());
- for (; it.valid(); ++it)
- for (vectoru::iterator p = ploidy.begin(); p != ploidy.end(); ++p) {
- if (m_haplotypes.empty()) {
- for (vectoru::const_iterator loc = loci.begin(); loc != loci.end(); ++loc)
- it->setAllele(ToAllele(ws.draw()), *loc, static_cast<int>(*p));
- } else {
- const vectori & haplotype = m_haplotypes[ws.draw()];
- size_t hapSz = haplotype.size();
- size_t j = 0;
- for (vectoru::const_iterator loc = loci.begin(); loc != loci.end(); ++loc, ++j)
- it->setAllele(ToAllele(haplotype[j % hapSz]), *loc, static_cast<int>(*p));
- }
- }
}
pop.deactivateVirtualSubPop(sp->subPop());
}
Modified: trunk/src/mating.h
===================================================================
--- trunk/src/mating.h 2011-06-07 15:22:29 UTC (rev 4205)
+++ trunk/src/mating.h 2011-06-07 15:48:29 UTC (rev 4206)
@@ -1293,6 +1293,11 @@
return "<simuPOP.CombinedParentsChooser> chooses parents using two parent choosers";
}
+ /// CPPONLY
+ virtual bool parallelizable() const
+ {
+ return m_fatherChooser->parallelizable() && m_motherChooser->parallelizable();
+ }
/// CPPONLY
void initialize(Population & pop, size_t sp);
Modified: trunk/src/stator.cpp
===================================================================
--- trunk/src/stator.cpp 2011-06-07 15:22:29 UTC (rev 4205)
+++ trunk/src/stator.cpp 2011-06-07 15:48:29 UTC (rev 4206)
@@ -515,12 +515,19 @@
size_t totalCnt = 0;
pop.activateVirtualSubPop(*sp);
- IndIterator it = pop.indIterator(sp->subPop());
- for (; it.valid(); ++it)
- if (it->sex() == MALE)
- maleCnt++;
- else
- femaleCnt++;
+#pragma omp parallel reduction (+ : maleCnt,femaleCnt) if(numThreads() > 1)
+ {
+#ifdef _OPENMP
+ IndIterator it = pop.indIterator(sp->subPop(), omp_get_thread_num());
+#else
+ IndIterator it = pop.indIterator(sp->subPop());
+#endif
+ for (; it.valid(); ++it)
+ if (it->sex() == MALE)
+ maleCnt++;
+ else
+ femaleCnt++;
+ }
pop.deactivateVirtualSubPop(sp->subPop());
@@ -595,12 +602,19 @@
size_t totalCnt = 0;
pop.activateVirtualSubPop(*sp);
- IndIterator it = pop.indIterator(sp->subPop());
- for (; it.valid(); ++it)
- if (it->affected())
- affectedCnt++;
- else
- unaffectedCnt++;
+#pragma omp parallel reduction (+ : affectedCnt,unaffectedCnt) if(numThreads() > 1)
+ {
+#ifdef _OPENMP
+ IndIterator it = pop.indIterator(sp->subPop(), omp_get_thread_num());
+#else
+ IndIterator it = pop.indIterator(sp->subPop());
+#endif
+ for (; it.valid(); ++it)
+ if (it->affected())
+ affectedCnt++;
+ else
+ unaffectedCnt++;
+ }
pop.deactivateVirtualSubPop(sp->subPop());
@@ -688,7 +702,8 @@
pop.activateVirtualSubPop(*it);
- for (size_t idx = 0; idx < loci.size(); ++idx) {
+#pragma omp parallel for if(numThreads() > 1)
+ for (ssize_t idx = 0; idx < static_cast<ssize_t>(loci.size()); ++idx) {
size_t loc = loci[idx];
#ifdef LONGALLELE
@@ -726,13 +741,16 @@
allAllelesCnt[idx] += allAlleles;
// output variable.
#ifdef LONGALLELE
- if (m_vars.contains(AlleleNum_sp_String))
+ if (m_vars.contains(AlleleNum_sp_String)) {
+# pragma omp critical
pop.getVars().setVar(subPopVar_String(*it, AlleleNum_String) + m_suffix + "{" + toStr(loc) + "}", alleles);
+ }
if (m_vars.contains(AlleleFreq_sp_String)) {
intDict::iterator cnt = alleles.begin();
intDict::iterator cntEnd = alleles.end();
for ( ; cnt != cntEnd; ++cnt)
cnt->second /= static_cast<double>(allAlleles);
+# pragma omp critical
pop.getVars().setVar(subPopVar_String(*it, AlleleFreq_String) + m_suffix + "{" + toStr(loc) + "}", alleles);
}
#else
@@ -741,6 +759,7 @@
for (size_t i = 0; i < alleles.size(); ++i)
if (alleles[i] != 0)
d[i] = static_cast<double>(alleles[i]);
+# pragma omp critical
pop.getVars().setVar(subPopVar_String(*it, AlleleNum_String) + m_suffix + "{" + toStr(loc) + "}", d);
}
if (m_vars.contains(AlleleFreq_sp_String)) {
@@ -748,6 +767,7 @@
for (size_t i = 0; i < alleles.size(); ++i)
if (alleles[i] != 0)
d[i] = alleles[i] / static_cast<double>(allAlleles);
+# pragma omp critical
pop.getVars().setVar(subPopVar_String(*it, AlleleFreq_String) + m_suffix + "{" + toStr(loc) + "}", d);
}
#endif
@@ -850,7 +870,8 @@
uintDict heteroCnt;
uintDict homoCnt;
- for (size_t idx = 0; idx < loci.size(); ++idx) {
+#pragma omp parallel for if(numThreads() > 1)
+ for (ssize_t idx = 0; idx < static_cast<ssize_t>(loci.size()); ++idx) {
size_t loc = loci[idx];
#ifndef OPTIMIZED
@@ -869,11 +890,14 @@
else
homo += 1;
}
- heteroCnt[loc] = static_cast<double>(hetero);
- homoCnt[loc] = static_cast<double>(homo);
- //
- allHeteroCnt[loc] += heteroCnt[loc];
- allHomoCnt[loc] += homoCnt[loc];
+#pragma omp critical
+ {
+ heteroCnt[loc] = static_cast<double>(hetero);
+ homoCnt[loc] = static_cast<double>(homo);
+ //
+ allHeteroCnt[loc] += heteroCnt[loc];
+ allHomoCnt[loc] += homoCnt[loc];
+ }
}
pop.deactivateVirtualSubPop(it->subPop());
// output subpopulation variable?
@@ -981,7 +1005,8 @@
pop.activateVirtualSubPop(*it);
- for (size_t idx = 0; idx < loci.size(); ++idx) {
+#pragma omp parallel for if(numThreads() > 1)
+ for (ssize_t idx = 0; idx < static_cast<ssize_t>(loci.size()); ++idx) {
size_t loc = loci[idx];
tupleDict genotypes;
@@ -1022,9 +1047,11 @@
genotypeCnt[idx][dct->first] += dct->second;
allGenotypeCnt[idx] += allGenotypes;
// output variable.
- if (m_vars.contains(GenotypeNum_sp_String))
+ if (m_vars.contains(GenotypeNum_sp_String)) {
+#pragma omp critical
pop.getVars().setVar(subPopVar_String(*it, GenotypeNum_String)
+ m_suffix + "{" + toStr(loc) + "}", genotypes);
+ }
// note that genotyeps is changed in place.
if (m_vars.contains(GenotypeFreq_sp_String)) {
if (allGenotypes != 0) {
@@ -1033,6 +1060,7 @@
for (; dct != dctEnd; ++dct)
dct->second /= allGenotypes;
}
+#pragma omp critical
pop.getVars().setVar(subPopVar_String(*it, GenotypeFreq_String)
+ m_suffix + "{" + toStr(loc) + "}", genotypes);
}
@@ -1128,7 +1156,8 @@
pop.activateVirtualSubPop(*it);
- for (size_t idx = 0; idx < m_loci.size(); ++idx) {
+#pragma omp parallel for if(numThreads() > 1)
+ for (ssize_t idx = 0; idx < static_cast<ssize_t>(m_loci.size()); ++idx) {
const vectori & loci = m_loci[idx];
size_t nLoci = loci.size();
if (nLoci == 0)
@@ -1171,9 +1200,11 @@
haplotypeCnt[idx][dct->first] += dct->second;
allHaplotypeCnt[idx] += allHaplotypes;
// output variable.
- if (m_vars.contains(HaplotypeNum_sp_String))
+ if (m_vars.contains(HaplotypeNum_sp_String)) {
+#pragma omp critical
pop.getVars().setVar(subPopVar_String(*it, HaplotypeNum_String) + m_suffix + "{"
+ key + "}", haplotypes);
+ }
// note that genotyeps is changed in place.
if (m_vars.contains(HaplotypeFreq_sp_String)) {
if (allHaplotypes != 0) {
@@ -1182,6 +1213,7 @@
for (; dct != dctEnd; ++dct)
dct->second /= allHaplotypes;
}
+#pragma omp critical
pop.getVars().setVar(subPopVar_String(*it, HaplotypeFreq_String) + m_suffix + "{"
+ key + "}", haplotypes);
}
@@ -1284,7 +1316,8 @@
tupleDict heteroCnt;
tupleDict homoCnt;
- for (size_t idx = 0; idx < m_loci.size(); ++idx) {
+#pragma omp parallel for if(numThreads() > 1)
+ for (ssize_t idx = 0; idx < static_cast<ssize_t>(m_loci.size()); ++idx) {
const vectori & loci = m_loci[idx];
size_t nLoci = loci.size();
if (nLoci == 0)
@@ -1318,11 +1351,14 @@
else
++homo;
}
- heteroCnt[loci] = static_cast<double>(hetero);
- homoCnt[loci] = static_cast<double>(homo);
+#pragma omp critical
+ {
+ heteroCnt[loci] = static_cast<double>(hetero);
+ homoCnt[loci] = static_cast<double>(homo);
- allHeteroCnt[loci] += hetero;
- allHomoCnt[loci] += homo;
+ allHeteroCnt[loci] += hetero;
+ allHomoCnt[loci] += homo;
+ }
}
pop.deactivateVirtualSubPop(it->subPop());
// output subpopulation variable?
@@ -2426,19 +2462,43 @@
double diffCnt = 0;
int numComparison = 0;
- HAPLOLIST::const_iterator it = begin;
+ size_t size = end - begin;
+ size_t nThreads = numThreads();
- for (; it != end; ++it) {
- HAPLOLIST::const_iterator it1 = it;
- for (++it1; it1 != end; ++it1) {
- const vectora & seq1 = *it;
- const vectora & seq2 = *it1;
- size_t sz = seq1.size();
- for (size_t i = 0; i < sz; ++i)
- diffCnt += seq1[i] != seq2[i];
- ++numComparison;
+ if (nThreads > 1)
+#ifdef _OPENMP
+# pragma omp parallel reduction(+ : diffCnt, numComparison)
+ {
+ size_t id = omp_get_thread_num();
+ HAPLOLIST::const_iterator it = begin + id * (size / nThreads);
+ HAPLOLIST::const_iterator itEnd = id == nThreads - 1 ? end : it + (size / nThreads);
+ for (; it != itEnd; ++it) {
+ HAPLOLIST::const_iterator it1 = it;
+ for (++it1; it1 != end; ++it1) {
+ const vectora & seq1 = *it;
+ const vectora & seq2 = *it1;
+ size_t sz = seq1.size();
+ for (size_t i = 0; i < sz; ++i)
+ diffCnt += seq1[i] != seq2[i];
+ ++numComparison;
+ }
}
}
+#endif
+ else {
+ HAPLOLIST::const_iterator it = begin;
+ for (; it != end; ++it) {
+ HAPLOLIST::const_iterator it1 = it;
+ for (++it1; it1 != end; ++it1) {
+ const vectora & seq1 = *it;
+ const vectora & seq2 = *it1;
+ size_t sz = seq1.size();
+ for (size_t i = 0; i < sz; ++i)
+ diffCnt += seq1[i] != seq2[i];
+ ++numComparison;
+ }
+ }
+ }
// return 0 if there is only one sequence
return numComparison == 0 ? 0 : diffCnt / numComparison;
}
Modified: trunk/src/utility.cpp
===================================================================
--- trunk/src/utility.cpp 2011-06-07 15:22:29 UTC (rev 4205)
+++ trunk/src/utility.cpp 2011-06-07 15:48:29 UTC (rev 4206)
@@ -492,17 +492,20 @@
ATOMICLONG fetchAndIncrement(ATOMICLONG * val)
{
+ if(g_numThreads == 1)
+ return (*val)++;
+ else
#ifdef _WIN64
- return InterlockedIncrement64(val) - 1;
+ return InterlockedIncrement64(val) - 1;
#elif defined(_WIN32)
- return InterlockedIncrement(val) - 1;
+ return InterlockedIncrement(val) - 1;
#else
// for Intel C++, see page 164 of
// http://softwarecommunity.intel.com/isn/downloads/softwareproducts/pdfs/347603.pdf
//
// for gcc, see
// http://gcc.gnu.org/onlinedocs/gcc-4.1.0/gcc/Atomic-Builtins.html
- return __sync_fetch_and_add(val, 1);
+ return __sync_fetch_and_add(val, 1);
#endif
}
@@ -3569,6 +3572,9 @@
{
DBG_FAILIF(m_algorithm == 0, ValueError,
"weighted sample is not initialized");
+#ifdef _OPENMP
+ ATOMICLONG index = 0;
+#endif
switch (m_algorithm) {
case 1:
@@ -3593,7 +3599,13 @@
// return according to proportion.
if (m_index == m_sequence.size())
m_index = 0;
+#ifdef _OPENMP
+ index = fetchAndIncrement(&m_index);
+ return m_sequence[index];
+#else
+
return m_sequence[m_index++];
+#endif
default:
throw RuntimeError("Invalid weighted sampler (empty weight?)");
}
Modified: trunk/src/utility.h
===================================================================
--- trunk/src/utility.h 2011-06-07 15:22:29 UTC (rev 4205)
+++ trunk/src/utility.h 2011-06-07 15:48:29 UTC (rev 4206)
@@ -1920,7 +1920,7 @@
///
vectoru m_sequence;
- ULONG m_index;
+ ATOMICLONG m_index;
};
Modified: trunk/test/performance.csv
===================================================================
--- trunk/test/performance.csv 2011-06-07 15:22:29 UTC (rev 4205)
+++ trunk/test/performance.csv 2011-06-07 15:48:29 UTC (rev 4206)
@@ -325,3 +325,126 @@
TestInheritTagger, 2011-05-18 17:01:51,673, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4173-intel, short, 26678, 2174, 23119, 1588, 677, 64
TestInheritTagger, 2011-05-18 17:04:27,692, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4173-intel, long, 25909, 1801, 15852, 1144, 179, 0
TestInheritTagger, 2011-05-18 17:07:35,036, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4173-intel, binary, 22938, 2168, 24949, 2026, 4616, 398
+TestStatAlleleFreq, 2011-05-25 14:16:24,057, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, short, 0.642503023148, 7.59624409676, 6.07503390312, 9.04420208931, 228.846941948, 89.078854084
+TestStatAlleleFreq, 2011-05-25 14:23:30,764, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, long, 1.01851701736, 17.1053318977, 10.8354318142, 12.6472120285, 240.113608122, 126.978461027
+TestStatAlleleFreq, 2011-05-25 14:28:33,636, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, binary, 1.08484101295, 10.7368938923, 10.8209798336, 11.4512810707, 132.637831926, 111.818598986
+TestStatAlleleFreq, 2011-05-25 14:30:39,283, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, short, 0.173316955566, 2.43554115295, 1.73279309273, 3.60566401482, 62.5272729397, 36.6046230793
+TestStatAlleleFreq, 2011-05-25 14:33:25,358, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, long, 0.287755966187, 4.98926496506, 3.02955412865, 6.11895489693, 71.2390468121, 61.2199239731
+TestStatAlleleFreq, 2011-05-25 14:35:07,703, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, binary, 0.307837963104, 3.0087928772, 3.05822300911, 3.17401409149, 36.7387290001, 31.7028801441
+TestStatNumOfMales, 2011-05-26 09:55:10,511, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, short, 16.8653411865, 17.209662199
+TestStatNumOfMales, 2011-05-26 09:55:46,138, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, long, 16.4387378693, 17.3230619431
+TestStatNumOfMales, 2011-05-26 09:56:23,810, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, binary, 17.4795110226, 17.6907908916
+TestStatNumOfMales, 2011-05-26 09:56:46,249, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, short, 9.28081488609, 10.3006439209
+TestStatNumOfMales, 2011-05-26 09:57:08,449, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, long, 9.30121707916, 10.2057070732
+TestStatNumOfMales, 2011-05-26 09:57:32,400, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, binary, 10.1437051296, 10.6698708534
+TestStatNumOfAffected, 2011-05-26 09:58:13,138, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, short, 18.7245531082, 19.554336071
+TestStatNumOfAffected, 2011-05-26 09:58:54,166, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, long, 18.9747388363, 19.5944628716
+TestStatNumOfAffected, 2011-05-26 09:59:36,526, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, binary, 19.5599150658, 20.22062397
+TestStatNumOfAffected, 2011-05-26 09:59:58,940, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, short, 9.38937807083, 10.0877468586
+TestStatNumOfAffected, 2011-05-26 10:00:20,933, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, long, 9.50907111168, 10.3536448479
+TestStatNumOfAffected, 2011-05-26 10:00:44,755, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, binary, 10.2223381996, 11.0147790909
+TestStatHaploFreq, 2011-05-26 10:21:44,402, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, short, 1.23293209076, 12.2021050453, 11.865776062, 1.29735088348, 21.6016001701, 15.2668449879
+TestStatHaploFreq, 2011-05-26 10:23:30,689, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, long, 1.41531896591, 23.2550559044, 17.4902069569, 1.51551508904, 25.3949120045, 16.8971569538
+TestStatHaploFreq, 2011-05-26 10:25:10,205, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, binary, 1.69325518608, 17.1936631203, 18.6411919594, 1.70309305191, 17.4465510845, 18.0900690556
+TestStatHaploFreq, 2011-05-26 10:26:01,853, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, short, 0.566158056259, 5.73171782494, 5.61322593689, 0.713933944702, 9.37162017822, 7.79208993912
+TestStatHaploFreq, 2011-05-26 10:26:56,395, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, long, 0.613075971603, 9.36668801308, 7.58966112137, 0.720818042755, 9.74222493172, 7.8867251873
+TestStatHaploFreq, 2011-05-26 10:27:52,943, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, binary, 0.768512964249, 7.49124717712, 7.55833601952, 0.781599998474, 7.85499882698, 7.7969429493
+TestStatHaploHomoFreq, 2011-05-26 10:28:28,350, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, short, 0.292308092117, 3.24175906181, 2.92852807045, 0.337744951248, 6.22854995728, 3.89006996155
+TestStatHaploHomoFreq, 2011-05-26 10:29:08,609, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, long, 0.31462597847, 5.88319706917, 3.6914870739, 0.325666904449, 7.17342495918, 4.69271183014
+TestStatHaploHomoFreq, 2011-05-26 10:29:59,679, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, binary, 0.631763935089, 6.12271213531, 6.13581681252, 0.631522893906, 6.96468997002, 6.4281539917
+TestStatHaploHomoFreq, 2011-05-26 10:30:26,105, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, short, 0.139616966248, 1.46904397011, 1.41087889671, 0.158464193344, 2.5026910305, 1.93978285789
+TestStatHaploHomoFreq, 2011-05-26 10:30:53,443, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, long, 0.147619009018, 2.38445401192, 1.86939907074, 0.15052485466, 2.83502817154, 2.09009408951
+TestStatHaploHomoFreq, 2011-05-26 10:31:30,481, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, binary, 0.287275075912, 2.73110985756, 2.7528860569, 0.292492866516, 3.02533006668, 2.91801309586
+TestStatGenoFreq, 2011-05-26 11:09:33,398, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, short, 0.460355997086, 4.32857394218, 4.52319002151, 0.482565879822, 6.7190079689, 6.86939692497
+TestStatGenoFreq, 2011-05-26 11:10:21,683, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, long, 0.500542163849, 6.76568007469, 6.89576387405, 0.500433206558, 7.35019493103, 7.48760890961
+TestStatGenoFreq, 2011-05-26 11:11:10,292, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, binary, 0.590523004532, 5.49827694893, 5.5768828392, 0.637578964233, 6.14054203033, 6.18443202972
+TestStatGenoFreq, 2011-05-26 11:14:14,234, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, short, 1.43687391281, 14.7355120182, 14.2837300301, 1.52868509293, 24.1452269554, 17.648113966
+TestStatGenoFreq, 2011-05-26 11:16:09,379, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, long, 1.64711523056, 25.8571681976, 18.9256169796, 1.66001415253, 28.0234498978, 19.0963768959
+TestStatGenoFreq, 2011-05-26 11:17:55,313, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4182-intel, binary, 1.89334607124, 18.6318368912, 18.7467119694, 1.92588806152, 21.1599271297, 19.6372129917
+TestStatHeteroFreq, 2011-05-26 13:08:13,920, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4184-intel, short, 0.441030979156, 5.07090187073, 4.35444688797, 5.11432695389, 117.634579182, 51.200012207
+TestStatHeteroFreq, 2011-05-26 13:12:40,530, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4184-intel, long, 0.556185007095, 9.46308708191, 5.34688615799, 6.48223590851, 162.691661835, 63.0534501076
+TestStatHeteroFreq, 2011-05-26 13:16:29,162, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4184-intel, binary, 0.831079959869, 8.2782459259, 8.30177307129, 8.63011312485, 93.6239349842, 84.6393620968
+TestStatHeteroFreq, 2011-05-26 13:18:27,983, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4184-intel, short, 0.127473115921, 1.61057591438, 1.26040196419, 1.40715408325, 33.8272380829, 13.8213179111
+TestStatHeteroFreq, 2011-05-26 13:19:57,092, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4184-intel, long, 0.136440992355, 2.69143199921, 1.42887401581, 1.70447492599, 45.7699849606, 17.6911768913
+TestStatHeteroFreq, 2011-05-26 13:21:18,570, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4184-intel, binary, 0.234434127808, 2.50543117523, 2.3329770565, 2.43857598305, 26.4068300724, 23.9802000523
+TestStatNeutrality, 2011-05-27 12:07:40,930, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4187-intel, short, 9.03047394753, 8.99528694153, 27.8919439316, 27.8793339729, 162.322354078, 161.907181978
+TestStatNeutrality, 2011-05-27 12:12:47,358, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4187-intel, long, 11.8714928627, 11.7830820084, 30.3244822025, 30.1393539906, 109.87086916, 111.744431973
+TestStatNeutrality, 2011-05-27 12:36:43,441, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4187-intel, binary, 38.0854780674, 38.7297050953, 84.4918601513, 84.3150889874, 597.092149973, 592.624132156
+TestStatNeutrality, 2011-05-27 12:47:16,722, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4187-intel, short, 3.13563299179, 3.20556497574, 27.0847280025, 27.1585049629, 267.419605017, 268.027008057
+TestStatNeutrality, 2011-05-27 12:57:26,253, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4187-intel, long, 3.10889577866, 3.15888404846, 26.967279911, 26.9330770969, 273.505503893, 275.049628019
+TestStatNeutrality, 2011-05-27 13:07:35,760, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4187-intel, binary, 8.32187199593, 8.2234890461, 32.0274319649, 31.5282058716, 265.823650122, 262.824134827
+TestStatAlleleFreq, 2011-05-30 22:36:02,049, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, short, 0.156656771779, 1.27655273963, 0.772660287815, 2.37574158829, 61.8670897501, 22.9204747493
+TestStatHaploFreq, 2011-05-30 22:36:39,930, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, short, 0.516961671952, 5.07994453068, 5.05862403715, 0.543532975813, 8.80322124159, 6.99310467028
+TestStatHaploHomoFreq, 2011-05-30 22:36:56,315, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, short, 0.089213063666, 1.02716445375, 0.939058905066, 0.101590728388, 1.95475398316, 1.38428928569
+TestStatNeutrality, 2011-05-30 22:40:04,670, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, short, 1.63284142643, 1.61529354731, 9.36116640133, 9.26592282954, 82.7843907702, 83.5741105317
+TestStatNumOfAffected, 2011-05-30 22:40:32,180, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, short, 12.5538024681, 14.0043555011
+TestStatNumOfMales, 2011-05-30 22:40:59,032, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, short, 12.1569785518, 13.7430625612
+TestStatAlleleFreq, 2011-05-30 22:42:50,881, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, long, 0.220509281815, 4.18473675917, 2.32420848449, 2.93125649371, 61.5509994198, 30.0181917411
+TestStatHaploFreq, 2011-05-30 22:43:34,875, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, long, 0.526113989825, 8.50943485645, 6.82598914158, 0.549702036511, 9.71940961513, 7.44523822892
+TestStatHaploHomoFreq, 2011-05-30 22:43:52,589, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, long, 0.0952381383606, 1.640990672, 1.33187294699, 0.116611155082, 2.41424260042, 1.69099849011
+TestStatNeutrality, 2011-05-30 22:47:03,999, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, long, 1.76370840329, 1.7402884912, 9.68770733834, 9.7137196022, 83.7511417758, 84.6337454895
+TestStatNumOfAffected, 2011-05-30 22:47:31,562, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, long, 12.5345379257, 14.0830832444
+TestStatNumOfMales, 2011-05-30 22:47:58,328, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, long, 12.1148138958, 13.7313332862
+TestStatAlleleFreq, 2011-05-30 22:48:56,724, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, binary, 0.12388803262, 1.45832435307, 1.32294249434, 1.57181067984, 23.3392189499, 15.4070457151
+TestStatHaploFreq, 2011-05-30 22:49:38,438, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, binary, 0.635344730263, 6.14874750288, 6.11202654414, 0.643167969785, 6.50306445683, 6.59007939455
+TestStatHaploHomoFreq, 2011-05-30 22:50:02,937, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, binary, 0.188049342826, 1.7590105958, 1.80983161788, 0.201168973159, 2.93850409107, 2.4963571843
+TestStatNeutrality, 2011-05-30 23:03:11,364, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, binary, 11.648486698, 11.7215078263, 40.8976600614, 40.9682174291, 341.107198032, 341.91136288
+TestStatNumOfAffected, 2011-05-30 23:03:39,740, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, binary, 12.6815394851, 14.3641107189
+TestStatNumOfMales, 2011-05-30 23:04:07,559, BoPeng-PC, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4188-vc, binary, 12.2875931758, 14.2055386616
+TestStatNeutrality, 2011-05-31 11:04:27,264, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4189-intel, short, 6.89465403557, 6.83319497108, 59.4530448914, 58.7852652073, 582.544010878, 575.242040157
+TestStatNeutrality, 2011-05-31 11:26:06,905, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4189-intel, long, 6.49560403824, 6.46290183067, 58.2610440254, 58.1104929447, 580.978451014, 588.665710926
+TestStatNeutrality, 2011-05-31 11:47:47,179, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4189-intel, binary, 17.2013239861, 17.1441349983, 66.1994318962, 66.1883180141, 564.6483531, 568.191828012
+TestCombinedParentsChooser, 2011-05-31 12:24:18,072, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4190-intel, short, 16601, 1443, 15558, 1021, 715, 55
+TestCombinedParentsChooser, 2011-05-31 12:26:53,397, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4190-intel, long, 17644, 1233, 9825, 804, 183, 0
+TestCombinedParentsChooser, 2011-05-31 12:30:00,590, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4190-intel, binary, 12489, 1132, 13914, 1176, 3589, 338
+TestCombinedParentsChooser, 2011-05-31 12:36:04,961, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4190-intel, short, 52566, 4674, 48309, 3269, 788, 70
+TestCombinedParentsChooser, 2011-05-31 12:38:40,375, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4190-intel, long, 52725, 4021, 19461, 1602, 205, 0
+TestCombinedParentsChooser, 2011-05-31 12:41:47,862, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4190-intel, binary, 36988, 3779, 43414, 3928, 6050, 554
+TestStatNeutrality, 2011-06-01 12:19:12,461, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4191-intel, short, 5.57430195808, 5.54049086571, 23.4916911125, 23.5364370346, 157.407531977, 157.336145878
+TestStatNeutrality, 2011-06-01 12:23:30,558, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4191-intel, long, 6.09040188789, 5.92418003082, 19.0062968731, 19.4905800819, 103.946276903, 102.977053881
+TestStatNeutrality, 2011-06-01 12:45:16,569, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4191-intel, binary, 17.0345540047, 17.1601970196, 66.7122030258, 66.5635910034, 569.442780972, 568.384868145
+TestStatNeutrality, 2011-06-01 13:15:52,983, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4191-intel, short, 3.03625702858, 3.06062293053, 26.9129579067, 26.9386310577, 266.358695984, 268.104444981
+TestStatNeutrality, 2011-06-01 13:25:52,287, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4191-intel, long, 3.10122394562, 3.10917305946, 26.9314918518, 26.8245511055, 270.068092108, 268.488473892
+TestStatNeutrality, 2011-06-01 13:35:54,684, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4191-intel, binary, 7.92105603218, 7.99158787727, 30.9572019577, 31.2986159325, 261.169814825, 262.290413141
+TestHeteroMating, 2011-06-02 13:03:44,077, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4192-intel, short, 9574, 799, 8610, 645, 680, 1
+TestHeteroMating, 2011-06-02 13:06:20,597, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4192-intel, long, 9322, 706, 6626, 529, 182, 0
+TestHeteroMating, 2011-06-02 13:09:28,174, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4192-intel, binary, 8048, 740, 8468, 711, 2888, 256
+TestHeteroMating, 2011-06-02 13:12:52,461, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4192-intel, short, 20484, 1388, 11540, 1498, 804, 44
+TestHeteroMating, 2011-06-02 13:15:30,025, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4192-intel, long, 19089, 1637, 15357, 1357, 198, 0
+TestHeteroMating, 2011-06-02 13:18:36,396, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4192-intel, binary, 17963, 1668, 19806, 1729, 5586, 532
+TestInitGenotypeCase1, 2011-06-03 10:03:58,047, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, short, 20.0126931667, 20.2507748604
+TestInitGenotypeCase1, 2011-06-03 10:04:48,348, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, long, 20.1913919449, 20.4295210838
+TestInitGenotypeCase1, 2011-06-03 10:06:18,425, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, binary, 44.585860014, 44.6598989964
+TestInitGenotypeCase1, 2011-06-03 10:06:31,379, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, short, 5.68694496155, 5.69882082939
+TestInitGenotypeCase1, 2011-06-03 10:06:44,668, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, long, 5.97290492058, 6.30002713203
+TestInitGenotypeCase1, 2011-06-03 10:07:10,443, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, binary, 12.9159140587, 12.3552010059
+TestInitGenotypeCase2, 2011-06-03 10:11:05,127, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, short, 128.611124992, 104.630683184
+TestInitGenotypeCase2, 2011-06-03 10:15:02,793, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, long, 128.964793921, 107.590738058
+TestInitGenotypeCase2, 2011-06-03 10:19:13,348, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, binary, 133.749624968, 116.280220985
+TestInitGenotypeCase2, 2011-06-03 10:23:46,829, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, short, 136.778111935, 135.20889616
+TestInitGenotypeCase2, 2011-06-03 10:28:20,802, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, long, 137.331019163, 133.9238801
+TestInitGenotypeCase2, 2011-06-03 10:32:49,232, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, binary, 135.631910086, 132.102210045
+TestInitGenotypeCase3, 2011-06-03 10:33:32,227, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, short, 20.7163860798, 20.7371339798
+TestInitGenotypeCase3, 2011-06-03 10:34:15,306, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, long, 21.2412390709, 21.0875110626
+TestInitGenotypeCase3, 2011-06-03 10:35:50,274, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, binary, 47.2954690456, 47.1605689526
+TestInitGenotypeCase3, 2011-06-03 10:36:02,968, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, short, 5.51451182365, 5.6633439064
+TestInitGenotypeCase3, 2011-06-03 10:36:15,091, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, long, 5.6491651535, 5.6448340416
+TestInitGenotypeCase3, 2011-06-03 10:36:38,723, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, binary, 11.493434906, 11.7346558571
+TestInitGenotypeCase4, 2011-06-03 10:39:15,629, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, short, 77.3453309536, 78.1487438679
+TestInitGenotypeCase4, 2011-06-03 10:41:55,561, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, long, 79.8385441303, 79.1435091496
+TestInitGenotypeCase4, 2011-06-03 10:45:27,401, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, binary, 105.690921068, 105.673449993
+TestInitGenotypeCase4, 2011-06-03 10:46:12,888, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, short, 21.8644630909, 22.1283450127
+TestInitGenotypeCase4, 2011-06-03 10:46:58,953, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, long, 22.5271499157, 22.7279741764
+TestInitGenotypeCase4, 2011-06-03 10:47:59,678, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4195-intel, binary, 29.9604380131, 30.151968956
+TestInitSex, 2011-06-06 10:22:20,721, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4197-intel, short, 14.3448200226, 14.728511095
+TestInitSex, 2011-06-06 10:22:54,606, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4197-intel, long, 14.6376848221, 14.6885848045
+TestInitSex, 2011-06-06 10:23:23,739, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4197-intel, binary, 14.1411120892, 14.4127311707
+TestInitSex, 2011-06-06 10:26:24,857, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4197-intel, short, 4.17382383347, 4.48227882385
+TestInitSex, 2011-06-06 10:26:38,022, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4197-intel, long, 4.08154797554, 4.58521986008
+TestInitSex, 2011-06-06 10:26:48,164, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4197-intel, binary, 4.46001601219, 5.02257704735
+TestInitSex, 2011-06-06 15:38:55,266, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4200-intel, short, 46.7628421783, 46.9360320568
+TestInitSex, 2011-06-06 15:40:50,926, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4200-intel, long, 47.1968901157, 47.7802641392
+TestInitSex, 2011-06-06 15:42:28,424, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4200-intel, binary, 47.520539999, 47.8896892071
+TestInitSex, 2011-06-06 15:43:11,943, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4200-intel, short, 13.1370029449, 13.5422229767
+TestInitSex, 2011-06-06 15:43:59,207, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4200-intel, long, 13.7384490967, 15.3715240955
+TestInitSex, 2011-06-06 15:44:27,405, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4200-intel, binary, 12.9587409496, 13.3092448711
Modified: trunk/test/performance.log
===================================================================
--- trunk/test/performance.log 2011-06-07 15:22:29 UTC (rev 4205)
+++ trunk/test/performance.log 2011-06-07 15:48:29 UTC (rev 4206)
@@ -5192,3 +5192,1401 @@
TestInheritTagger : loci=10000, size=100000: 398
TestInheritTagger : 22938, 2168, 24949, 2026, 4616, 398
TestInheritTagger : End of test TestInheritTagger
+TestStatAlleleFreq : Host: bp9 (Linux, x86_64, x86_64)
+TestStatAlleleFreq : Time: Wed May 25 14:10:25 2011
+TestStatAlleleFreq : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatAlleleFreq : simuPOP: 1.0.6svn (rev 4182, module short, optimized, 1 threads)
+TestStatAlleleFreq : Test: Stat AlleleFreq, results are time (not processor time) to apply operator for 30 times.
+TestStatAlleleFreq : loci=100, size=10000: 0.642503023148
+TestStatAlleleFreq : loci=100, size=100000: 7.59624409676
+TestStatAlleleFreq : loci=100, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 6.07503390312
+TestStatAlleleFreq : loci=1000, size=10000: 9.04420208931
+TestStatAlleleFreq : loci=1000, size=100000: 228.846941948
+TestStatAlleleFreq : loci=1000, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 89.078854084
+TestStatAlleleFreq : 0.642503023148, 7.59624409676, 6.07503390312, 9.04420208931, 228.846941948, 89.078854084
+TestStatAlleleFreq : End of test TestStatAlleleFreq
+TestStatAlleleFreq : Host: bp9 (Linux, x86_64, x86_64)
+TestStatAlleleFreq : Time: Wed May 25 14:16:25 2011
+TestStatAlleleFreq : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatAlleleFreq : simuPOP: 1.0.6svn (rev 4182, module long, optimized, 1 threads)
+TestStatAlleleFreq : Test: Stat AlleleFreq, results are time (not processor time) to apply operator for 30 times.
+TestStatAlleleFreq : loci=100, size=10000: 1.01851701736
+TestStatAlleleFreq : loci=100, size=100000: 17.1053318977
+TestStatAlleleFreq : loci=100, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 10.8354318142
+TestStatAlleleFreq : loci=1000, size=10000: 12.6472120285
+TestStatAlleleFreq : loci=1000, size=100000: 240.113608122
+TestStatAlleleFreq : loci=1000, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 126.978461027
+TestStatAlleleFreq : 1.01851701736, 17.1053318977, 10.8354318142, 12.6472120285, 240.113608122, 126.978461027
+TestStatAlleleFreq : End of test TestStatAlleleFreq
+TestStatAlleleFreq : Host: bp9 (Linux, x86_64, x86_64)
+TestStatAlleleFreq : Time: Wed May 25 14:23:31 2011
+TestStatAlleleFreq : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatAlleleFreq : simuPOP: 1.0.6svn (rev 4182, module binary, optimized, 1 threads)
+TestStatAlleleFreq : Test: Stat AlleleFreq, results are time (not processor time) to apply operator for 30 times.
+TestStatAlleleFreq : loci=100, size=10000: 1.08484101295
+TestStatAlleleFreq : loci=100, size=100000: 10.7368938923
+TestStatAlleleFreq : loci=100, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 10.8209798336
+TestStatAlleleFreq : loci=1000, size=10000: 11.4512810707
+TestStatAlleleFreq : loci=1000, size=100000: 132.637831926
+TestStatAlleleFreq : loci=1000, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 111.818598986
+TestStatAlleleFreq : 1.08484101295, 10.7368938923, 10.8209798336, 11.4512810707, 132.637831926, 111.818598986
+TestStatAlleleFreq : End of test TestStatAlleleFreq
+TestStatAlleleFreq : Host: bp9 (Linux, x86_64, x86_64)
+TestStatAlleleFreq : Time: Wed May 25 14:28:34 2011
+TestStatAlleleFreq : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatAlleleFreq : simuPOP: 1.0.6svn (rev 4182, module short, optimized, 4 threads)
+TestStatAlleleFreq : Test: Stat AlleleFreq, results are time (not processor time) to apply operator for 30 times.
+TestStatAlleleFreq : loci=100, size=10000: 0.173316955566
+TestStatAlleleFreq : loci=100, size=100000: 2.43554115295
+TestStatAlleleFreq : loci=100, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 1.73279309273
+TestStatAlleleFreq : loci=1000, size=10000: 3.60566401482
+TestStatAlleleFreq : loci=1000, size=100000: 62.5272729397
+TestStatAlleleFreq : loci=1000, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 36.6046230793
+TestStatAlleleFreq : 0.173316955566, 2.43554115295, 1.73279309273, 3.60566401482, 62.5272729397, 36.6046230793
+TestStatAlleleFreq : End of test TestStatAlleleFreq
+TestStatAlleleFreq : Host: bp9 (Linux, x86_64, x86_64)
+TestStatAlleleFreq : Time: Wed May 25 14:30:40 2011
+TestStatAlleleFreq : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatAlleleFreq : simuPOP: 1.0.6svn (rev 4182, module long, optimized, 4 threads)
+TestStatAlleleFreq : Test: Stat AlleleFreq, results are time (not processor time) to apply operator for 30 times.
+TestStatAlleleFreq : loci=100, size=10000: 0.287755966187
+TestStatAlleleFreq : loci=100, size=100000: 4.98926496506
+TestStatAlleleFreq : loci=100, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 3.02955412865
+TestStatAlleleFreq : loci=1000, size=10000: 6.11895489693
+TestStatAlleleFreq : loci=1000, size=100000: 71.2390468121
+TestStatAlleleFreq : loci=1000, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 61.2199239731
+TestStatAlleleFreq : 0.287755966187, 4.98926496506, 3.02955412865, 6.11895489693, 71.2390468121, 61.2199239731
+TestStatAlleleFreq : End of test TestStatAlleleFreq
+TestStatAlleleFreq : Host: bp9 (Linux, x86_64, x86_64)
+TestStatAlleleFreq : Time: Wed May 25 14:33:25 2011
+TestStatAlleleFreq : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatAlleleFreq : simuPOP: 1.0.6svn (rev 4182, module binary, optimized, 4 threads)
+TestStatAlleleFreq : Test: Stat AlleleFreq, results are time (not processor time) to apply operator for 30 times.
+TestStatAlleleFreq : loci=100, size=10000: 0.307837963104
+TestStatAlleleFreq : loci=100, size=100000: 3.0087928772
+TestStatAlleleFreq : loci=100, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 3.05822300911
+TestStatAlleleFreq : loci=1000, size=10000: 3.17401409149
+TestStatAlleleFreq : loci=1000, size=100000: 36.7387290001
+TestStatAlleleFreq : loci=1000, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 31.7028801441
+TestStatAlleleFreq : 0.307837963104, 3.0087928772, 3.05822300911, 3.17401409149, 36.7387290001, 31.7028801441
+TestStatAlleleFreq : End of test TestStatAlleleFreq
+TestStatNumOfMales : Host: bp9 (Linux, x86_64, x86_64)
+TestStatNumOfMales : Time: Thu May 26 09:54:34 2011
+TestStatNumOfMales : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatNumOfMales : simuPOP: 1.0.6svn (rev 4182, module short, optimized, 1 threads)
+TestStatNumOfMales : Test: Stat NumOfMales, results are time (not processor time) to apply operator for 5000 times.
+TestStatNumOfMales : size=100000: 16.8653411865
+TestStatNumOfMales : size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 17.209662199
+TestStatNumOfMales : 16.8653411865, 17.209662199
+TestStatNumOfMales : End of test TestStatNumOfMales
+TestStatNumOfMales : Host: bp9 (Linux, x86_64, x86_64)
+TestStatNumOfMales : Time: Thu May 26 09:55:10 2011
+TestStatNumOfMales : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatNumOfMales : simuPOP: 1.0.6svn (rev 4182, module long, optimized, 1 threads)
+TestStatNumOfMales : Test: Stat NumOfMales, results are time (not processor time) to apply operator for 5000 times.
+TestStatNumOfMales : size=100000: 16.4387378693
+TestStatNumOfMales : size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 17.3230619431
+TestStatNumOfMales : 16.4387378693, 17.3230619431
+TestStatNumOfMales : End of test TestStatNumOfMales
+TestStatNumOfMales : Host: bp9 (Linux, x86_64, x86_64)
+TestStatNumOfMales : Time: Thu May 26 09:55:46 2011
+TestStatNumOfMales : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatNumOfMales : simuPOP: 1.0.6svn (rev 4182, module binary, optimized, 1 threads)
+TestStatNumOfMales : Test: Stat NumOfMales, results are time (not processor time) to apply operator for 5000 times.
+TestStatNumOfMales : size=100000: 17.4795110226
+TestStatNumOfMales : size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 17.6907908916
+TestStatNumOfMales : 17.4795110226, 17.6907908916
+TestStatNumOfMales : End of test TestStatNumOfMales
+TestStatNumOfMales : Host: bp9 (Linux, x86_64, x86_64)
+TestStatNumOfMales : Time: Thu May 26 09:56:24 2011
+TestStatNumOfMales : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatNumOfMales : simuPOP: 1.0.6svn (rev 4182, module short, optimized, 4 threads)
+TestStatNumOfMales : Test: Stat NumOfMales, results are time (not processor time) to apply operator for 5000 times.
+TestStatNumOfMales : size=100000: 9.28081488609
+TestStatNumOfMales : size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 10.3006439209
+TestStatNumOfMales : 9.28081488609, 10.3006439209
+TestStatNumOfMales : End of test TestStatNumOfMales
+TestStatNumOfMales : Host: bp9 (Linux, x86_64, x86_64)
+TestStatNumOfMales : Time: Thu May 26 09:56:47 2011
+TestStatNumOfMales : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatNumOfMales : simuPOP: 1.0.6svn (rev 4182, module long, optimized, 4 threads)
+TestStatNumOfMales : Test: Stat NumOfMales, results are time (not processor time) to apply operator for 5000 times.
+TestStatNumOfMales : size=100000: 9.30121707916
+TestStatNumOfMales : size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 10.2057070732
+TestStatNumOfMales : 9.30121707916, 10.2057070732
+TestStatNumOfMales : End of test TestStatNumOfMales
+TestStatNumOfMales : Host: bp9 (Linux, x86_64, x86_64)
+TestStatNumOfMales : Time: Thu May 26 09:57:09 2011
+TestStatNumOfMales : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatNumOfMales : simuPOP: 1.0.6svn (rev 4182, module binary, optimized, 4 threads)
+TestStatNumOfMales : Test: Stat NumOfMales, results are time (not processor time) to apply operator for 5000 times.
+TestStatNumOfMales : size=100000: 10.1437051296
+TestStatNumOfMales : size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 10.6698708534
+TestStatNumOfMales : 10.1437051296, 10.6698708534
+TestStatNumOfMales : End of test TestStatNumOfMales
+TestStatNumOfAffected : Host: bp9 (Linux, x86_64, x86_64)
+TestStatNumOfAffected : Time: Thu May 26 09:57:33 2011
+TestStatNumOfAffected : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatNumOfAffected : simuPOP: 1.0.6svn (rev 4182, module short, optimized, 1 threads)
+TestStatNumOfAffected : Test: Stat NumOfAffected, results are time (not processor time) to apply operator for 5000 times.
+TestStatNumOfAffected : size=100000: 18.7245531082
+TestStatNumOfAffected : size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 19.554336071
+TestStatNumOfAffected : 18.7245531082, 19.554336071
+TestStatNumOfAffected : End of test TestStatNumOfAffected
+TestStatNumOfAffected : Host: bp9 (Linux, x86_64, x86_64)
+TestStatNumOfAffected : Time: Thu May 26 09:58:14 2011
+TestStatNumOfAffected : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatNumOfAffected : simuPOP: 1.0.6svn (rev 4182, module long, optimized, 1 threads)
+TestStatNumOfAffected : Test: Stat NumOfAffected, results are time (not processor time) to apply operator for 5000 times.
+TestStatNumOfAffected : size=100000: 18.9747388363
+TestStatNumOfAffected : size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 19.5944628716
+TestStatNumOfAffected : 18.9747388363, 19.5944628716
+TestStatNumOfAffected : End of test TestStatNumOfAffected
+TestStatNumOfAffected : Host: bp9 (Linux, x86_64, x86_64)
+TestStatNumOfAffected : Time: Thu May 26 09:58:54 2011
+TestStatNumOfAffected : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatNumOfAffected : simuPOP: 1.0.6svn (rev 4182, module binary, optimized, 1 threads)
+TestStatNumOfAffected : Test: Stat NumOfAffected, results are time (not processor time) to apply operator for 5000 times.
+TestStatNumOfAffected : size=100000: 19.5599150658
+TestStatNumOfAffected : size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 20.22062397
+TestStatNumOfAffected : 19.5599150658, 20.22062397
+TestStatNumOfAffected : End of test TestStatNumOfAffected
+TestStatNumOfAffected : Host: bp9 (Linux, x86_64, x86_64)
+TestStatNumOfAffected : Time: Thu May 26 09:59:37 2011
+TestStatNumOfAffected : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatNumOfAffected : simuPOP: 1.0.6svn (rev 4182, module short, optimized, 4 threads)
+TestStatNumOfAffected : Test: Stat NumOfAffected, results are time (not processor time) to apply operator for 5000 times.
+TestStatNumOfAffected : size=100000: 9.38937807083
+TestStatNumOfAffected : size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 10.0877468586
+TestStatNumOfAffected : 9.38937807083, 10.0877468586
+TestStatNumOfAffected : End of test TestStatNumOfAffected
+TestStatNumOfAffected : Host: bp9 (Linux, x86_64, x86_64)
+TestStatNumOfAffected : Time: Thu May 26 09:59:59 2011
+TestStatNumOfAffected : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatNumOfAffected : simuPOP: 1.0.6svn (rev 4182, module long, optimized, 4 threads)
+TestStatNumOfAffected : Test: Stat NumOfAffected, results are time (not processor time) to apply operator for 5000 times.
+TestStatNumOfAffected : size=100000: 9.50907111168
+TestStatNumOfAffected : size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 10.3536448479
+TestStatNumOfAffected : 9.50907111168, 10.3536448479
+TestStatNumOfAffected : End of test TestStatNumOfAffected
+TestStatNumOfAffected : Host: bp9 (Linux, x86_64, x86_64)
+TestStatNumOfAffected : Time: Thu May 26 10:00:21 2011
+TestStatNumOfAffected : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatNumOfAffected : simuPOP: 1.0.6svn (rev 4182, module binary, optimized, 4 threads)
+TestStatNumOfAffected : Test: Stat NumOfAffected, results are time (not processor time) to apply operator for 5000 times.
+TestStatNumOfAffected : size=100000: 10.2223381996
+TestStatNumOfAffected : size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 11.0147790909
+TestStatNumOfAffected : 10.2223381996, 11.0147790909
+TestStatNumOfAffected : End of test TestStatNumOfAffected
+TestStatHaploFreq : Host: bp9 (Linux, x86_64, x86_64)
+TestStatHaploFreq : Time: Thu May 26 10:20:21 2011
+TestStatHaploFreq : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatHaploFreq : simuPOP: 1.0.6svn (rev 4182, module short, optimized, 1 threads)
+TestStatHaploFreq : Test: Stat HaploFreq, results are time (not processor time) to apply operator for 200 times.
+TestStatHaploFreq : loci=100, size=10000: 1.23293209076
+TestStatHaploFreq : loci=100, size=100000: 12.2021050453
+TestStatHaploFreq : loci=100, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 11.865776062
+TestStatHaploFreq : loci=1000, size=10000: 1.29735088348
+TestStatHaploFreq : loci=1000, size=100000: 21.6016001701
+TestStatHaploFreq : loci=1000, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 15.2668449879
+TestStatHaploFreq : 1.23293209076, 12.2021050453, 11.865776062, 1.29735088348, 21.6016001701, 15.2668449879
+TestStatHaploFreq : End of test TestStatHaploFreq
+TestStatHaploFreq : Host: bp9 (Linux, x86_64, x86_64)
+TestStatHaploFreq : Time: Thu May 26 10:21:45 2011
+TestStatHaploFreq : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatHaploFreq : simuPOP: 1.0.6svn (rev 4182, module long, optimized, 1 threads)
+TestStatHaploFreq : Test: Stat HaploFreq, results are time (not processor time) to apply operator for 200 times.
+TestStatHaploFreq : loci=100, size=10000: 1.41531896591
+TestStatHaploFreq : loci=100, size=100000: 23.2550559044
+TestStatHaploFreq : loci=100, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 17.4902069569
+TestStatHaploFreq : loci=1000, size=10000: 1.51551508904
+TestStatHaploFreq : loci=1000, size=100000: 25.3949120045
+TestStatHaploFreq : loci=1000, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 16.8971569538
+TestStatHaploFreq : 1.41531896591, 23.2550559044, 17.4902069569, 1.51551508904, 25.3949120045, 16.8971569538
+TestStatHaploFreq : End of test TestStatHaploFreq
+TestStatHaploFreq : Host: bp9 (Linux, x86_64, x86_64)
+TestStatHaploFreq : Time: Thu May 26 10:23:31 2011
+TestStatHaploFreq : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatHaploFreq : simuPOP: 1.0.6svn (rev 4182, module binary, optimized, 1 threads)
+TestStatHaploFreq : Test: Stat HaploFreq, results are time (not processor time) to apply operator for 200 times.
+TestStatHaploFreq : loci=100, size=10000: 1.69325518608
+TestStatHaploFreq : loci=100, size=100000: 17.1936631203
+TestStatHaploFreq : loci=100, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 18.6411919594
+TestStatHaploFreq : loci=1000, size=10000: 1.70309305191
+TestStatHaploFreq : loci=1000, size=100000: 17.4465510845
+TestStatHaploFreq : loci=1000, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 18.0900690556
+TestStatHaploFreq : 1.69325518608, 17.1936631203, 18.6411919594, 1.70309305191, 17.4465510845, 18.0900690556
+TestStatHaploFreq : End of test TestStatHaploFreq
+TestStatHaploFreq : Host: bp9 (Linux, x86_64, x86_64)
+TestStatHaploFreq : Time: Thu May 26 10:25:12 2011
+TestStatHaploFreq : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatHaploFreq : simuPOP: 1.0.6svn (rev 4182, module short, optimized, 4 threads)
+TestStatHaploFreq : Test: Stat HaploFreq, results are time (not processor time) to apply operator for 200 times.
+TestStatHaploFreq : loci=100, size=10000: 0.566158056259
+TestStatHaploFreq : loci=100, size=100000: 5.73171782494
+TestStatHaploFreq : loci=100, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 5.61322593689
+TestStatHaploFreq : loci=1000, size=10000: 0.713933944702
+TestStatHaploFreq : loci=1000, size=100000: 9.37162017822
+TestStatHaploFreq : loci=1000, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 7.79208993912
+TestStatHaploFreq : 0.566158056259, 5.73171782494, 5.61322593689, 0.713933944702, 9.37162017822, 7.79208993912
+TestStatHaploFreq : End of test TestStatHaploFreq
+TestStatHaploFreq : Host: bp9 (Linux, x86_64, x86_64)
+TestStatHaploFreq : Time: Thu May 26 10:26:02 2011
+TestStatHaploFreq : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatHaploFreq : simuPOP: 1.0.6svn (rev 4182, module long, optimized, 4 threads)
+TestStatHaploFreq : Test: Stat HaploFreq, results are time (not processor time) to apply operator for 200 times.
+TestStatHaploFreq : loci=100, size=10000: 0.613075971603
+TestStatHaploFreq : loci=100, size=100000: 9.36668801308
+TestStatHaploFreq : loci=100, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 7.58966112137
+TestStatHaploFreq : loci=1000, size=10000: 0.720818042755
+TestStatHaploFreq : loci=1000, size=100000: 9.74222493172
+TestStatHaploFreq : loci=1000, size=[10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000, 10000]: 7.8867251873
+TestStatHaploFreq : 0.613075971603, 9.36668801308, 7.58966112137, 0.720818042755, 9.74222493172, 7.8867251873
+TestStatHaploFreq : End of test TestStatHaploFreq
+TestStatHaploFreq : Host: bp9 (Linux, x86_64, x86_64)
+TestStatHaploFreq : Time: Thu May 26 10:26:57 2011
+TestStatHaploFreq : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestStatHaploFreq : simuPOP: 1.0.6svn (rev 4182, module binary, optimized, 4 threads)
+TestStatHaploFreq : Test: Stat HaploFreq, results are time (not processor time) to apply operator for 200 times.
+TestStatHaploFreq : loci=100, size=10000: 0.768512964249
+TestStatHaploFreq : loci=10...
[truncated message content] |
|
From: <si...@us...> - 2011-06-29 21:34:52
|
Revision: 4242
http://simupop.svn.sourceforge.net/simupop/?rev=4242&view=rev
Author: simupop
Date: 2011-06-29 21:34:43 +0000 (Wed, 29 Jun 2011)
Log Message:
-----------
Merge the openMP branch to trunk
Modified Paths:
--------------
trunk/setup.py
trunk/src/customizedTypes.c
trunk/src/individual.h
trunk/src/initializer.cpp
trunk/src/mating.cpp
trunk/src/mating.h
trunk/src/migrator.cpp
trunk/src/penetrance.cpp
trunk/src/penetrance.h
trunk/src/population.cpp
trunk/src/selector.cpp
trunk/src/selector.h
trunk/src/stator.cpp
trunk/src/transmitter.cpp
trunk/src/transmitter.h
trunk/src/utility.cpp
trunk/src/utility.h
trunk/test/performance.csv
trunk/test/performance.log
trunk/test/performance.py
trunk/test/test_03_operator.py
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/openMP:3999-4205
+ /branches/openMP:3999-4241
Modified: trunk/setup.py
===================================================================
--- trunk/setup.py 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/setup.py 2011-06-29 21:34:43 UTC (rev 4242)
@@ -41,13 +41,22 @@
"""
import os, sys, platform, shutil, glob, re, tempfile, subprocess
import distutils.sysconfig
+USE_DISTRIBUTE = False
+try:
+ from distribute_setup import use_setuptools
+ use_setuptools()
+ from setuptools import setup, find_packages, Extension
+ USE_DISTRIBUTE = True
+except ImportError:
+ from distutils.core import setup, Extension
+ print("fail to import distribute/setuptools, build the program with distutils")
if sys.version_info[0] <= 2 and sys.version_info[1] <= 4:
print("simuPOP supports Python version 2.5 or higher, including Python 3.x. Please upgrade your Python installation and try again.")
sys.exit(1)
# Change this to False if you would like to compile simuPOP without openMP support
-USE_OPENMP = True
+USE_OPENMP = False
if os.name == 'nt':
VS9PATH = os.environ.get('VS90COMNTOOLS')
@@ -113,7 +122,6 @@
#
############################################################################
-from distutils.core import setup, Extension
from distutils.sysconfig import get_config_var
try:
from distutils.command.build_py import build_py_2to3 as build_py
@@ -468,7 +476,7 @@
else:
res['libraries'] = ['stdc++', 'z']
if USE_OPENMP:
- res['libraries'].append('iomp5' if USE_ICC else 'gomp')
+ res['libraries'].append(['iomp5','tbb'] if USE_ICC else 'gomp')
res['libraries'].extend(boost_lib_names)
res['include_dirs'] = ['.', 'gsl', boost_inc_path]
res['library_dirs'] = ['build']
@@ -506,6 +514,10 @@
# this one disables a lot of warnings about VC Checked iterators.
#('_SCL_SECURE_NO_WARNINGS', None)
])
+ else:
+ if not USE_ICC:
+ if USE_OPENMP:
+ res['define_macros'].append(('_GLIBCXX_PARALLEL', None))
res['undef_macros'] = []
return res
@@ -515,6 +527,8 @@
# Build extensions
#
############################################################################
+import filecmp
+
if os.name == 'nt': # Windows
# copy platform dependent dll files
machine = platform.uname()[4].lower()
@@ -571,8 +585,8 @@
os.mkdir('build/%s' % modu)
for src in SOURCE_FILES:
mod_src = 'build/%s/%s' % (modu, src)
- shutil.copy('src/' + src, mod_src)
- copied_files.append(mod_src)
+ if not os.path.isfile(mod_src) or not filecmp.cmp(mod_src,'src/'+src):
+ shutil.copy('src/'+src, mod_src)
# build
# For module simuPOP.gsl
EXT_MODULES = [
@@ -595,6 +609,13 @@
undef_macros = info['undef_macros'],
)
)
+ if USE_DISTRIBUTE :
+ setup_params = dict(packages = find_packages(), include_package_data = True,
+ exclude_package_data = {'':['README.txt']}, zip_safe = False,
+ install_requires = ['distribute'])
+ else :
+ setup_params = dict(packages = ['simuPOP'])
+
setup(
name = "simuPOP",
version = SIMUPOP_VER,
@@ -621,7 +642,6 @@
],
platforms = ['all'],
#
- packages = ['simuPOP'],
package_dir = {'simuPOP': 'src'},
package_data = {'simuPOP': PACKAGE_DATA},
py_modules = [
@@ -633,10 +653,9 @@
'simuPOP.sandbox',
] + ['simuPOP.simuPOP_%s' % x for x in MODULES],
ext_modules = EXT_MODULES,
- cmdclass = {'build_py': build_py}
+ cmdclass = {'build_py': build_py},
+ **setup_params
)
- # remove copied files
- for file in copied_files:
- os.remove(file)
+
Modified: trunk/src/customizedTypes.c
===================================================================
--- trunk/src/customizedTypes.c 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/customizedTypes.c 2011-06-29 21:34:43 UTC (rev 4242)
@@ -1395,11 +1395,17 @@
}
else if (PySlice_Check(item)) {
Py_ssize_t start, stop, step, slicelength;
-
+#if PY_VERSION_HEX >= 0x03020000
+ if (PySlice_GetIndicesEx((PyObject*)item, Py_SIZE(self),
+ &start, &stop, &step, &slicelength) < 0) {
+ return NULL;
+ }
+#else
if (PySlice_GetIndicesEx((PySliceObject*)item, Py_SIZE(self),
&start, &stop, &step, &slicelength) < 0) {
return NULL;
}
+#endif
if (step > 1) {
PyErr_SetString(PyExc_TypeError,
"Slice with step > 1 is not supported for type simuPOP.array");
@@ -1448,11 +1454,19 @@
return setarrayitem(self, i, value);
}
else if (PySlice_Check(item)) {
+#if PY_VERSION_HEX >= 0x03020000
+ if (PySlice_GetIndicesEx((PyObject *)item,
+ Py_SIZE(self), &start, &stop,
+ &step, &slicelength) < 0) {
+ return -1;
+ }
+#else
if (PySlice_GetIndicesEx((PySliceObject *)item,
Py_SIZE(self), &start, &stop,
&step, &slicelength) < 0) {
return -1;
}
+#endif
}
else {
PyErr_SetString(PyExc_TypeError,
Modified: trunk/src/individual.h
===================================================================
--- trunk/src/individual.h 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/individual.h 2011-06-29 21:34:43 UTC (rev 4242)
@@ -515,7 +515,7 @@
indCompare(const vectoru & idx) : m_fields(idx) {}
- bool operator()(const Individual & lhs, const Individual & rhs)
+ bool operator()(const Individual & lhs, const Individual & rhs) const
{
for (size_t i = 0; i < m_fields.size(); ++i) {
double v1 = lhs.info(m_fields[i]);
Modified: trunk/src/initializer.cpp
===================================================================
--- trunk/src/initializer.cpp 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/initializer.cpp 2011-06-29 21:34:43 UTC (rev 4242)
@@ -70,12 +70,14 @@
ind->setSex(m_sex[idx % sexSz] == 1 ? MALE : FEMALE);
else {
if (numThreads() > 1) {
+#ifdef _OPENMP
#pragma omp parallel private(ind)
{
ind = pop.indIterator(sp->subPop(), omp_get_thread_num());
for (; ind.valid(); ++ind)
ind->setSex(ws.draw() == 0 ? MALE : FEMALE);
}
+#endif
} else
for (; ind.valid(); ++ind)
ind->setSex(ws.draw() == 0 ? MALE : FEMALE);
Modified: trunk/src/mating.cpp
===================================================================
--- trunk/src/mating.cpp 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/mating.cpp 2011-06-29 21:34:43 UTC (rev 4242)
@@ -627,7 +627,7 @@
DBG_ASSERT(m_ind.valid(), RuntimeError, "No valid individual if found.")
}
return ParentChooser::IndividualPair(&*m_ind++, NULL);
- }else {
+ } else {
if (m_curInd == m_index.size())
m_curInd = 0;
@@ -1270,7 +1270,6 @@
// scrtach will have the right structure.
if (!prepareScratchPop(pop, scratch))
return false;
-
for (size_t sp = 0; sp < static_cast<size_t>(pop.numSubPop()); ++sp)
if (!mateSubPop(pop, scratch, sp, scratch.rawIndBegin(sp), scratch.rawIndEnd(sp)))
return false;
@@ -1431,46 +1430,64 @@
for (; it != it_end; ++it)
idMap[toID(it->info(idIdx))] = &*it;
- it = scratch.rawIndBegin();
- it_end = scratch.rawIndEnd();
- for (size_t i = 0; it != it_end; ++it, ++i) {
- const Individual & pedInd = m_ped.individual(static_cast<double>(i));
+ // initialize operator before entering parallel region in order to avoid race condition
+ opList::const_iterator iop = m_transmitters.begin();
+ opList::const_iterator iopEnd = m_transmitters.end();
+ for (; iop != iopEnd; ++iop)
+ (*iop)->initializeIfNeeded(*pop.rawIndBegin());
- size_t my_id = toID(pedInd.info(m_ped.idIdx()));
- size_t father_id = m_ped.fatherOf(my_id);
- size_t mother_id = m_ped.motherOf(my_id);
- Individual * dad = NULL;
- Individual * mom = NULL;
+#pragma omp parallel private(it, it_end) if (numThreads() > 1 && parallelizable())
+ {
+#ifdef _OPENMP
+ size_t id = omp_get_thread_num();
+ size_t offPopSize = scratch.rawIndEnd() - scratch.rawIndBegin();
+ it = scratch.rawIndBegin() + id * (offPopSize / numThreads());
+ it_end = id == numThreads() - 1 ? scratch.rawIndEnd() : it + (offPopSize / numThreads());
+ size_t i = id * (offPopSize / numThreads());
+#else
+ it = scratch.rawIndBegin();
+ it_end = scratch.rawIndEnd();
+ size_t i = 0;
+#endif
+ for (; it != it_end; ++it, ++i) {
+ const Individual & pedInd = m_ped.individual(static_cast<double>(i));
- if (father_id) {
- IdMap::iterator dad_it = idMap.find(father_id);
- DBG_FAILIF(dad_it == idMap.end(), RuntimeError,
- "Could not locate individual with ID " + toStr(father_id));
- dad = &*(dad_it->second);
- }
- if (mother_id) {
- IdMap::iterator mom_it = idMap.find(mother_id);
- DBG_FAILIF(mom_it == idMap.end(), RuntimeError,
- "Could not locate individual with ID " + toStr(mother_id));
- mom = &*(mom_it->second);
- }
- DBG_DO(DBG_MATING, cerr << "Choosing parents " << father_id << " and "
- << mother_id << " for offspring " << my_id << endl);
+ size_t my_id = toID(pedInd.info(m_ped.idIdx()));
+ size_t father_id = m_ped.fatherOf(my_id);
+ size_t mother_id = m_ped.motherOf(my_id);
+ Individual * dad = NULL;
+ Individual * mom = NULL;
- // copy sex
- it->setSex(pedInd.sex());
- // copy id
- it->setInfo(static_cast<double>(my_id), m_idField);
- //
- opList::const_iterator iop = m_transmitters.begin();
- opList::const_iterator iopEnd = m_transmitters.end();
- for (; iop != iopEnd; ++iop) {
- if ((*iop)->isActive(pop.rep(), pop.gen()))
- (*iop)->applyDuringMating(pop, scratch, it, dad, mom);
+ if (father_id) {
+ IdMap::iterator dad_it = idMap.find(father_id);
+ DBG_FAILIF(dad_it == idMap.end(), RuntimeError,
+ "Could not locate individual with ID " + toStr(father_id));
+ dad = &*(dad_it->second);
+ }
+ if (mother_id) {
+ IdMap::iterator mom_it = idMap.find(mother_id);
+ DBG_FAILIF(mom_it == idMap.end(), RuntimeError,
+ "Could not locate individual with ID " + toStr(mother_id));
+ mom = &*(mom_it->second);
+ }
+ DBG_DO(DBG_MATING, cerr << "Choosing parents " << father_id << " and "
+ << mother_id << " for offspring " << my_id << endl);
+
+ // copy sex
+ it->setSex(pedInd.sex());
+ // copy id
+ it->setInfo(static_cast<double>(my_id), m_idField);
+ //
+ opList::const_iterator iop = m_transmitters.begin();
+ opList::const_iterator iopEnd = m_transmitters.end();
+ for (; iop != iopEnd; ++iop) {
+ if ((*iop)->isActive(pop.rep(), pop.gen()))
+ (*iop)->applyDuringMating(pop, scratch, it, dad, mom);
+ }
+ // copy individual ID again, just to make sure that even if during mating operators
+ // changes ID, pedigree mating could proceed normally.
+ it->setInfo(static_cast<double>(my_id), m_idField);
}
- // copy individual ID again, just to make sure that even if during mating operators
- // changes ID, pedigree mating could proceed normally.
- it->setInfo(static_cast<double>(my_id), m_idField);
}
const_cast<Pedigree &>(m_ped).useAncestralGen(oldGen);
submitScratch(pop, scratch);
@@ -1492,6 +1509,19 @@
}
+bool PedigreeMating::parallelizable() const
+{
+ opList::const_iterator iop = m_transmitters.begin();
+ opList::const_iterator iopEnd = m_transmitters.end();
+
+ for (; iop != iopEnd; ++iop) {
+ if (!(*iop)->parallelizable())
+ return false;
+ }
+ return true;
+}
+
+
HeteroMating::HeteroMating(const vectormating & matingSchemes,
const uintListFunc & subPopSize,
bool shuffleOffspring)
Modified: trunk/src/mating.h
===================================================================
--- trunk/src/mating.h 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/mating.h 2011-06-29 21:34:43 UTC (rev 4242)
@@ -1293,12 +1293,14 @@
return "<simuPOP.CombinedParentsChooser> chooses parents using two parent choosers";
}
+
/// CPPONLY
virtual bool parallelizable() const
{
return m_fatherChooser->parallelizable() && m_motherChooser->parallelizable();
}
+
/// CPPONLY
void initialize(Population & pop, size_t sp);
@@ -1639,6 +1641,8 @@
*/
virtual bool mate(Population & pop, Population & scratch);
+ bool parallelizable() const;
+
private:
const Pedigree & m_ped;
Modified: trunk/src/migrator.cpp
===================================================================
--- trunk/src/migrator.cpp 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/migrator.cpp 2011-06-29 21:34:43 UTC (rev 4242)
@@ -70,9 +70,24 @@
for (size_t sp = 0; sp < pop.numSubPop(); ++sp) {
RawIndIterator it = pop.rawIndBegin(sp);
RawIndIterator it_end = pop.rawIndEnd(sp);
- for (; it != it_end; ++it)
- it->setInfo(static_cast<double>(sp), info);
+ if (numThreads() > 1) {
+#ifdef _OPENMP
+ size_t popSize = it_end - it;
+# pragma omp parallel firstprivate(it, it_end)
+ {
+ size_t id = omp_get_thread_num();
+ it = it + id * (popSize / numThreads());
+ it_end = id == numThreads() - 1 ? it_end : it + popSize / numThreads();
+ for (; it != it_end; ++it)
+ it->setInfo(static_cast<double>(sp), info);
+ }
+#endif
+ } else {
+ for (; it != it_end; ++it)
+ it->setInfo(static_cast<double>(sp), info);
+ }
}
+
}
DBG_FAILIF(pop.hasActivatedVirtualSubPop(), RuntimeError,
@@ -150,26 +165,51 @@
// restore information fields set by user so that other individuals
// can stay at their original subpopulation.
if (!oldInfo.empty()) {
- for (IndIterator ind = pop.indIterator(spFrom); ind.valid(); ++ind)
- ind->setInfo(oldInfo[&*ind - &*pop.rawIndBegin()], info);
+ if (numThreads() > 1) {
+#ifdef _OPENMP
+# pragma omp parallel
+ {
+ for (IndIterator ind = pop.indIterator(spFrom, omp_get_thread_num()); ind.valid(); ++ind)
+ ind->setInfo(oldInfo[&*ind - &*pop.rawIndBegin()], info);
+ }
+#endif
+ } else {
+ for (IndIterator ind = pop.indIterator(spFrom); ind.valid(); ++ind)
+ ind->setInfo(oldInfo[&*ind - &*pop.rawIndBegin()], info);
+ }
}
} else if (m_mode == BY_PROBABILITY) {
WeightedSampler ws(migrationRate[from]);
// for each individual, migrate according to migration probability
- for (IndIterator ind = pop.indIterator(spFrom); ind.valid(); ++ind) {
- //toIndex = getRNG().randIntByFreq( rateSize, &migrationRate[from][0] ) ;
- toIndex = ws.draw();
+ if (numThreads() > 1) {
+#ifdef _OPENMP
+# pragma omp parallel private(toIndex)
+ {
+ for (IndIterator ind = pop.indIterator(spFrom, omp_get_thread_num()); ind.valid(); ++ind) {
+ toIndex = ws.draw();
+ DBG_ASSERT(toIndex < migrationRate[from].size(), ValueError,
+ "Return index out of range.");
+ if (toIndex < toSize && toSubPops[toIndex] != spFrom)
+ ind->setInfo(static_cast<double>(toSubPops[toIndex]), info);
+ }
+ }
+#endif
+ } else {
+ for (IndIterator ind = pop.indIterator(spFrom); ind.valid(); ++ind) {
+ //toIndex = getRNG().randIntByFreq( rateSize, &migrationRate[from][0] ) ;
+ toIndex = ws.draw();
- DBG_ASSERT(toIndex < migrationRate[from].size(), ValueError,
- "Return index out of range.");
+ DBG_ASSERT(toIndex < migrationRate[from].size(), ValueError,
+ "Return index out of range.");
- // rateSize == toSize (no i->i addition)
- // toIndex < toSize
- // rateSize = toSize + 1, ignore i->1 (last one)
- // toIndex < toSize
- if (toIndex < toSize && toSubPops[toIndex] != spFrom)
- ind->setInfo(static_cast<double>(toSubPops[toIndex]), info);
+ // rateSize == toSize (no i->i addition)
+ // toIndex < toSize
+ // rateSize = toSize + 1, ignore i->1 (last one)
+ // toIndex < toSize
+ if (toIndex < toSize && toSubPops[toIndex] != spFrom)
+ ind->setInfo(static_cast<double>(toSubPops[toIndex]), info);
+ }
}
} else {
// 2nd, or 3rd method
Modified: trunk/src/penetrance.cpp
===================================================================
--- trunk/src/penetrance.cpp 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/penetrance.cpp 2011-06-29 21:34:43 UTC (rev 4242)
@@ -60,17 +60,37 @@
if (sp->isVirtual())
pop.activateVirtualSubPop(*sp);
- IndIterator ind = pop.indIterator(sp->subPop());
- for (; ind.valid(); ++ind) {
- double p = penet(&pop, &*ind);
+ if (numThreads() > 1 && parallelizable()) {
+#pragma omp parallel
+ {
+#ifdef _OPENMP
+ IndIterator ind = pop.indIterator(sp->subPop(), omp_get_thread_num());
+ for (; ind.valid(); ++ind) {
+ double p = penet(&pop, &*ind);
- if (savePene)
- ind->setInfo(p, infoIdx);
+ if (savePene)
+ ind->setInfo(p, infoIdx);
- if (getRNG().randUniform() < p)
- ind->setAffected(true);
- else
- ind->setAffected(false);
+ if (getRNG().randUniform() < p)
+ ind->setAffected(true);
+ else
+ ind->setAffected(false);
+ }
+#endif
+ }
+ } else {
+ IndIterator ind = pop.indIterator(sp->subPop());
+ for (; ind.valid(); ++ind) {
+ double p = penet(&pop, &*ind);
+
+ if (savePene)
+ ind->setInfo(p, infoIdx);
+
+ if (getRNG().randUniform() < p)
+ ind->setAffected(true);
+ else
+ ind->setAffected(false);
+ }
}
if (sp->isVirtual())
pop.deactivateVirtualSubPop(sp->subPop());
Modified: trunk/src/penetrance.h
===================================================================
--- trunk/src/penetrance.h 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/penetrance.h 2011-06-29 21:34:43 UTC (rev 4242)
@@ -191,6 +191,13 @@
}
+ /// CPPONLY
+ bool parallelizable() const
+ {
+ return true;
+ }
+
+
private:
/// one locus
const lociList m_loci;
@@ -261,6 +268,13 @@
/// HIDDEN
string describe(bool format = true) const;
+ /// CPPONLY
+ bool parallelizable() const
+ {
+ return true;
+ }
+
+
private:
/// one locus
const lociList m_loci;
@@ -333,6 +347,13 @@
}
+ /// CPPONLY
+ bool parallelizable() const
+ {
+ return true;
+ }
+
+
private:
/// a list of peneOps
const opList m_peneOps;
@@ -395,6 +416,13 @@
}
+ /// CPPONLY
+ bool parallelizable() const
+ {
+ return false;
+ }
+
+
private:
/// user supplied python function
const pyFunc m_func;
Modified: trunk/src/population.cpp
===================================================================
--- trunk/src/population.cpp 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/population.cpp 2011-06-29 21:34:43 UTC (rev 4242)
@@ -787,7 +787,7 @@
for (size_t i = 0; i < infoFields.size(); ++i)
fields[i] = infoIdx(infoFields[i]);
for (size_t sp = 0; sp < numSubPop(); ++sp)
- std::sort(rawIndBegin(sp), rawIndEnd(sp), indCompare(fields));
+ parallelSort(rawIndBegin(sp), rawIndEnd(sp), indCompare(fields));
setIndOrdered(false);
}
@@ -798,10 +798,9 @@
"This operation is not allowed when there is an activated virtual subpopulation");
size_t info = infoIdx(field);
-
DBG_DO(DBG_POPULATION, cerr << "Sorting individuals." << endl);
// sort individuals first
- std::sort(rawIndBegin(), rawIndEnd(), indCompare(info));
+ parallelSort(rawIndBegin(), rawIndEnd(), indCompare(info));
setIndOrdered(false);
// sort individuals first
Modified: trunk/src/selector.cpp
===================================================================
--- trunk/src/selector.cpp 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/selector.cpp 2011-06-29 21:34:43 UTC (rev 4242)
@@ -42,9 +42,21 @@
for (; sp != spEnd; ++sp) {
if (sp->isVirtual())
pop.activateVirtualSubPop(*sp);
- IndIterator ind = pop.indIterator(sp->subPop());
- for (; ind.valid(); ++ind)
- ind->setInfo(indFitness(pop, &*ind), fit_id);
+ if (numThreads() > 1 && parallelizable()) {
+#pragma omp parallel
+ {
+#ifdef _OPENMP
+ IndIterator ind = pop.indIterator(sp->subPop(), omp_get_thread_num());
+ for (; ind.valid(); ++ind)
+ ind->setInfo(indFitness(pop, &*ind), fit_id);
+#endif
+ }
+
+ } else {
+ IndIterator ind = pop.indIterator(sp->subPop());
+ for (; ind.valid(); ++ind)
+ ind->setInfo(indFitness(pop, &*ind), fit_id);
+ }
if (sp->isVirtual())
pop.deactivateVirtualSubPop(sp->subPop());
}
@@ -253,3 +265,5 @@
}
+
+
Modified: trunk/src/selector.h
===================================================================
--- trunk/src/selector.h 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/selector.h 2011-06-29 21:34:43 UTC (rev 4242)
@@ -225,6 +225,13 @@
}
+ /// CPPONLY
+ bool parallelizable() const
+ {
+ return true;
+ }
+
+
private:
///
const lociList m_loci;
@@ -297,6 +304,13 @@
}
+ /// CPPONLY
+ bool parallelizable() const
+ {
+ return true;
+ }
+
+
private:
/// one locus
const lociList m_loci;
@@ -366,6 +380,13 @@
}
+ /// CPPONLY
+ bool parallelizable() const
+ {
+ return true;
+ }
+
+
private:
/// a list of selectors
const opList m_selectors;
@@ -425,6 +446,13 @@
}
+ /// CPPONLY
+ bool parallelizable() const
+ {
+ return false;
+ }
+
+
private:
/// user supplied python function
const pyFunc m_func;
Modified: trunk/src/stator.cpp
===================================================================
--- trunk/src/stator.cpp 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/stator.cpp 2011-06-29 21:34:43 UTC (rev 4242)
@@ -2462,32 +2462,15 @@
double diffCnt = 0;
int numComparison = 0;
- size_t size = end - begin;
- size_t nThreads = numThreads();
-
- if (nThreads > 1)
+ if (numThreads() > 1) {
#ifdef _OPENMP
+ size_t size = end - begin;
# pragma omp parallel reduction(+ : diffCnt, numComparison)
- {
- size_t id = omp_get_thread_num();
- HAPLOLIST::const_iterator it = begin + id * (size / nThreads);
- HAPLOLIST::const_iterator itEnd = id == nThreads - 1 ? end : it + (size / nThreads);
- for (; it != itEnd; ++it) {
- HAPLOLIST::const_iterator it1 = it;
- for (++it1; it1 != end; ++it1) {
- const vectora & seq1 = *it;
- const vectora & seq2 = *it1;
- size_t sz = seq1.size();
- for (size_t i = 0; i < sz; ++i)
- diffCnt += seq1[i] != seq2[i];
- ++numComparison;
- }
- }
- }
-#endif
- else {
- HAPLOLIST::const_iterator it = begin;
- for (; it != end; ++it) {
+ {
+ size_t id = omp_get_thread_num();
+ HAPLOLIST::const_iterator it = begin + id * (size / numThreads());
+ HAPLOLIST::const_iterator itEnd = id == numThreads() - 1 ? end : it + (size / numThreads());
+ for (; it != itEnd; ++it) {
HAPLOLIST::const_iterator it1 = it;
for (++it1; it1 != end; ++it1) {
const vectora & seq1 = *it;
@@ -2499,6 +2482,21 @@
}
}
}
+#endif
+ } else {
+ HAPLOLIST::const_iterator it = begin;
+ for (; it != end; ++it) {
+ HAPLOLIST::const_iterator it1 = it;
+ for (++it1; it1 != end; ++it1) {
+ const vectora & seq1 = *it;
+ const vectora & seq2 = *it1;
+ size_t sz = seq1.size();
+ for (size_t i = 0; i < sz; ++i)
+ diffCnt += seq1[i] != seq2[i];
+ ++numComparison;
+ }
+ }
+ }
// return 0 if there is only one sequence
return numComparison == 0 ? 0 : diffCnt / numComparison;
}
Modified: trunk/src/transmitter.cpp
===================================================================
--- trunk/src/transmitter.cpp 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/transmitter.cpp 2011-06-29 21:34:43 UTC (rev 4242)
@@ -417,11 +417,15 @@
const stringFunc & output, int begin, int end, int step, const intList & at,
const intList & reps, const subPopList & subPops, const stringList & infoFields)
:
- GenoTransmitter(output, begin, end, step, at, reps, subPops, infoFields)
- , m_intensity(intensity), m_rates(rates.elems()), m_loci(loci),
- m_recBeforeLoci(0), m_convMode(convMode.elems()),
- m_bt(numThreads(), getRNG()), m_chromX(-1), m_chromY(-1), m_customizedBegin(-1), m_customizedEnd(-1),
- m_algorithm(0), m_debugOutput(NULL)
+ GenoTransmitter(output, begin, end, step, at, reps, subPops, infoFields),
+ m_intensity(intensity), m_rates(rates.elems()), m_loci(loci),
+ m_recBeforeLoci(0), m_convMode(convMode.elems()), m_chromX(-1), m_chromY(-1),
+ m_customizedBegin(-1), m_customizedEnd(-1), m_algorithm(0), m_debugOutput(NULL),
+#ifdef _OPENMP
+ m_bt(numThreads(), getRNG())
+#else
+ m_bt(getRNG())
+#endif
{
DBG_FAILIF(m_convMode.empty(), ValueError,
@@ -589,9 +593,13 @@
// if the operator is called directly, there is no way to know population size so we
// a variable to tell it.
+#ifdef _OPENMP
for (size_t i = 0; i < numThreads(); i++)
m_bt[i].setParameter(vecP, 0 /* obsolete m_intendedSize */);
+#else
+ m_bt.setParameter(vecP, 0 /* obsolete m_intendedSize */);
+#endif
// choose an algorithm
// if recombinations are dense. use the first algorithm
// For example 10 chromoes, regular 0.5*10=5
@@ -614,7 +622,11 @@
initializeIfNeeded(offspring);
//Bernullitrial for each thread
+#ifdef _OPENMP
Bernullitrials & bt = m_bt[omp_get_thread_num()];
+#else
+ Bernullitrials & bt = m_bt;
+#endif
// use which copy of chromosome
GenoIterator cp[2], off;
Modified: trunk/src/transmitter.h
===================================================================
--- trunk/src/transmitter.h 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/transmitter.h 2011-06-29 21:34:43 UTC (rev 4242)
@@ -623,9 +623,6 @@
const vectorf m_convMode;
- /// bernulli trials
- mutable vector<Bernullitrials> m_bt;
-
// locataion of special chromosomes
mutable int m_chromX;
mutable int m_chromY;
@@ -637,6 +634,14 @@
mutable ostream * m_debugOutput;
+ /// bernulli trials
+#ifdef _OPENMP
+ mutable vector<Bernullitrials> m_bt;
+#else
+ mutable Bernullitrials m_bt;
+#endif
+
+
};
}
Modified: trunk/src/utility.cpp
===================================================================
--- trunk/src/utility.cpp 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/utility.cpp 2011-06-29 21:34:43 UTC (rev 4242)
@@ -2263,7 +2263,11 @@
PyObject * res = NULL;
if (m_stmts != NULL) {
+#if PY_VERSION_HEX >= 0x03020000
+ res = PyEval_EvalCode((PyObject *)m_stmts, m_locals, m_locals);
+#else
res = PyEval_EvalCode((PyCodeObject *)m_stmts, m_locals, m_locals);
+#endif
if (res == NULL) {
#ifndef OPTIMIZED
if (debug(DBG_GENERAL)) {
@@ -2279,7 +2283,11 @@
}
if (m_expr != NULL) {
+#if PY_VERSION_HEX >= 0x03020000
+ res = PyEval_EvalCode((PyObject *)m_expr, m_locals, m_locals);
+#else
res = PyEval_EvalCode((PyCodeObject *)m_expr, m_locals, m_locals);
+#endif
if (res == NULL) {
#ifndef OPTIMIZED
if (debug(DBG_GENERAL)) {
Modified: trunk/src/utility.h
===================================================================
--- trunk/src/utility.h 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/src/utility.h 2011-06-29 21:34:43 UTC (rev 4242)
@@ -76,6 +76,12 @@
/// for openMP
#ifdef _OPENMP
# include "omp.h"
+# if defined(__INTEL_COMPILER)
+# include "tbb/parallel_sort.h"
+# include "tbb/task_scheduler_init.h"
+# elif defined(GCC_VERSION) && GCC_VERSION >= 40300
+# include "parallel/algorithm"
+# endif
#endif
/// for bernulli trials.
// use vector<bool> instead of dynamic_bitset since I can manipulate
@@ -145,6 +151,26 @@
/// CPPONLY return val and increase val by 1, ensuring thread safety
ATOMICLONG fetchAndIncrement(ATOMICLONG * val);
+/// CPPONLY parallel sort by using tbb or gnu parallel
+template<class T1, class T2>
+void parallelSort(T1 start, T1 end, T2 cmp)
+{
+ if (numThreads() > 1) {
+#ifdef _OPENMP
+# if defined(__INTEL_COMPILER)
+ tbb::task_scheduler_init init(numThreads());
+ tbb::parallel_sort(start, end, cmp);
+# elif defined(GCC_VERSION) && GCC_VERSION >= 40300
+ __gnu_parallel::sort(start, end, cmp);
+# else
+ std::sort(start, end, cmp);
+# endif
+#endif
+ } else {
+ std::sort(start, end, cmp);
+ }
+}
+
/// a utility function to check keyboard stroke
/// CPPONLY
int simuPOP_kbhit();
@@ -1202,6 +1228,12 @@
if (expr.empty() && stmts.empty())
return;
+ //detect leading spaces from python expressions
+ DBG_FAILIF(!expr.empty() && (expr[0] == ' ' || expr[0] == '\t'), ValueError,
+ "Can not include leading space in python expression '" + expr + "'");
+ DBG_FAILIF(!stmts.empty() && (stmts[0] == ' ' || stmts[0] == '\t'), ValueError,
+ "Can not include leading space in python statement '" + stmts + "'");
+
compileExpr(expr);
compileStmts(stmts);
}
Modified: trunk/test/performance.csv
===================================================================
--- trunk/test/performance.csv 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/test/performance.csv 2011-06-29 21:34:43 UTC (rev 4242)
@@ -448,3 +448,120 @@
TestInitSex, 2011-06-06 15:43:11,943, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4200-intel, short, 13.1370029449, 13.5422229767
TestInitSex, 2011-06-06 15:43:59,207, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4200-intel, long, 13.7384490967, 15.3715240955
TestInitSex, 2011-06-06 15:44:27,405, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4200-intel, binary, 12.9587409496, 13.3092448711
+TestInitInfo, 2011-06-07 10:50:29,049, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4205-intel, short, 28.5263929367, 28.5497779846
+TestInitInfo, 2011-06-07 10:51:25,868, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4205-intel, long, 27.8562178612, 28.108784914
+TestInitInfo, 2011-06-07 10:52:22,403, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4205-intel, binary, 27.9055569172, 27.9653069973
+TestInitInfo, 2011-06-07 11:01:39,745, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4205-intel, short, 8.08958816528, 8.34579896927
+TestInitInfo, 2011-06-07 11:01:57,159, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4205-intel, long, 8.00524497032, 8.44241905212
+TestInitInfo, 2011-06-07 11:02:13,861, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4205-intel, binary, 8.06356215477, 8.2104408741
+TestInitInfo, 2011-06-07 11:52:02,098, EPI7-0541302, AMD64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4205-vc, short, 42.5138275974, 42.0906409373
+TestInitInfo, 2011-06-07 11:53:30,035, EPI7-0541302, AMD64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4205-vc, long, 42.7154268612, 43.2257380443
+TestInitInfo, 2011-06-07 11:55:01,380, EPI7-0541302, AMD64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4205-vc, binary, 45.0157581313, 44.4060398472
+TestInitInfo, 2011-06-07 11:55:52,381, EPI7-0541302, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4205-vc, short, 12.986396842, 14.089627703
+TestInitInfo, 2011-06-07 11:56:20,819, EPI7-0541302, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4205-vc, long, 13.1444051231, 13.6804705765
+TestInitInfo, 2011-06-07 11:56:49,009, EPI7-0541302, AMD64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4205-vc, binary, 12.6781480139, 13.7568184564
+TestMapSelector, 2011-06-08 12:32:43,362, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4212-intel, short, 137.560660124, 136.669243097
+TestMapSelector, 2011-06-08 12:37:05,477, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4212-intel, long, 131.439245939, 129.801275969
+TestMapSelector, 2011-06-08 12:42:04,585, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4212-intel, binary, 149.361258984, 148.818060875
+TestMapSelector, 2011-06-08 12:48:18,478, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4212-intel, short, 45.7759559155, 52.9312109947
+TestMapSelector, 2011-06-08 12:49:53,758, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4212-intel, long, 46.7970941067, 47.7334721088
+TestMapSelector, 2011-06-08 12:51:42,545, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4212-intel, binary, 52.5352201462, 55.497841835
+TestMaSelector, 2011-06-08 14:28:08,546, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4214-intel, short, 25.4252510071, 25.5701878071
+TestMaSelector, 2011-06-08 14:29:05,049, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4214-intel, long, 27.9332430363, 27.9779438972
+TestMaSelector, 2011-06-08 14:30:42,441, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4214-intel, binary, 48.2308118343, 48.3816211224
+TestMaSelector, 2011-06-08 14:31:09,735, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4214-intel, short, 7.88334703445, 8.11231207848
+TestMaSelector, 2011-06-08 14:31:26,819, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4214-intel, long, 8.17427706718, 8.4179918766
+TestMaSelector, 2011-06-08 14:31:57,265, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4214-intel, binary, 15.1356091499, 14.8043692112
+TestMlSelector, 2011-06-08 15:46:22,150, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4215-intel, short, 50.193365097, 50.2650611401
+TestMlSelector, 2011-06-08 15:48:09,026, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4215-intel, long, 51.6552660465, 54.0810310841
+TestMlSelector, 2011-06-08 15:50:16,152, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4215-intel, binary, 62.9643480778, 62.9600830078
+TestMlSelector, 2011-06-08 15:58:01,759, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4215-intel, short, 20.2570528984, 18.9420928955
+TestMlSelector, 2011-06-08 15:58:42,519, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4215-intel, long, 19.7100989819, 20.2147932053
+TestMlSelector, 2011-06-08 15:59:33,111, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4215-intel, binary, 24.4318461418, 25.4335269928
+TestMapPenetrance, 2011-06-09 13:29:16,820, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4217-intel, short, 30.1838719845, 29.9526631832
+TestMapPenetrance, 2011-06-09 13:30:24,110, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4217-intel, long, 32.5619549751, 32.8275830746
+TestMapPenetrance, 2011-06-09 13:31:39,551, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4217-intel, binary, 36.6352450848, 36.3903110027
+TestMapPenetrance, 2011-06-09 13:34:04,566, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4217-intel, short, 13.2235410213, 13.5193769932
+TestMapPenetrance, 2011-06-09 13:34:30,985, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4217-intel, long, 12.4324560165, 13.0819602013
+TestMapPenetrance, 2011-06-09 13:34:59,703, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4217-intel, binary, 13.6132779121, 14.0616240501
+TestMaPenetrance, 2011-06-09 14:15:27,807, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4218-intel, short, 9.05448889732, 9.03937888145
+TestMaPenetrance, 2011-06-09 14:15:49,226, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4218-intel, long, 9.61507201195, 9.80975604057
+TestMaPenetrance, 2011-06-09 14:16:19,546, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4218-intel, binary, 13.9117228985, 14.0005609989
+TestMaPenetrance, 2011-06-09 14:16:26,804, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4218-intel, short, 2.95468306541, 3.07803201675
+TestMaPenetrance, 2011-06-09 14:16:33,916, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4218-intel, long, 3.09952521324, 3.21534013748
+TestMaPenetrance, 2011-06-09 14:16:44,022, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4218-intel, binary, 4.47951889038, 4.53425717354
+TestMlPenetrance, 2011-06-09 14:18:44,988, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4218-intel, short, 59.3637518883, 59.5009410381
+TestMlPenetrance, 2011-06-09 14:20:48,471, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4218-intel, long, 61.0185468197, 60.5403618813
+TestMlPenetrance, 2011-06-09 14:23:09,441, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4218-intel, binary, 69.4342930317, 69.1806800365
+TestMlPenetrance, 2011-06-09 14:23:57,203, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4218-intel, short, 22.7854809761, 23.7821338177
+TestMlPenetrance, 2011-06-09 14:24:45,537, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4218-intel, long, 22.8191227913, 24.6416099072
+TestMlPenetrance, 2011-06-09 14:25:41,754, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4218-intel, binary, 26.4700949192, 28.6646509171
+TestMigratorByProbability, 2011-06-14 15:22:26,387, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4226-intel, short, 25.6720509529, 289.408267021
+TestMigratorByProbability, 2011-06-14 15:27:43,088, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4226-intel, long, 26.1059360504, 289.273638964
+TestMigratorByProbability, 2011-06-14 15:33:03,204, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4226-intel, binary, 26.363268137, 292.225383997
+TestMigratorByProbability, 2011-06-14 15:36:25,599, bp9, x86_64-2threads, python2.7.1, simuPOP-1.0.6svn, rev4226-intel, short, 3.85128188133, 37.7105200291
+TestMigratorByProbability, 2011-06-14 15:37:09,576, bp9, x86_64-2threads, python2.7.1, simuPOP-1.0.6svn, rev4226-intel, long, 3.8537299633, 38.7310800552
+TestMigratorByProbability, 2011-06-14 15:37:52,903, bp9, x86_64-2threads, python2.7.1, simuPOP-1.0.6svn, rev4226-intel, binary, 3.89192581177, 37.8206448555
+TestMigratorByProbability, 2011-06-14 15:39:51,191, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4226-intel, short, 3.68470191956, 36.2090260983
+TestMigratorByProbability, 2011-06-14 15:40:32,838, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4226-intel, long, 3.67241191864, 36.6956839561
+TestMigratorByProbability, 2011-06-14 15:41:14,535, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4226-intel, binary, 3.70908212662, 36.3693478107
+TestMigratorByProbability, 2011-06-14 16:00:42,787, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4226-gcc, short, 19.2052230835, 213.073572874
+TestMigratorByProbability, 2011-06-14 16:04:33,578, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4226-gcc, long, 19.0889210701, 210.232218981
+TestMigratorByProbability, 2011-06-14 16:08:30,824, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4226-gcc, binary, 19.5818870068, 215.983033895
+TestMigratorByProbability, 2011-06-14 16:11:28,255, bp9, x86_64-2threads, python2.7.1, simuPOP-1.0.6svn, rev4226-gcc, short, 11.753456831, 129.562813044
+TestMigratorByProbability, 2011-06-14 16:13:45,338, bp9, x86_64-2threads, python2.7.1, simuPOP-1.0.6svn, rev4226-gcc, long, 11.34167099, 124.56328702
+TestMigratorByProbability, 2011-06-14 16:16:09,380, bp9, x86_64-2threads, python2.7.1, simuPOP-1.0.6svn, rev4226-gcc, binary, 11.8418748379, 130.746499777
+TestMigratorByProbability, 2011-06-14 16:17:49,311, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4226-gcc, short, 7.99957203865, 84.460050106
+TestMigratorByProbability, 2011-06-14 16:19:20,940, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4226-gcc, long, 7.60408210754, 82.7148649693
+TestMigratorByProbability, 2011-06-14 16:20:57,946, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4226-gcc, binary, 8.37837600708, 87.1949620247
+TestMigratorByProbability, 2011-06-15 12:26:38,514, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4229-intel, short, 1.9312608242, 17.998347044
+TestMigratorByProbability, 2011-06-15 12:26:59,075, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4229-intel, long, 1.87130308151, 17.1944150925
+TestMigratorByProbability, 2011-06-15 12:27:20,130, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4229-intel, binary, 1.89324998856, 17.7626860142
+TestMigratorByProbability, 2011-06-15 13:42:10,927, bp9, x86_64-2threads, python2.7.1, simuPOP-1.0.6svn, rev4229-intel, short, 2.60852098465, 25.8612132072
+TestMigratorByProbability, 2011-06-15 13:42:44,813, bp9, x86_64-2threads, python2.7.1, simuPOP-1.0.6svn, rev4229-intel, long, 2.70065402985, 25.6916520596
+TestMigratorByProbability, 2011-06-15 13:43:15,274, bp9, x86_64-2threads, python2.7.1, simuPOP-1.0.6svn, rev4229-intel, binary, 2.63936305046, 25.8546738625
+TestMigratorByProbability, 2011-06-15 14:03:33,076, bp9, x86_64-2threads, python2.7.1, simuPOP-1.0.6svn, rev4229-gcc, short, 11.1535990238, 123.792095184
+TestMigratorByProbability, 2011-06-15 14:08:02,558, bp9, x86_64-2threads, python2.7.1, simuPOP-1.0.6svn, rev4229-gcc, long, 10.8459448814, 119.107388973
+TestMigratorByProbability, 2011-06-15 14:12:34,146, bp9, x86_64-2threads, python2.7.1, simuPOP-1.0.6svn, rev4229-gcc, binary, 11.3297309875, 125.051301003
+TestMigratorByProbability, 2011-06-15 14:44:25,953, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4229-gcc, short, 6.46779084206, 73.2599718571
+TestMigratorByProbability, 2011-06-15 14:45:48,805, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4229-gcc, long, 6.84860181808, 74.6199998856
+TestMigratorByProbability, 2011-06-15 14:47:15,090, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4229-gcc, binary, 7.11267113686, 77.6748759747
+TestMigratorByIndInfo, 2011-06-15 15:26:07,842, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, short, 26.1453762054, 293.74267602
+TestMigratorByIndInfo, 2011-06-15 15:31:32,104, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, long, 26.3325400352, 295.03544116
+TestMigratorByIndInfo, 2011-06-15 15:37:02,364, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, binary, 27.2269229889, 299.873353958
+TestMigratorByIndInfo, 2011-06-15 15:37:35,940, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, short, 2.99913883209, 27.3614680767
+TestMigratorByIndInfo, 2011-06-15 15:38:13,350, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, long, 3.31677007675, 31.3634848595
+TestMigratorByIndInfo, 2011-06-15 15:38:52,125, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, binary, 3.51236987114, 32.3257880211
+TestMigratorByCount, 2011-06-15 15:44:37,405, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, short, 27.3829629421, 313.405131102
+TestMigratorByCount, 2011-06-15 15:50:18,503, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, long, 27.1348381042, 312.564651012
+TestMigratorByCount, 2011-06-15 15:56:05,059, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, binary, 28.0947768688, 316.94431901
+TestMigratorByCount, 2011-06-15 15:57:04,649, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, short, 4.43328809738, 53.2696549892
+TestMigratorByCount, 2011-06-15 15:58:03,514, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, long, 4.49258899689, 53.0905818939
+TestMigratorByCount, 2011-06-15 15:59:03,128, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, binary, 4.42320084572, 53.5732860565
+TestMigratorByProportion, 2011-06-16 09:31:14,071, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, short, 27.1460089684, 311.949622869
+TestMigratorByProportion, 2011-06-16 09:37:00,421, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, long, 27.462939024, 316.891449928
+TestMigratorByProportion, 2011-06-16 09:42:50,875, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, binary, 28.1410610676, 320.35036397
+TestMigratorByProportion, 2011-06-16 09:43:50,063, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, short, 4.38145494461, 53.0418229103
+TestMigratorByProportion, 2011-06-16 09:44:49,681, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, long, 4.43273711205, 53.8642539978
+TestMigratorByProportion, 2011-06-16 09:45:50,018, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4230-intel, binary, 4.50796914101, 54.1398379803
+TestMigratorByIndInfo, 2011-06-16 12:18:46,099, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4232-intel, short, 2.966381073, 27.7702920437
+TestMigratorByIndInfo, 2011-06-16 12:19:19,834, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4232-intel, long, 2.91467499733, 28.0086240768
+TestMigratorByIndInfo, 2011-06-16 12:19:54,456, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4232-intel, binary, 3.1325969696, 28.1677310467
+TestMigratorByProportion, 2011-06-16 12:20:50,553, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4232-intel, short, 4.09359002113, 50.0307469368
+TestMigratorByProportion, 2011-06-16 12:21:45,803, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4232-intel, long, 4.10800004005, 49.5832879543
+TestMigratorByProportion, 2011-06-16 12:22:42,183, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4232-intel, binary, 4.32871103287, 50.3448860645
+TestMigratorByCount, 2011-06-16 12:23:39,026, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4232-intel, short, 4.16416311264, 50.6448938847
+TestMigratorByCount, 2011-06-16 12:24:34,253, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4232-intel, long, 4.0694630146, 49.7850799561
+TestMigratorByCount, 2011-06-16 12:25:30,668, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4232-intel, binary, 4.26471400261, 50.2679200172
+TestSortIndividuals, 2011-06-17 14:19:38,738, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4236-intel, short, 53.682005167, 33.6767070293
+TestSortIndividuals, 2011-06-17 14:21:20,066, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4236-intel, long, 52.7289278507, 33.5573928356
+TestSortIndividuals, 2011-06-17 14:23:07,867, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4236-intel, binary, 56.0339119434, 36.2461290359
+TestSortIndividuals, 2011-06-17 14:24:03,903, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4236-intel, short, 1.04947304726, 1.13233399391
+TestSortIndividuals, 2011-06-17 14:24:21,066, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4236-intel, long, 1.03604102135, 1.10664105415
+TestSortIndividuals, 2011-06-17 14:24:38,181, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4236-intel, binary, 1.10549497604, 1.12094712257
+TestPedigreeMating, 2011-06-22 15:43:19,001, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4238-intel, short, 39.6762161255, 88.2637140751
+TestPedigreeMating, 2011-06-22 15:48:12,256, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4238-intel, long, 46.6159968376, 99.869631052
+TestPedigreeMating, 2011-06-22 15:52:44,522, bp9, x86_64-1threads, python2.7.1, simuPOP-1.0.6svn, rev4238-intel, binary, 41.4395649433, 85.7024009228
+TestPedigreeMating, 2011-06-22 16:05:06,221, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4238-intel, short, 25.8149080276, 61.1918590069
+TestPedigreeMating, 2011-06-22 16:10:02,036, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4238-intel, long, 28.0662469864, 62.3663561344
+TestPedigreeMating, 2011-06-22 16:14:42,413, bp9, x86_64-4threads, python2.7.1, simuPOP-1.0.6svn, rev4238-intel, binary, 26.5212380886, 54.3880081177
Modified: trunk/test/performance.log
===================================================================
--- trunk/test/performance.log 2011-06-29 21:13:49 UTC (rev 4241)
+++ trunk/test/performance.log 2011-06-29 21:34:43 UTC (rev 4242)
@@ -6590,3 +6590,1056 @@
TestInitSex : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 13.3092448711
TestInitSex : 12.9587409496, 13.3092448711
TestInitSex : End of test TestInitSex
+TestInitInfo : Host: bp9 (Linux, x86_64, x86_64)
+TestInitInfo : Time: Tue Jun 7 10:49:31 2011
+TestInitInfo : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestInitInfo : simuPOP: 1.0.6svn (rev 4205, module short, optimized, 1 threads)
+TestInitInfo : Test: InitInfo, results are time (not processor time) to apply operator for 1000 times.
+TestInitInfo : size=1000000: 28.5263929367
+TestInitInfo : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 28.5497779846
+TestInitInfo : 28.5263929367, 28.5497779846
+TestInitInfo : End of test TestInitInfo
+TestInitInfo : Host: bp9 (Linux, x86_64, x86_64)
+TestInitInfo : Time: Tue Jun 7 10:50:29 2011
+TestInitInfo : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestInitInfo : simuPOP: 1.0.6svn (rev 4205, module long, optimized, 1 threads)
+TestInitInfo : Test: InitInfo, results are time (not processor time) to apply operator for 1000 times.
+TestInitInfo : size=1000000: 27.8562178612
+TestInitInfo : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 28.108784914
+TestInitInfo : 27.8562178612, 28.108784914
+TestInitInfo : End of test TestInitInfo
+TestInitInfo : Host: bp9 (Linux, x86_64, x86_64)
+TestInitInfo : Time: Tue Jun 7 10:51:26 2011
+TestInitInfo : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestInitInfo : simuPOP: 1.0.6svn (rev 4205, module binary, optimized, 1 threads)
+TestInitInfo : Test: InitInfo, results are time (not processor time) to apply operator for 1000 times.
+TestInitInfo : size=1000000: 27.9055569172
+TestInitInfo : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 27.9653069973
+TestInitInfo : 27.9055569172, 27.9653069973
+TestInitInfo : End of test TestInitInfo
+TestInitInfo : Host: bp9 (Linux, x86_64, x86_64)
+TestInitInfo : Time: Tue Jun 7 11:01:22 2011
+TestInitInfo : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestInitInfo : simuPOP: 1.0.6svn (rev 4205, module short, optimized, 4 threads)
+TestInitInfo : Test: InitInfo, results are time (not processor time) to apply operator for 1000 times.
+TestInitInfo : size=1000000: 8.08958816528
+TestInitInfo : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 8.34579896927
+TestInitInfo : 8.08958816528, 8.34579896927
+TestInitInfo : End of test TestInitInfo
+TestInitInfo : Host: bp9 (Linux, x86_64, x86_64)
+TestInitInfo : Time: Tue Jun 7 11:01:40 2011
+TestInitInfo : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestInitInfo : simuPOP: 1.0.6svn (rev 4205, module long, optimized, 4 threads)
+TestInitInfo : Test: InitInfo, results are time (not processor time) to apply operator for 1000 times.
+TestInitInfo : size=1000000: 8.00524497032
+TestInitInfo : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 8.44241905212
+TestInitInfo : 8.00524497032, 8.44241905212
+TestInitInfo : End of test TestInitInfo
+TestInitInfo : Host: bp9 (Linux, x86_64, x86_64)
+TestInitInfo : Time: Tue Jun 7 11:01:57 2011
+TestInitInfo : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestInitInfo : simuPOP: 1.0.6svn (rev 4205, module binary, optimized, 4 threads)
+TestInitInfo : Test: InitInfo, results are time (not processor time) to apply operator for 1000 times.
+TestInitInfo : size=1000000: 8.06356215477
+TestInitInfo : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 8.2104408741
+TestInitInfo : 8.06356215477, 8.2104408741
+TestInitInfo : End of test TestInitInfo
+TestInitInfo : Host: EPI7-0541302 (Windows, AMD64, Intel64 Family 6 Model 30 Stepping 5, GenuineIntel)
+TestInitInfo : Time: Tue Jun 07 11:50:36 2011
+TestInitInfo : Python: 2.7.1 [MSC v.1500 64 bit (AMD64)]
+TestInitInfo : simuPOP: 1.0.6svn (rev 4205, module short, optimized, 1 threads)
+TestInitInfo : Test: InitInfo, results are time (not processor time) to apply operator for 1000 times.
+TestInitInfo : size=1000000: 42.5138275974
+TestInitInfo : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 42.0906409373
+TestInitInfo : 42.5138275974, 42.0906409373
+TestInitInfo : End of test TestInitInfo
+TestInitInfo : Host: EPI7-0541302 (Windows, AMD64, Intel64 Family 6 Model 30 Stepping 5, GenuineIntel)
+TestInitInfo : Time: Tue Jun 07 11:52:02 2011
+TestInitInfo : Python: 2.7.1 [MSC v.1500 64 bit (AMD64)]
+TestInitInfo : simuPOP: 1.0.6svn (rev 4205, module long, optimized, 1 threads)
+TestInitInfo : Test: InitInfo, results are time (not processor time) to apply operator for 1000 times.
+TestInitInfo : size=1000000: 42.7154268612
+TestInitInfo : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 43.2257380443
+TestInitInfo : 42.7154268612, 43.2257380443
+TestInitInfo : End of test TestInitInfo
+TestInitInfo : Host: EPI7-0541302 (Windows, AMD64, Intel64 Family 6 Model 30 Stepping 5, GenuineIntel)
+TestInitInfo : Time: Tue Jun 07 11:53:30 2011
+TestInitInfo : Python: 2.7.1 [MSC v.1500 64 bit (AMD64)]
+TestInitInfo : simuPOP: 1.0.6svn (rev 4205, module binary, optimized, 1 threads)
+TestInitInfo : Test: InitInfo, results are time (not processor time) to apply operator for 1000 times.
+TestInitInfo : size=1000000: 45.0157581313
+TestInitInfo : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 44.4060398472
+TestInitInfo : 45.0157581313, 44.4060398472
+TestInitInfo : End of test TestInitInfo
+TestInitInfo : Host: EPI7-0541302 (Windows, AMD64, Intel64 Family 6 Model 30 Stepping 5, GenuineIntel)
+TestInitInfo : Time: Tue Jun 07 11:55:24 2011
+TestInitInfo : Python: 2.7.1 [MSC v.1500 64 bit (AMD64)]
+TestInitInfo : simuPOP: 1.0.6svn (rev 4205, module short, optimized, 4 threads)
+TestInitInfo : Test: InitInfo, results are time (not processor time) to apply operator for 1000 times.
+TestInitInfo : size=1000000: 12.986396842
+TestInitInfo : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 14.089627703
+TestInitInfo : 12.986396842, 14.089627703
+TestInitInfo : End of test TestInitInfo
+TestInitInfo : Host: EPI7-0541302 (Windows, AMD64, Intel64 Family 6 Model 30 Stepping 5, GenuineIntel)
+TestInitInfo : Time: Tue Jun 07 11:55:52 2011
+TestInitInfo : Python: 2.7.1 [MSC v.1500 64 bit (AMD64)]
+TestInitInfo : simuPOP: 1.0.6svn (rev 4205, module long, optimized, 4 threads)
+TestInitInfo : Test: InitInfo, results are time (not processor time) to apply operator for 1000 times.
+TestInitInfo : size=1000000: 13.1444051231
+TestInitInfo : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 13.6804705765
+TestInitInfo : 13.1444051231, 13.6804705765
+TestInitInfo : End of test TestInitInfo
+TestInitInfo : Host: EPI7-0541302 (Windows, AMD64, Intel64 Family 6 Model 30 Stepping 5, GenuineIntel)
+TestInitInfo : Time: Tue Jun 07 11:56:21 2011
+TestInitInfo : Python: 2.7.1 [MSC v.1500 64 bit (AMD64)]
+TestInitInfo : simuPOP: 1.0.6svn (rev 4205, module binary, optimized, 4 threads)
+TestInitInfo : Test: InitInfo, results are time (not processor time) to apply operator for 1000 times.
+TestInitInfo : size=1000000: 12.6781480139
+TestInitInfo : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 13.7568184564
+TestInitInfo : 12.6781480139, 13.7568184564
+TestInitInfo : End of test TestInitInfo
+TestMapSelector : Host: bp9 (Linux, x86_64, x86_64)
+TestMapSelector : Time: Wed Jun 8 12:28:08 2011
+TestMapSelector : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestMapSelector : simuPOP: 1.0.6svn (rev 4212, module short, optimized, 1 threads)
+TestMapSelector : Test: MapSelector, results are time (not processor time) to apply operator for 1000 times.
+TestMapSelector : size=1000000: 137.560660124
+TestMapSelector : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 136.669243097
+TestMapSelector : 137.560660124, 136.669243097
+TestMapSelector : End of test TestMapSelector
+TestMapSelector : Host: bp9 (Linux, x86_64, x86_64)
+TestMapSelector : Time: Wed Jun 8 12:32:43 2011
+TestMapSelector : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestMapSelector : simuPOP: 1.0.6svn (rev 4212, module long, optimized, 1 threads)
+TestMapSelector : Test: MapSelector, results are time (not processor time) to apply operator for 1000 times.
+TestMapSelector : size=1000000: 131.439245939
+TestMapSelector : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 129.801275969
+TestMapSelector : 131.439245939, 129.801275969
+TestMapSelector : End of test TestMapSelector
+TestMapSelector : Host: bp9 (Linux, x86_64, x86_64)
+TestMapSelector : Time: Wed Jun 8 12:37:06 2011
+TestMapSelector : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestMapSelector : simuPOP: 1.0.6svn (rev 4212, module binary, optimized, 1 threads)
+TestMapSelector : Test: MapSelector, results are time (not processor time) to apply operator for 1000 times.
+TestMapSelector : size=1000000: 149.361258984
+TestMapSelector : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 148.818060875
+TestMapSelector : 149.361258984, 148.818060875
+TestMapSelector : End of test TestMapSelector
+TestMapSelector : Host: bp9 (Linux, x86_64, x86_64)
+TestMapSelector : Time: Wed Jun 8 12:46:39 2011
+TestMapSelector : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestMapSelector : simuPOP: 1.0.6svn (rev 4212, module short, optimized, 4 threads)
+TestMapSelector : Test: MapSelector, results are time (not processor time) to apply operator for 1000 times.
+TestMapSelector : size=1000000: 45.7759559155
+TestMapSelector : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 52.9312109947
+TestMapSelector : 45.7759559155, 52.9312109947
+TestMapSelector : End of test TestMapSelector
+TestMapSelector : Host: bp9 (Linux, x86_64, x86_64)
+TestMapSelector : Time: Wed Jun 8 12:48:19 2011
+TestMapSelector : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestMapSelector : simuPOP: 1.0.6svn (rev 4212, module long, optimized, 4 threads)
+TestMapSelector : Test: MapSelector, results are time (not processor time) to apply operator for 1000 times.
+TestMapSelector : size=1000000: 46.7970941067
+TestMapSelector : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 47.7334721088
+TestMapSelector : 46.7970941067, 47.7334721088
+TestMapSelector : End of test TestMapSelector
+TestMapSelector : Host: bp9 (Linux, x86_64, x86_64)
+TestMapSelector : Time: Wed Jun 8 12:49:54 2011
+TestMapSelector : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestMapSelector : simuPOP: 1.0.6svn (rev 4212, module binary, optimized, 4 threads)
+TestMapSelector : Test: MapSelector, results are time (not processor time) to apply operator for 1000 times.
+TestMapSelector : size=1000000: 52.5352201462
+TestMapSelector : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 55.497841835
+TestMapSelector : 52.5352201462, 55.497841835
+TestMapSelector : End of test TestMapSelector
+TestMaSelector : Host: bp9 (Linux, x86_64, x86_64)
+TestMaSelector : Time: Wed Jun 8 14:27:17 2011
+TestMaSelector : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestMaSelector : simuPOP: 1.0.6svn (rev 4214, module short, optimized, 1 threads)
+TestMaSelector : Test: MaSelector, results are time (not processor time) to apply operator for 1000 times.
+TestMaSelector : size=1000000: 25.4252510071
+TestMaSelector : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 25.5701878071
+TestMaSelector : 25.4252510071, 25.5701878071
+TestMaSelector : End of test TestMaSelector
+TestMaSelector : Host: bp9 (Linux, x86_64, x86_64)
+TestMaSelector : Time: Wed Jun 8 14:28:08 2011
+TestMaSelector : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestMaSelector : simuPOP: 1.0.6svn (rev 4214, module long, optimized, 1 threads)
+TestMaSelector : Test: MaSelector, results are time (not processor time) to apply operator for 1000 times.
+TestMaSelector : size=1000000: 27.9332430363
+TestMaSelector : size=[100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000, 100000]: 27.9779438972
+TestMaSelector : 27.9332430363, 27.9779438972
+TestMaSelector : End of test TestMaSelector
+TestMaSelector : Host: bp9 (Linux, x86_64, x86_64)
+TestMaSelector : Time: Wed Jun 8 14:29:05 2011
+TestMaSelector : Python: 2.7.1 [GCC Intel(R) C++ g++ 4.4 mode]
+TestMaSelector : simuPOP: 1.0.6svn...
[truncated message content] |
|
From: <si...@us...> - 2011-07-06 16:23:42
|
Revision: 4244
http://simupop.svn.sourceforge.net/simupop/?rev=4244&view=rev
Author: simupop
Date: 2011-07-06 15:33:58 +0000 (Wed, 06 Jul 2011)
Log Message:
-----------
Rename src to simuPOP so that the development mode of setup.py/distribute will work directly
Added Paths:
-----------
trunk/simuPOP/
Removed Paths:
-------------
trunk/src/
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <si...@us...> - 2011-07-06 16:24:18
|
Revision: 4245
http://simupop.svn.sourceforge.net/simupop/?rev=4245&view=rev
Author: simupop
Date: 2011-07-06 15:46:04 +0000 (Wed, 06 Jul 2011)
Log Message:
-----------
Update manifest and setup.py for the rename
Modified Paths:
--------------
trunk/MANIFEST.in
trunk/setup.py
Modified: trunk/MANIFEST.in
===================================================================
--- trunk/MANIFEST.in 2011-07-06 15:33:58 UTC (rev 4244)
+++ trunk/MANIFEST.in 2011-07-06 15:46:04 UTC (rev 4245)
@@ -18,86 +18,86 @@
include config_win32.h
include config_linux.h
include config_mac.h
-include src/simuPOP_cfg.h
-include src/utility.h
-include src/genoStru.h
-include src/individual.h
-include src/population.h
-include src/simulator.h
-include src/mating.h
-include src/operator.h
-include src/initializer.h
-include src/migrator.h
-include src/outputer.h
-include src/selector.h
-include src/penetrance.h
-include src/qtrait.h
-include src/stator.h
-include src/mutator.h
-include src/transmitter.h
-include src/tagger.h
-include src/pedigree.h
-include src/virtualSubPop.h
-include src/sandbox.h
+include simuPOP/simuPOP_cfg.h
+include simuPOP/utility.h
+include simuPOP/genoStru.h
+include simuPOP/individual.h
+include simuPOP/population.h
+include simuPOP/simulator.h
+include simuPOP/mating.h
+include simuPOP/operator.h
+include simuPOP/initializer.h
+include simuPOP/migrator.h
+include simuPOP/outputer.h
+include simuPOP/selector.h
+include simuPOP/penetrance.h
+include simuPOP/qtrait.h
+include simuPOP/stator.h
+include simuPOP/mutator.h
+include simuPOP/transmitter.h
+include simuPOP/tagger.h
+include simuPOP/pedigree.h
+include simuPOP/virtualSubPop.h
+include simuPOP/sandbox.h
# source files
-include src/customizedTypes.c
-include src/utility.cpp
-include src/genoStru.cpp
-include src/individual.cpp
-include src/population.cpp
-include src/simulator.cpp
-include src/mating.cpp
-include src/operator.cpp
-include src/initializer.cpp
-include src/migrator.cpp
-include src/outputer.cpp
-include src/selector.cpp
-include src/penetrance.cpp
-include src/qtrait.cpp
-include src/stator.cpp
-include src/mutator.cpp
-include src/transmitter.cpp
-include src/tagger.cpp
-include src/pedigree.cpp
-include src/virtualSubPop.cpp
-include src/sandbox.cpp
-include src/main.cpp
+include simuPOP/customizedTypes.c
+include simuPOP/utility.cpp
+include simuPOP/genoStru.cpp
+include simuPOP/individual.cpp
+include simuPOP/population.cpp
+include simuPOP/simulator.cpp
+include simuPOP/mating.cpp
+include simuPOP/operator.cpp
+include simuPOP/initializer.cpp
+include simuPOP/migrator.cpp
+include simuPOP/outputer.cpp
+include simuPOP/selector.cpp
+include simuPOP/penetrance.cpp
+include simuPOP/qtrait.cpp
+include simuPOP/stator.cpp
+include simuPOP/mutator.cpp
+include simuPOP/transmitter.cpp
+include simuPOP/tagger.cpp
+include simuPOP/pedigree.cpp
+include simuPOP/virtualSubPop.cpp
+include simuPOP/sandbox.cpp
+include simuPOP/main.cpp
# source generated files
-include src/swigpyrun.h
-include src/simuPOP_std_wrap.cpp
-include src/simuPOP_op_wrap.cpp
-include src/simuPOP_la_wrap.cpp
-include src/simuPOP_laop_wrap.cpp
-include src/simuPOP_ba_wrap.cpp
-include src/simuPOP_baop_wrap.cpp
-include src/simuPOP_std.py
-include src/simuPOP_op.py
-include src/simuPOP_la.py
-include src/simuPOP_laop.py
-include src/simuPOP_ba.py
-include src/simuPOP_baop.py
-include src/gsl_wrap.c
+include simuPOP/swigpyrun.h
+include simuPOP/simuPOP_std_wrap.cpp
+include simuPOP/simuPOP_op_wrap.cpp
+include simuPOP/simuPOP_la_wrap.cpp
+include simuPOP/simuPOP_laop_wrap.cpp
+include simuPOP/simuPOP_ba_wrap.cpp
+include simuPOP/simuPOP_baop_wrap.cpp
+include simuPOP/simuPOP_std.py
+include simuPOP/simuPOP_op.py
+include simuPOP/simuPOP_la.py
+include simuPOP/simuPOP_laop.py
+include simuPOP/simuPOP_ba.py
+include simuPOP/simuPOP_baop.py
+include simuPOP/gsl_wrap.c
# source wrap files
-include src/simuPOP_common.i
-include src/simuPOP_doc.i
-include src/simuPOP_std.i
-include src/simuPOP_op.i
-include src/simuPOP_la.i
-include src/simuPOP_laop.i
-include src/simuPOP_ba.i
-include src/simuPOP_baop.i
-include src/gsl.i
+include simuPOP/simuPOP_common.i
+include simuPOP/simuPOP_doc.i
+include simuPOP/simuPOP_std.i
+include simuPOP/simuPOP_op.i
+include simuPOP/simuPOP_la.i
+include simuPOP/simuPOP_laop.i
+include simuPOP/simuPOP_ba.i
+include simuPOP/simuPOP_baop.i
+include simuPOP/gsl.i
# source python files (modules)
include simuOpt.py
-include src/__init__.py
-include src/utils.py
-include src/plotter.py
-include src/sampling.py
-include src/sandbox.py
+include simuPOP/__init__.py
+include simuPOP/utils.py
+include simuPOP/plotter.py
+include simuPOP/sampling.py
+include simuPOP/sandbox.py
# gsl files
include gsl/gsl_machine.h
Modified: trunk/setup.py
===================================================================
--- trunk/setup.py 2011-07-06 15:33:58 UTC (rev 4244)
+++ trunk/setup.py 2011-07-06 15:46:04 UTC (rev 4245)
@@ -399,9 +399,9 @@
SWIG_CC_FLAGS += ' -py3'
SWIG_RUNTIME_FLAGS = '-python -external-runtime'
-# python setup.py reads py_modules from src so we have to produce simuPOP_std.py
+# python setup.py reads py_modules from simuPOP so we have to produce simuPOP_std.py
# etc to this directory.
-SWIG_OUTDIR = 'src'
+SWIG_OUTDIR = 'simuPOP'
if not os.path.isdir('build'):
os.mkdir('build')
@@ -421,12 +421,12 @@
}
WRAP_INFO = {
- 'std': ['src/simuPOP_std_wrap.cpp', 'src/simuPOP_std.i', ''],
- 'op': ['src/simuPOP_op_wrap.cpp', 'src/simuPOP_op.i', '-DOPTIMIZED'],
- 'la': ['src/simuPOP_la_wrap.cpp', 'src/simuPOP_la.i', '-DLONGALLELE'],
- 'laop': ['src/simuPOP_laop_wrap.cpp', 'src/simuPOP_laop.i', '-DLONGALLELE -DOPTIMIZED'],
- 'ba': ['src/simuPOP_ba_wrap.cpp', 'src/simuPOP_ba.i', '-DBINARYALLELE'],
- 'baop': ['src/simuPOP_baop_wrap.cpp', 'src/simuPOP_baop.i', '-DBINARYALLELE -DOPTIMIZED'],
+ 'std': ['simuPOP/simuPOP_std_wrap.cpp', 'simuPOP/simuPOP_std.i', ''],
+ 'op': ['simuPOP/simuPOP_op_wrap.cpp', 'simuPOP/simuPOP_op.i', '-DOPTIMIZED'],
+ 'la': ['simuPOP/simuPOP_la_wrap.cpp', 'simuPOP/simuPOP_la.i', '-DLONGALLELE'],
+ 'laop': ['simuPOP/simuPOP_laop_wrap.cpp', 'simuPOP/simuPOP_laop.i', '-DLONGALLELE -DOPTIMIZED'],
+ 'ba': ['simuPOP/simuPOP_ba_wrap.cpp', 'simuPOP/simuPOP_ba.i', '-DBINARYALLELE'],
+ 'baop': ['simuPOP/simuPOP_baop_wrap.cpp', 'simuPOP/simuPOP_baop.i', '-DBINARYALLELE -DOPTIMIZED'],
}
if os.name == 'nt':
@@ -466,7 +466,7 @@
boost_lib_names = []
boost_lib_path = None
res = {}
- res['src'] = ['src/simuPOP_' + modu + '_wrap.cpp']
+ res['src'] = ['simuPOP/simuPOP_' + modu + '_wrap.cpp']
for src in SOURCE_FILES:
res['src'].append('build/%s/%s' % (modu, src))
res['src'].extend(LIB_FILES)
@@ -534,8 +534,8 @@
machine = platform.uname()[4].lower()
if machine == '': # have to guess
machine = 'x86'
- shutil.copy('win32/%s/vcomp90.dll' % machine, 'src/vcomp90.dll')
- shutil.copy('win32/%s/msvcr90.dll' % machine, 'src/msvcr90.dll')
+ shutil.copy('win32/%s/vcomp90.dll' % machine, 'simuPOP/vcomp90.dll')
+ shutil.copy('win32/%s/msvcr90.dll' % machine, 'simuPOP/msvcr90.dll')
if __name__ == '__main__':
SIMUPOP_VER, SIMUPOP_REV = simuPOP_version()
@@ -546,9 +546,9 @@
#
# if any of the wrap files does not exist
# or if the wrap files are older than any of the source files.
- if (not os.path.isfile('src/gsl_wrap.c') or (not os.path.isfile('src/swigpyrun.h')) or \
+ if (not os.path.isfile('simuPOP/gsl_wrap.c') or (not os.path.isfile('simuPOP/swigpyrun.h')) or \
False in [os.path.isfile(WRAP_INFO[x][0]) for x in MODULES]) or \
- (max( [os.path.getmtime('src/' + x) for x in HEADER_FILES] ) > \
+ (max( [os.path.getmtime('simuPOP/' + x) for x in HEADER_FILES] ) > \
min( [os.path.getmtime(WRAP_INFO[x][0]) for x in MODULES])):
(v1, v2, v3) = swig_version()
if (v1, v2, v3) < (1, 3, 35):
@@ -558,8 +558,8 @@
print('Swig >= 2.0.4 is required for Python 3.2 or higher')
sys.exit(1)
# generate header file
- print("Generating external runtime header file src/swigpyrun.h...")
- os.system('%s %s src/swigpyrun.h' % (SWIG, SWIG_RUNTIME_FLAGS))
+ print("Generating external runtime header file simuPOP/swigpyrun.h...")
+ os.system('%s %s simuPOP/swigpyrun.h' % (SWIG, SWIG_RUNTIME_FLAGS))
# try the first option set with the first library
for lib in MODULES:
print("Generating wrapper file " + WRAP_INFO[lib][0])
@@ -567,9 +567,9 @@
SWIG_OUTDIR, WRAP_INFO[lib][2], WRAP_INFO[lib][0], WRAP_INFO[lib][1])) != 0:
print("Calling swig failed. Please check your swig version.")
sys.exit(1)
- print("Generating wrapper file src/gsl_wrap.c")
+ print("Generating wrapper file simuPOP/gsl_wrap.c")
if os.system('%s %s -outdir %s %s -o %s %s' % (SWIG, SWIG_CC_FLAGS, \
- SWIG_OUTDIR, '', 'src/gsl_wrap.c', 'src/gsl.i')) != 0:
+ SWIG_OUTDIR, '', 'simuPOP/gsl_wrap.c', 'simuPOP/gsl.i')) != 0:
print("Calling swig failed. Please check your swig version.")
sys.exit(1)
print("\nAll wrap files are generated successfully.\n")
@@ -585,13 +585,13 @@
os.mkdir('build/%s' % modu)
for src in SOURCE_FILES:
mod_src = 'build/%s/%s' % (modu, src)
- if not os.path.isfile(mod_src) or not filecmp.cmp(mod_src,'src/'+src):
- shutil.copy('src/'+src, mod_src)
+ if not os.path.isfile(mod_src) or not filecmp.cmp(mod_src,'simuPOP/'+src):
+ shutil.copy('simuPOP/'+src, mod_src)
# build
# For module simuPOP.gsl
EXT_MODULES = [
Extension('simuPOP._gsl',
- sources = GSL_FILES + ['src/gsl_wrap.c'],
+ sources = GSL_FILES + ['simuPOP/gsl_wrap.c'],
include_dirs = ['gsl', 'gsl/specfunc', 'build', '.'],
)
]
@@ -602,7 +602,7 @@
sources = info['src'],
extra_compile_args = info['extra_compile_args'],
# src for config.h etc, build for swigpyrun.h
- include_dirs = info['include_dirs'] + ['src', 'build'],
+ include_dirs = info['include_dirs'] + ['simuPOP', 'build'],
library_dirs = info['library_dirs'],
libraries = info['libraries'],
define_macros = info['define_macros'],
@@ -642,7 +642,7 @@
],
platforms = ['all'],
#
- package_dir = {'simuPOP': 'src'},
+ package_dir = {'simuPOP': 'simuPOP'},
package_data = {'simuPOP': PACKAGE_DATA},
py_modules = [
'simuOpt',
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <si...@us...> - 2011-07-06 16:52:38
|
Revision: 4248
http://simupop.svn.sourceforge.net/simupop/?rev=4248&view=rev
Author: simupop
Date: 2011-07-06 16:52:32 +0000 (Wed, 06 Jul 2011)
Log Message:
-----------
Update processing scripts. Prepare for a release
Modified Paths:
--------------
trunk/Doxy_web
trunk/Doxyfile
trunk/Makefile
trunk/simuPOP/initializer.cpp
trunk/simuPOP/simuPOP_doc.i
trunk/simuPOP/stator.cpp
trunk/simuPOP/transmitter.cpp
trunk/simuPOP/transmitter.h
trunk/simuPOP/utility.cpp
trunk/simuPOP/utility.h
trunk/tools/doxy2swig.py
Modified: trunk/Doxy_web
===================================================================
--- trunk/Doxy_web 2011-07-06 16:18:23 UTC (rev 4247)
+++ trunk/Doxy_web 2011-07-06 16:52:32 UTC (rev 4248)
@@ -578,7 +578,7 @@
# directories like "/usr/src/myproject". Separate the files or directories
# with spaces.
-INPUT = src
+INPUT = simuPOP
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
Modified: trunk/Doxyfile
===================================================================
--- trunk/Doxyfile 2011-07-06 16:18:23 UTC (rev 4247)
+++ trunk/Doxyfile 2011-07-06 16:52:32 UTC (rev 4248)
@@ -578,7 +578,7 @@
# directories like "/usr/src/myproject". Separate the files or directories
# with spaces.
-INPUT = src \
+INPUT = simuPOP \
config_linux.h
# This tag can be used to specify the character encoding of the source files
Modified: trunk/Makefile
===================================================================
--- trunk/Makefile 2011-07-06 16:18:23 UTC (rev 4247)
+++ trunk/Makefile 2011-07-06 16:52:32 UTC (rev 4248)
@@ -4,7 +4,7 @@
rebuild:
- bcpp src/*.h src/*.cpp
+ bcpp simuPOP/*.h simuPOP/*.cpp
doxygen
tools/doxy2swig.py
scons install -j4 std
@@ -17,7 +17,7 @@
clean:
@rm -rf build
- @rm -f src/*wrap* src/simuPOP_*.py
+ @rm -f simuPOP/*wrap* simuPOP/simuPOP_*.py
@find . -name '*~' -exec rm -f {} \;
@find . -name '*.bak' -exec rm -f {} \;
@find . -name '*.py?' -exec rm -f {} \;
Modified: trunk/simuPOP/initializer.cpp
===================================================================
--- trunk/simuPOP/initializer.cpp 2011-07-06 16:18:23 UTC (rev 4247)
+++ trunk/simuPOP/initializer.cpp 2011-07-06 16:52:32 UTC (rev 4248)
@@ -71,13 +71,13 @@
else {
if (numThreads() > 1) {
#ifdef _OPENMP
-#pragma omp parallel private(ind)
+# pragma omp parallel private(ind)
{
ind = pop.indIterator(sp->subPop(), omp_get_thread_num());
for (; ind.valid(); ++ind)
ind->setSex(ws.draw() == 0 ? MALE : FEMALE);
}
-#endif
+#endif
} else
for (; ind.valid(); ++ind)
ind->setSex(ws.draw() == 0 ? MALE : FEMALE);
Modified: trunk/simuPOP/simuPOP_doc.i
===================================================================
--- trunk/simuPOP/simuPOP_doc.i 2011-07-06 16:18:23 UTC (rev 4247)
+++ trunk/simuPOP/simuPOP_doc.i 2011-07-06 16:52:32 UTC (rev 4248)
@@ -740,13 +740,13 @@
";
-%ignore simuPOP::Bernullitrials::Bernullitrials(RNG &rng);
+%ignore simuPOP::Bernullitrials::Bernullitrials(RNG &);
%feature("docstring") simuPOP::Bernullitrials::Bernullitrials "
Usage:
- Bernullitrials(rng, prob, trials)
+ Bernullitrials(, prob, trials=0)
";
@@ -768,7 +768,7 @@
";
-%ignore simuPOP::Bernullitrials::setParameter(const vectorf &prob, size_t trials);
+%ignore simuPOP::Bernullitrials::setParameter(const vectorf &prob, size_t trials=0);
%feature("docstring") simuPOP::Bernullitrials::doTrial "
@@ -1032,6 +1032,8 @@
%feature("docstring") simuPOP::CombinedParentsChooser::describe "Obsolete or undocumented function."
+%ignore simuPOP::CombinedParentsChooser::parallelizable() const;
+
%ignore simuPOP::CombinedParentsChooser::initialize(Population &pop, size_t sp);
%ignore simuPOP::CombinedParentsChooser::finalize(Population &pop, size_t sp);
@@ -3191,6 +3193,8 @@
%feature("docstring") simuPOP::InheritTagger::clone "Obsolete or undocumented function."
+%ignore simuPOP::InheritTagger::parallelizable() const;
+
%feature("docstring") simuPOP::InitGenotype "
Details:
@@ -3547,6 +3551,8 @@
%feature("docstring") simuPOP::MaPenetrance::describe "Obsolete or undocumented function."
+%ignore simuPOP::MaPenetrance::parallelizable() const;
+
%feature("docstring") simuPOP::MapPenetrance "
Details:
@@ -3595,6 +3601,8 @@
%feature("docstring") simuPOP::MapPenetrance::describe "Obsolete or undocumented function."
+%ignore simuPOP::MapPenetrance::parallelizable() const;
+
%feature("docstring") simuPOP::MapSelector "
Details:
@@ -3644,6 +3652,8 @@
%feature("docstring") simuPOP::MapSelector::describe "Obsolete or undocumented function."
+%ignore simuPOP::MapSelector::parallelizable() const;
+
%feature("docstring") simuPOP::MaSelector "
Details:
@@ -3700,6 +3710,8 @@
%feature("docstring") simuPOP::MaSelector::describe "Obsolete or undocumented function."
+%ignore simuPOP::MaSelector::parallelizable() const;
+
%feature("docstring") simuPOP::MatingScheme "
Details:
@@ -4065,6 +4077,8 @@
%ignore simuPOP::MitochondrialGenoTransmitter::applyDuringMating(Population &pop, Population &offPop, RawIndIterator offspring, Individual *dad=NULL, Individual *mom=NULL) const;
+%ignore simuPOP::MitochondrialGenoTransmitter::parallelizable() const;
+
%feature("docstring") simuPOP::MixedMutator "
Details:
@@ -4158,6 +4172,8 @@
%feature("docstring") simuPOP::MlPenetrance::describe "Obsolete or undocumented function."
+%ignore simuPOP::MlPenetrance::parallelizable() const;
+
%feature("docstring") simuPOP::MlSelector "
Details:
@@ -4208,6 +4224,8 @@
%feature("docstring") simuPOP::MlSelector::describe "Obsolete or undocumented function."
+%ignore simuPOP::MlSelector::parallelizable() const;
+
%feature("docstring") simuPOP::MutSpaceMutator "
Details:
@@ -4838,6 +4856,8 @@
%ignore simuPOP::ParentsTagger::applyDuringMating(Population &pop, Population &offPop, RawIndIterator offspring, Individual *dad=NULL, Individual *mom=NULL) const;
+%ignore simuPOP::ParentsTagger::parallelizable() const;
+
%feature("docstring") simuPOP::Pause "
Details:
@@ -5256,6 +5276,14 @@
%ignore simuPOP::PedigreeMating::mate(Population &pop, Population &scratch);
+%feature("docstring") simuPOP::PedigreeMating::parallelizable "
+
+Usage:
+
+ x.parallelizable()
+
+";
+
%feature("docstring") simuPOP::PedigreeTagger "
Details:
@@ -5330,6 +5358,8 @@
%ignore simuPOP::PedigreeTagger::applyDuringMating(Population &pop, Population &offPop, RawIndIterator offspring, Individual *dad=NULL, Individual *mom=NULL) const;
+%ignore simuPOP::PedigreeTagger::parallelizable() const;
+
%feature("docstring") simuPOP::PointMutator "
Details:
@@ -5445,6 +5475,8 @@
%feature("docstring") simuPOP::PolyParentsChooser::describe "Obsolete or undocumented function."
+%ignore simuPOP::PolyParentsChooser::parallelizable() const;
+
%ignore simuPOP::PolyParentsChooser::initialize(Population &pop, size_t sp);
%ignore simuPOP::PolyParentsChooser::chooseParents(RawIndIterator basePtr);
@@ -7190,6 +7222,8 @@
%feature("docstring") simuPOP::PyParentsChooser::describe "Obsolete or undocumented function."
+%ignore simuPOP::PyParentsChooser::parallelizable() const;
+
%ignore simuPOP::PyParentsChooser::initialize(Population &pop, size_t sp);
%ignore simuPOP::PyParentsChooser::finalize(Population &pop, size_t sp);
@@ -7251,6 +7285,8 @@
%feature("docstring") simuPOP::PyPenetrance::describe "Obsolete or undocumented function."
+%ignore simuPOP::PyPenetrance::parallelizable() const;
+
%feature("docstring") simuPOP::pyPopIterator "
Details:
@@ -7383,6 +7419,8 @@
%feature("docstring") simuPOP::PySelector::describe "Obsolete or undocumented function."
+%ignore simuPOP::PySelector::parallelizable() const;
+
%feature("docstring") simuPOP::PyTagger "
Details:
@@ -7424,6 +7462,8 @@
%ignore simuPOP::PyTagger::applyDuringMating(Population &pop, Population &offPop, RawIndIterator offspring, Individual *dad=NULL, Individual *mom=NULL) const;
+%ignore simuPOP::PyTagger::parallelizable() const;
+
%feature("docstring") simuPOP::RandomParentChooser "
Details:
@@ -7767,6 +7807,8 @@
%ignore simuPOP::Recombinator::applyDuringMating(Population &pop, Population &offPop, RawIndIterator offspring, Individual *dad, Individual *mom) const;
+%ignore simuPOP::Recombinator::parallelizable() const;
+
%feature("docstring") simuPOP::ResizeSubPops "
Details:
@@ -7942,8 +7984,6 @@
";
-%ignore simuPOP::RNG::generateRandomSeed();
-
%feature("docstring") simuPOP::RNG::randUniform "
Usage:
@@ -10378,6 +10418,8 @@
%ignore simuPOP::fetchAndIncrement(ATOMICLONG *val);
+%ignore simuPOP::parallelSort(T1 start, T1 end, T2 cmp);
+
%ignore simuPOP::simuPOPkbhit();
%ignore simuPOP::simuPOPgetch();
Modified: trunk/simuPOP/stator.cpp
===================================================================
--- trunk/simuPOP/stator.cpp 2011-07-06 16:18:23 UTC (rev 4247)
+++ trunk/simuPOP/stator.cpp 2011-07-06 16:52:32 UTC (rev 4248)
@@ -2483,7 +2483,7 @@
}
}
#endif
- } else {
+ } else{
HAPLOLIST::const_iterator it = begin;
for (; it != end; ++it) {
HAPLOLIST::const_iterator it1 = it;
Modified: trunk/simuPOP/transmitter.cpp
===================================================================
--- trunk/simuPOP/transmitter.cpp 2011-07-06 16:18:23 UTC (rev 4247)
+++ trunk/simuPOP/transmitter.cpp 2011-07-06 16:52:32 UTC (rev 4248)
@@ -420,7 +420,7 @@
GenoTransmitter(output, begin, end, step, at, reps, subPops, infoFields),
m_intensity(intensity), m_rates(rates.elems()), m_loci(loci),
m_recBeforeLoci(0), m_convMode(convMode.elems()), m_chromX(-1), m_chromY(-1),
- m_customizedBegin(-1), m_customizedEnd(-1), m_algorithm(0), m_debugOutput(NULL),
+ m_customizedBegin(-1), m_customizedEnd(-1), m_algorithm(0), m_debugOutput(NULL),
#ifdef _OPENMP
m_bt(numThreads(), getRNG())
#else
Modified: trunk/simuPOP/transmitter.h
===================================================================
--- trunk/simuPOP/transmitter.h 2011-07-06 16:18:23 UTC (rev 4247)
+++ trunk/simuPOP/transmitter.h 2011-07-06 16:52:32 UTC (rev 4248)
@@ -638,7 +638,7 @@
#ifdef _OPENMP
mutable vector<Bernullitrials> m_bt;
#else
- mutable Bernullitrials m_bt;
+ mutable Bernullitrials m_bt;
#endif
Modified: trunk/simuPOP/utility.cpp
===================================================================
--- trunk/simuPOP/utility.cpp 2011-07-06 16:18:23 UTC (rev 4247)
+++ trunk/simuPOP/utility.cpp 2011-07-06 16:52:32 UTC (rev 4248)
@@ -492,7 +492,7 @@
ATOMICLONG fetchAndIncrement(ATOMICLONG * val)
{
- if(g_numThreads == 1)
+ if (g_numThreads == 1)
return (*val)++;
else
#ifdef _WIN64
@@ -500,11 +500,11 @@
#elif defined(_WIN32)
return InterlockedIncrement(val) - 1;
#else
- // for Intel C++, see page 164 of
- // http://softwarecommunity.intel.com/isn/downloads/softwareproducts/pdfs/347603.pdf
- //
- // for gcc, see
- // http://gcc.gnu.org/onlinedocs/gcc-4.1.0/gcc/Atomic-Builtins.html
+ // for Intel C++, see page 164 of
+ // http://softwarecommunity.intel.com/isn/downloads/softwareproducts/pdfs/347603.pdf
+ //
+ // for gcc, see
+ // http://gcc.gnu.org/onlinedocs/gcc-4.1.0/gcc/Atomic-Builtins.html
return __sync_fetch_and_add(val, 1);
#endif
}
@@ -2265,9 +2265,9 @@
if (m_stmts != NULL) {
#if PY_VERSION_HEX >= 0x03020000
res = PyEval_EvalCode((PyObject *)m_stmts, m_locals, m_locals);
-#else
+#else
res = PyEval_EvalCode((PyCodeObject *)m_stmts, m_locals, m_locals);
-#endif
+#endif
if (res == NULL) {
#ifndef OPTIMIZED
if (debug(DBG_GENERAL)) {
@@ -2287,7 +2287,7 @@
res = PyEval_EvalCode((PyObject *)m_expr, m_locals, m_locals);
#else
res = PyEval_EvalCode((PyCodeObject *)m_expr, m_locals, m_locals);
-#endif
+#endif
if (res == NULL) {
#ifndef OPTIMIZED
if (debug(DBG_GENERAL)) {
Modified: trunk/simuPOP/utility.h
===================================================================
--- trunk/simuPOP/utility.h 2011-07-06 16:18:23 UTC (rev 4247)
+++ trunk/simuPOP/utility.h 2011-07-06 16:52:32 UTC (rev 4248)
@@ -80,7 +80,7 @@
# include "tbb/parallel_sort.h"
# include "tbb/task_scheduler_init.h"
# elif defined(GCC_VERSION) && GCC_VERSION >= 40300
-# include "parallel/algorithm"
+# include "parallel/algorithm"
# endif
#endif
/// for bernulli trials.
@@ -171,6 +171,7 @@
}
}
+
/// a utility function to check keyboard stroke
/// CPPONLY
int simuPOP_kbhit();
@@ -1228,7 +1229,7 @@
if (expr.empty() && stmts.empty())
return;
- //detect leading spaces from python expressions
+ //detect leading spaces from python expressions
DBG_FAILIF(!expr.empty() && (expr[0] == ' ' || expr[0] == '\t'), ValueError,
"Can not include leading space in python expression '" + expr + "'");
DBG_FAILIF(!stmts.empty() && (stmts[0] == ' ' || stmts[0] == '\t'), ValueError,
Modified: trunk/tools/doxy2swig.py
===================================================================
--- trunk/tools/doxy2swig.py 2011-07-06 16:18:23 UTC (rev 4247)
+++ trunk/tools/doxy2swig.py 2011-07-06 16:52:32 UTC (rev 4248)
@@ -1375,7 +1375,7 @@
xml_file = sys.argv[1]
# output interface file
if len(sys.argv) < 3:
- interface_file = os.path.join(src_path, 'src', 'simuPOP_doc.i')
+ interface_file = os.path.join(src_path, 'simuPOP', 'simuPOP_doc.i')
else:
interface_file = sys.argv[2]
# output ref_single.tex file
@@ -1400,7 +1400,7 @@
# write interface file to output interface file.
print 'Writing SWIG interface file to', interface_file
p.write(interface_file, type='swig')
- sys.path = [os.path.join(src_path, 'src')] + sys.path
+ sys.path = [os.path.join(src_path, 'simuPOP')] + sys.path
p.scan_module('simuPOP')
p.scan_module('simuOpt')
p.scan_module('simuPOP.utils')
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <si...@us...> - 2011-07-06 17:25:01
|
Revision: 4251
http://simupop.svn.sourceforge.net/simupop/?rev=4251&view=rev
Author: simupop
Date: 2011-07-06 17:24:55 +0000 (Wed, 06 Jul 2011)
Log Message:
-----------
Prepare a release
Modified Paths:
--------------
trunk/ChangeLog
trunk/doc/refManual.lyx
trunk/doc/userGuide.lyx
trunk/doc/userGuide.pdf
trunk/simuPOP_version.py
trunk/tools/build.py
Modified: trunk/ChangeLog
===================================================================
--- trunk/ChangeLog 2011-07-06 17:10:22 UTC (rev 4250)
+++ trunk/ChangeLog 2011-07-06 17:24:55 UTC (rev 4251)
@@ -4,7 +4,12 @@
- BUG: simuPOP does not respond well to Ctrl-C under windows.
- BUG: Textbox in Tkinter help dialog does not resize.
-version 1.0.6 - Not released, available at https://simupop.svn.sourceforge.net/svnroot/simupop/trunk
+version 1.0.7 - Not released, available at https://simupop.svn.sourceforge.net/svnroot/simupop/trunk
+
+version 1.0.6 - Rev 4250 (July 6, 2011)
+Major new feature:
+ - Multi-thread support that allows simuPOP to take advantage of multi-core CPUs.
+
New features:
- Expose function Population::virtualSplitter
- Allow single input for parameters cutoff and values of operator InfoSplitter.
Modified: trunk/doc/refManual.lyx
===================================================================
--- trunk/doc/refManual.lyx 2011-07-06 17:10:22 UTC (rev 4250)
+++ trunk/doc/refManual.lyx 2011-07-06 17:24:55 UTC (rev 4251)
@@ -5,7 +5,7 @@
\textclass manual
\begin_preamble
\renewcommand{\py@ptsize}{12pt}
-\setreleaseinfo{Release 1.0.5 (\mbox{Rev: 3918})}
+\setreleaseinfo{Release 1.0.6 (\mbox{Rev: 4250})}
% file revision $Rev: 3372$
\authoraddress{
{\bf Department of Epidemiology, U.T. M.D. Anderson Cancer Center}\\
Modified: trunk/doc/userGuide.lyx
===================================================================
--- trunk/doc/userGuide.lyx 2011-07-06 17:10:22 UTC (rev 4250)
+++ trunk/doc/userGuide.lyx 2011-07-06 17:24:55 UTC (rev 4251)
@@ -6,7 +6,7 @@
\begin_preamble
\renewcommand{\py@ptsize}{12pt}
-\setreleaseinfo{Release 1.0.5 (\mbox{Rev: 3918})}
+\setreleaseinfo{Release 1.0.6 (\mbox{Rev: 4250})}
% file revision $Rev: 3372$
\authoraddress{
{\bf Department of Epidemiology, U.T. M.D. Anderson Cancer Center}\\
Modified: trunk/doc/userGuide.pdf
===================================================================
(Binary files differ)
Modified: trunk/simuPOP_version.py
===================================================================
--- trunk/simuPOP_version.py 2011-07-06 17:10:22 UTC (rev 4250)
+++ trunk/simuPOP_version.py 2011-07-06 17:24:55 UTC (rev 4251)
@@ -1,2 +1,2 @@
-SIMUPOP_VER = "1.0.6svn"
-SIMUPOP_REV = "3918"
+SIMUPOP_VER = "1.0.6"
+SIMUPOP_REV = "4250"
Modified: trunk/tools/build.py
===================================================================
--- trunk/tools/build.py 2011-07-06 17:10:22 UTC (rev 4250)
+++ trunk/tools/build.py 2011-07-06 17:24:55 UTC (rev 4251)
@@ -13,6 +13,7 @@
release_file = 'simuPOP_version.py'
user_guide = 'doc/userGuide.lyx'
ref_manual = 'doc/refManual.lyx'
+download_directory = 'download'
def setReleaseInManual(filename, rel, rev):
'''Replace Release x.x.x with Rev: with proper value during release'''
@@ -258,7 +259,6 @@
'''
if __name__ == '__main__':
- config_file = 'build.cfg'
release = 'snapshot'
actions = []
dryrun = False
@@ -274,8 +274,6 @@
sys.exit(0)
elif '--release' in op:
release = op[10:]
- elif '--config' in op:
- config_file = op[9:]
elif op == 'all':
actions.extend(['src', 'doc', 'svn', 'x86_64', 'rhel4', 'mac', 'win', 'fedora5', 'suse'])
elif op in all_actions and op not in actions:
@@ -286,12 +284,6 @@
print "Unknown option", op
sys.exit(1)
#
- if os.path.isfile(config_file):
- execfile(config_file)
- else:
- print 'Configuration file not found'
- sys.exit(1)
- #
os.chdir('..')
# get revision number and update last_revision_file
(ver, rev, old_ver, old_rev) = setVersionRevision(release)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <si...@us...> - 2011-07-07 03:06:02
|
Revision: 4253
http://simupop.svn.sourceforge.net/simupop/?rev=4253&view=rev
Author: simupop
Date: 2011-07-07 03:05:52 +0000 (Thu, 07 Jul 2011)
Log Message:
-----------
Revert src -> simuPOP directory change
Modified Paths:
--------------
trunk/Doxy_web
trunk/Doxyfile
trunk/MANIFEST.in
trunk/Makefile
trunk/SConstruct
trunk/setup.py
trunk/tools/doxy2swig.py
Added Paths:
-----------
trunk/src/
trunk/src/__init__.py
trunk/src/customizedTypes.c
trunk/src/genoStru.cpp
trunk/src/genoStru.h
trunk/src/gsl.i
trunk/src/individual.cpp
trunk/src/individual.h
trunk/src/initializer.cpp
trunk/src/initializer.h
trunk/src/main.cpp
trunk/src/mating.cpp
trunk/src/mating.h
trunk/src/migrator.cpp
trunk/src/migrator.h
trunk/src/mutator.cpp
trunk/src/mutator.h
trunk/src/operator.cpp
trunk/src/operator.h
trunk/src/outputer.cpp
trunk/src/outputer.h
trunk/src/pedigree.cpp
trunk/src/pedigree.h
trunk/src/penetrance.cpp
trunk/src/penetrance.h
trunk/src/plotter.py
trunk/src/population.cpp
trunk/src/population.h
trunk/src/qtrait.cpp
trunk/src/qtrait.h
trunk/src/sampling.py
trunk/src/sandbox.cpp
trunk/src/sandbox.h
trunk/src/sandbox.py
trunk/src/selector.cpp
trunk/src/selector.h
trunk/src/simuPOP_ba.i
trunk/src/simuPOP_baop.i
trunk/src/simuPOP_cfg.h
trunk/src/simuPOP_common.i
trunk/src/simuPOP_doc.i
trunk/src/simuPOP_la.i
trunk/src/simuPOP_laop.i
trunk/src/simuPOP_op.i
trunk/src/simuPOP_std.i
trunk/src/simulator.cpp
trunk/src/simulator.h
trunk/src/stator.cpp
trunk/src/stator.h
trunk/src/tagger.cpp
trunk/src/tagger.h
trunk/src/transmitter.cpp
trunk/src/transmitter.h
trunk/src/utility.cpp
trunk/src/utility.h
trunk/src/utils.py
trunk/src/virtualSubPop.cpp
trunk/src/virtualSubPop.h
Removed Paths:
-------------
trunk/simuPOP/
trunk/src/__init__.py
trunk/src/customizedTypes.c
trunk/src/genoStru.cpp
trunk/src/genoStru.h
trunk/src/gsl.i
trunk/src/individual.cpp
trunk/src/individual.h
trunk/src/initializer.cpp
trunk/src/initializer.h
trunk/src/main.cpp
trunk/src/mating.cpp
trunk/src/mating.h
trunk/src/migrator.cpp
trunk/src/migrator.h
trunk/src/mutator.cpp
trunk/src/mutator.h
trunk/src/operator.cpp
trunk/src/operator.h
trunk/src/outputer.cpp
trunk/src/outputer.h
trunk/src/pedigree.cpp
trunk/src/pedigree.h
trunk/src/penetrance.cpp
trunk/src/penetrance.h
trunk/src/plotter.py
trunk/src/population.cpp
trunk/src/population.h
trunk/src/qtrait.cpp
trunk/src/qtrait.h
trunk/src/sampling.py
trunk/src/sandbox.cpp
trunk/src/sandbox.h
trunk/src/sandbox.py
trunk/src/selector.cpp
trunk/src/selector.h
trunk/src/simuPOP_ba.i
trunk/src/simuPOP_baop.i
trunk/src/simuPOP_cfg.h
trunk/src/simuPOP_common.i
trunk/src/simuPOP_doc.i
trunk/src/simuPOP_la.i
trunk/src/simuPOP_laop.i
trunk/src/simuPOP_op.i
trunk/src/simuPOP_std.i
trunk/src/simulator.cpp
trunk/src/simulator.h
trunk/src/stator.cpp
trunk/src/stator.h
trunk/src/tagger.cpp
trunk/src/tagger.h
trunk/src/transmitter.cpp
trunk/src/transmitter.h
trunk/src/utility.cpp
trunk/src/utility.h
trunk/src/utils.py
trunk/src/virtualSubPop.cpp
trunk/src/virtualSubPop.h
Modified: trunk/Doxy_web
===================================================================
--- trunk/Doxy_web 2011-07-06 17:26:44 UTC (rev 4252)
+++ trunk/Doxy_web 2011-07-07 03:05:52 UTC (rev 4253)
@@ -578,7 +578,7 @@
# directories like "/usr/src/myproject". Separate the files or directories
# with spaces.
-INPUT = simuPOP
+INPUT = src
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
Modified: trunk/Doxyfile
===================================================================
--- trunk/Doxyfile 2011-07-06 17:26:44 UTC (rev 4252)
+++ trunk/Doxyfile 2011-07-07 03:05:52 UTC (rev 4253)
@@ -578,7 +578,7 @@
# directories like "/usr/src/myproject". Separate the files or directories
# with spaces.
-INPUT = simuPOP \
+INPUT = src \
config_linux.h
# This tag can be used to specify the character encoding of the source files
Modified: trunk/MANIFEST.in
===================================================================
--- trunk/MANIFEST.in 2011-07-06 17:26:44 UTC (rev 4252)
+++ trunk/MANIFEST.in 2011-07-07 03:05:52 UTC (rev 4253)
@@ -18,86 +18,86 @@
include config_win32.h
include config_linux.h
include config_mac.h
-include simuPOP/simuPOP_cfg.h
-include simuPOP/utility.h
-include simuPOP/genoStru.h
-include simuPOP/individual.h
-include simuPOP/population.h
-include simuPOP/simulator.h
-include simuPOP/mating.h
-include simuPOP/operator.h
-include simuPOP/initializer.h
-include simuPOP/migrator.h
-include simuPOP/outputer.h
-include simuPOP/selector.h
-include simuPOP/penetrance.h
-include simuPOP/qtrait.h
-include simuPOP/stator.h
-include simuPOP/mutator.h
-include simuPOP/transmitter.h
-include simuPOP/tagger.h
-include simuPOP/pedigree.h
-include simuPOP/virtualSubPop.h
-include simuPOP/sandbox.h
+include src/simuPOP_cfg.h
+include src/utility.h
+include src/genoStru.h
+include src/individual.h
+include src/population.h
+include src/simulator.h
+include src/mating.h
+include src/operator.h
+include src/initializer.h
+include src/migrator.h
+include src/outputer.h
+include src/selector.h
+include src/penetrance.h
+include src/qtrait.h
+include src/stator.h
+include src/mutator.h
+include src/transmitter.h
+include src/tagger.h
+include src/pedigree.h
+include src/virtualSubPop.h
+include src/sandbox.h
# source files
-include simuPOP/customizedTypes.c
-include simuPOP/utility.cpp
-include simuPOP/genoStru.cpp
-include simuPOP/individual.cpp
-include simuPOP/population.cpp
-include simuPOP/simulator.cpp
-include simuPOP/mating.cpp
-include simuPOP/operator.cpp
-include simuPOP/initializer.cpp
-include simuPOP/migrator.cpp
-include simuPOP/outputer.cpp
-include simuPOP/selector.cpp
-include simuPOP/penetrance.cpp
-include simuPOP/qtrait.cpp
-include simuPOP/stator.cpp
-include simuPOP/mutator.cpp
-include simuPOP/transmitter.cpp
-include simuPOP/tagger.cpp
-include simuPOP/pedigree.cpp
-include simuPOP/virtualSubPop.cpp
-include simuPOP/sandbox.cpp
-include simuPOP/main.cpp
+include src/customizedTypes.c
+include src/utility.cpp
+include src/genoStru.cpp
+include src/individual.cpp
+include src/population.cpp
+include src/simulator.cpp
+include src/mating.cpp
+include src/operator.cpp
+include src/initializer.cpp
+include src/migrator.cpp
+include src/outputer.cpp
+include src/selector.cpp
+include src/penetrance.cpp
+include src/qtrait.cpp
+include src/stator.cpp
+include src/mutator.cpp
+include src/transmitter.cpp
+include src/tagger.cpp
+include src/pedigree.cpp
+include src/virtualSubPop.cpp
+include src/sandbox.cpp
+include src/main.cpp
# source generated files
-include simuPOP/swigpyrun.h
-include simuPOP/simuPOP_std_wrap.cpp
-include simuPOP/simuPOP_op_wrap.cpp
-include simuPOP/simuPOP_la_wrap.cpp
-include simuPOP/simuPOP_laop_wrap.cpp
-include simuPOP/simuPOP_ba_wrap.cpp
-include simuPOP/simuPOP_baop_wrap.cpp
-include simuPOP/simuPOP_std.py
-include simuPOP/simuPOP_op.py
-include simuPOP/simuPOP_la.py
-include simuPOP/simuPOP_laop.py
-include simuPOP/simuPOP_ba.py
-include simuPOP/simuPOP_baop.py
-include simuPOP/gsl_wrap.c
+include src/swigpyrun.h
+include src/simuPOP_std_wrap.cpp
+include src/simuPOP_op_wrap.cpp
+include src/simuPOP_la_wrap.cpp
+include src/simuPOP_laop_wrap.cpp
+include src/simuPOP_ba_wrap.cpp
+include src/simuPOP_baop_wrap.cpp
+include src/simuPOP_std.py
+include src/simuPOP_op.py
+include src/simuPOP_la.py
+include src/simuPOP_laop.py
+include src/simuPOP_ba.py
+include src/simuPOP_baop.py
+include src/gsl_wrap.c
# source wrap files
-include simuPOP/simuPOP_common.i
-include simuPOP/simuPOP_doc.i
-include simuPOP/simuPOP_std.i
-include simuPOP/simuPOP_op.i
-include simuPOP/simuPOP_la.i
-include simuPOP/simuPOP_laop.i
-include simuPOP/simuPOP_ba.i
-include simuPOP/simuPOP_baop.i
-include simuPOP/gsl.i
+include src/simuPOP_common.i
+include src/simuPOP_doc.i
+include src/simuPOP_std.i
+include src/simuPOP_op.i
+include src/simuPOP_la.i
+include src/simuPOP_laop.i
+include src/simuPOP_ba.i
+include src/simuPOP_baop.i
+include src/gsl.i
# source python files (modules)
include simuOpt.py
-include simuPOP/__init__.py
-include simuPOP/utils.py
-include simuPOP/plotter.py
-include simuPOP/sampling.py
-include simuPOP/sandbox.py
+include src/__init__.py
+include src/utils.py
+include src/plotter.py
+include src/sampling.py
+include src/sandbox.py
# gsl files
include gsl/gsl_machine.h
Modified: trunk/Makefile
===================================================================
--- trunk/Makefile 2011-07-06 17:26:44 UTC (rev 4252)
+++ trunk/Makefile 2011-07-07 03:05:52 UTC (rev 4253)
@@ -4,7 +4,7 @@
rebuild:
- bcpp simuPOP/*.h simuPOP/*.cpp
+ bcpp src/*.h src/*.cpp
doxygen
tools/doxy2swig.py
scons install -j4 std
@@ -17,7 +17,7 @@
clean:
@rm -rf build
- @rm -f simuPOP/*wrap* simuPOP/simuPOP_*.py
+ @rm -f src/*wrap* src/simuPOP_*.py
@find . -name '*~' -exec rm -f {} \;
@find . -name '*.bak' -exec rm -f {} \;
@find . -name '*.py?' -exec rm -f {} \;
Modified: trunk/SConstruct
===================================================================
--- trunk/SConstruct 2011-07-06 17:26:44 UTC (rev 4252)
+++ trunk/SConstruct 2011-07-07 03:05:52 UTC (rev 4253)
@@ -159,11 +159,11 @@
#
gsl_env = env.Clone()
gsl_env.VariantDir('build/gsl', '.')
-gsl_env['SWIGOUTDIR'] = 'build/gsl/simuPOP'
+gsl_env['SWIGOUTDIR'] = 'build/gsl/src'
gsl_env['SWIGFLAGS'] = SWIG_CC_FLAGS
gsl = gsl_env.SharedLibrary(
target = 'build/gsl/_gsl%s' % so_ext,
- source = ['build/gsl/' + x for x in GSL_FILES] + ['build/gsl/simuPOP/gsl.i'],
+ source = ['build/gsl/' + x for x in GSL_FILES] + ['build/gsl/src/gsl.i'],
SHLIBPREFIX = "",
SHLIBSUFFIX = so_ext,
SHLINKFLAGS = comp.ldflags_shared,
@@ -176,7 +176,7 @@
Alias('gsl', gsl)
Alias('all', gsl)
Alias('install', gsl_env.InstallAs(os.path.join(dest_dir, '_gsl%s' % so_ext), gsl[0]))
-Alias('install', gsl_env.InstallAs(os.path.join(dest_dir, 'gsl.py'), 'build/gsl/simuPOP/gsl.py'))
+Alias('install', gsl_env.InstallAs(os.path.join(dest_dir, 'gsl.py'), 'build/gsl/src/gsl.py'))
#
#
# Building a library for common files
@@ -229,22 +229,22 @@
for mod in targets:
mod_env = env.Clone()
mod_env.VariantDir('build/' + mod, '.')
- mod_env['SWIGFLAGS'] = SWIG_CPP_FLAGS + ' -IsimuPOP' # -IsimuPOP for %include interface files under simuPOP
- mod_env['SWIGOUTDIR'] = 'build/%s/simuPOP' % mod
+ mod_env['SWIGFLAGS'] = SWIG_CPP_FLAGS + ' -Isrc' # -Isrc for %include interface files under src
+ mod_env['SWIGOUTDIR'] = 'build/%s/src' % mod
info = ModuInfo(mod, SIMUPOP_VER, SIMUPOP_REV)
- mod_env.Command('build/%s/simuPOP/swigpyrun.h' % mod, None, ['swig %s $TARGET' % SWIG_RUNTIME_FLAGS])
+ mod_env.Command('build/%s/src/swigpyrun.h' % mod, None, ['swig %s $TARGET' % SWIG_RUNTIME_FLAGS])
if 'op' in mod:
common_lib = op_common_lib
else:
common_lib = std_common_lib
mod_wrapper = mod_env.StaticLibrary(
- target = 'build/%s/simuPOP/_simuPOP_wrap_%s' % (mod, mod),
- source = ['build/%s/simuPOP/simuPOP_%s.i' % (mod, mod)],
+ target = 'build/%s/src/_simuPOP_wrap_%s' % (mod, mod),
+ source = ['build/%s/src/simuPOP_%s.i' % (mod, mod)],
SHLIBPREFIX = "",
SHLIBSUFFIX = so_ext,
SHLINKFLAGS = comp.ldflags_shared,
LIBPATH = info['library_dirs'] + extra_path,
- CPPPATH = [python_inc_dir, '.', 'simuPOP', 'build'] + info['include_dirs'],
+ CPPPATH = [python_inc_dir, '.', 'src', 'build'] + info['include_dirs'],
CPPDEFINES = convert_def(info['define_macros']),
# No extra-flags because it can have -Werror and we cannot guarantee that there is
# no warning coming out of the wrapper code.
@@ -253,22 +253,22 @@
)
mod_lib = mod_env.SharedLibrary(
target = 'build/%s/_simuPOP_%s' % (mod, mod),
- source = ['build/%s/simuPOP/%s' % (mod, x) for x in SOURCE_FILES],
+ source = ['build/%s/src/%s' % (mod, x) for x in SOURCE_FILES],
LIBS = info['libraries'] + [mod_wrapper, common_lib],
SHLIBPREFIX = "",
SHLIBSUFFIX = so_ext,
SHLINKFLAGS = comp.ldflags_shared,
LIBPATH = info['library_dirs'] + extra_path,
- CPPPATH = [python_inc_dir, '.', 'simuPOP', 'build'] + info['include_dirs'],
+ CPPPATH = [python_inc_dir, '.', 'src', 'build'] + info['include_dirs'],
CPPDEFINES = convert_def(info['define_macros']),
CCFLAGS = info['extra_compile_args'] + comp.compile_options + extra_flags,
CPPFLAGS = ' '.join([basicflags, ccshared, opt])
)
- env.Depends('build/%s/simuPOP/swigpyrun.h' % mod, 'build/%s/simuPOP/utility.cpp' % mod)
+ env.Depends('build/%s/src/swigpyrun.h' % mod, 'build/%s/src/utility.cpp' % mod)
Alias(mod, mod_lib)
Alias('all', mod_lib)
pyInstall = env.InstallAs(os.path.join(dest_dir, 'simuPOP_%s.py' % mod),
- 'build/%s/simuPOP/simuPOP_%s.py' % (mod, mod))
+ 'build/%s/src/simuPOP_%s.py' % (mod, mod))
libInstall = env.InstallAs(os.path.join(dest_dir, '_simuPOP_%s%s' % (mod, so_ext)),
mod_lib[0])
mod_env.Depends(pyInstall, libInstall)
@@ -285,8 +285,8 @@
mod_name = mod.split('_')[0]
exe_env = env.Clone()
exe_env.VariantDir('build/' + mod, '.')
- exe_env['SWIGFLAGS'] = SWIG_CPP_FLAGS + ' -IsimuPOP' # -IsimuPOP for %include interface files under simuPOP
- exe_env['SWIGOUTDIR'] = 'build/%s/simuPOP' % mod
+ exe_env['SWIGFLAGS'] = SWIG_CPP_FLAGS + ' -Isrc' # -Isrc for %include interface files under src
+ exe_env['SWIGOUTDIR'] = 'build/%s/src' % mod
info = ModuInfo(mod_name, SIMUPOP_VER, SIMUPOP_REV)
if 'op' in mod:
common_lib = op_common_lib
@@ -294,10 +294,10 @@
common_lib = std_common_lib
mod_executable = exe_env.Program(
target = 'build/simuPOP_%s' % mod,
- source = ['build/%s/simuPOP/%s' % (mod, x) for x in SOURCE_FILES],
+ source = ['build/%s/src/%s' % (mod, x) for x in SOURCE_FILES],
LIBS = info['libraries'] + [common_lib] + pylibs,
LIBPATH = info['library_dirs'] + extra_path,
- CPPPATH = [python_inc_dir, '.', 'simuPOP', 'build'] + info['include_dirs'],
+ CPPPATH = [python_inc_dir, '.', 'src', 'build'] + info['include_dirs'],
CPPDEFINES = convert_def(info['define_macros'] + [('STANDALONE_EXECUTABLE', None)]),
CCFLAGS = info['extra_compile_args'] + comp.compile_options + extra_flags,
CPPFLAGS = ' '.join([basicflags, ccshared, opt])
@@ -309,11 +309,11 @@
env.Install(pylib_dir, 'simuOpt.py')
Alias('install', pylib_dir)
for pyfile in ['__init__.py', 'utils.py', 'plotter.py', 'sampling.py', 'sandbox.py']:
- env.Install(dest_dir, 'simuPOP/%s' % pyfile)
+ env.Install(dest_dir, 'src/%s' % pyfile)
Alias('install', dest_dir)
for datafile in PACKAGE_DATA:
- env.Install(dest_dir, 'simuPOP/%s' % datafile)
+ env.Install(dest_dir, 'src/%s' % datafile)
Alias('install', dest_dir)
Default('install')
Modified: trunk/setup.py
===================================================================
--- trunk/setup.py 2011-07-06 17:26:44 UTC (rev 4252)
+++ trunk/setup.py 2011-07-07 03:05:52 UTC (rev 4253)
@@ -399,9 +399,9 @@
SWIG_CC_FLAGS += ' -py3'
SWIG_RUNTIME_FLAGS = '-python -external-runtime'
-# python setup.py reads py_modules from simuPOP so we have to produce simuPOP_std.py
+# python setup.py reads py_modules from src so we have to produce simuPOP_std.py
# etc to this directory.
-SWIG_OUTDIR = 'simuPOP'
+SWIG_OUTDIR = 'src'
if not os.path.isdir('build'):
os.mkdir('build')
@@ -421,12 +421,12 @@
}
WRAP_INFO = {
- 'std': ['simuPOP/simuPOP_std_wrap.cpp', 'simuPOP/simuPOP_std.i', ''],
- 'op': ['simuPOP/simuPOP_op_wrap.cpp', 'simuPOP/simuPOP_op.i', '-DOPTIMIZED'],
- 'la': ['simuPOP/simuPOP_la_wrap.cpp', 'simuPOP/simuPOP_la.i', '-DLONGALLELE'],
- 'laop': ['simuPOP/simuPOP_laop_wrap.cpp', 'simuPOP/simuPOP_laop.i', '-DLONGALLELE -DOPTIMIZED'],
- 'ba': ['simuPOP/simuPOP_ba_wrap.cpp', 'simuPOP/simuPOP_ba.i', '-DBINARYALLELE'],
- 'baop': ['simuPOP/simuPOP_baop_wrap.cpp', 'simuPOP/simuPOP_baop.i', '-DBINARYALLELE -DOPTIMIZED'],
+ 'std': ['src/simuPOP_std_wrap.cpp', 'src/simuPOP_std.i', ''],
+ 'op': ['src/simuPOP_op_wrap.cpp', 'src/simuPOP_op.i', '-DOPTIMIZED'],
+ 'la': ['src/simuPOP_la_wrap.cpp', 'src/simuPOP_la.i', '-DLONGALLELE'],
+ 'laop': ['src/simuPOP_laop_wrap.cpp', 'src/simuPOP_laop.i', '-DLONGALLELE -DOPTIMIZED'],
+ 'ba': ['src/simuPOP_ba_wrap.cpp', 'src/simuPOP_ba.i', '-DBINARYALLELE'],
+ 'baop': ['src/simuPOP_baop_wrap.cpp', 'src/simuPOP_baop.i', '-DBINARYALLELE -DOPTIMIZED'],
}
if os.name == 'nt':
@@ -466,7 +466,7 @@
boost_lib_names = []
boost_lib_path = None
res = {}
- res['src'] = ['simuPOP/simuPOP_' + modu + '_wrap.cpp']
+ res['src'] = ['src/simuPOP_' + modu + '_wrap.cpp']
for src in SOURCE_FILES:
res['src'].append('build/%s/%s' % (modu, src))
res['src'].extend(LIB_FILES)
@@ -534,8 +534,8 @@
machine = platform.uname()[4].lower()
if machine == '': # have to guess
machine = 'x86'
- shutil.copy('win32/%s/vcomp90.dll' % machine, 'simuPOP/vcomp90.dll')
- shutil.copy('win32/%s/msvcr90.dll' % machine, 'simuPOP/msvcr90.dll')
+ shutil.copy('win32/%s/vcomp90.dll' % machine, 'src/vcomp90.dll')
+ shutil.copy('win32/%s/msvcr90.dll' % machine, 'src/msvcr90.dll')
if __name__ == '__main__':
SIMUPOP_VER, SIMUPOP_REV = simuPOP_version()
@@ -546,9 +546,9 @@
#
# if any of the wrap files does not exist
# or if the wrap files are older than any of the source files.
- if (not os.path.isfile('simuPOP/gsl_wrap.c') or (not os.path.isfile('simuPOP/swigpyrun.h')) or \
+ if (not os.path.isfile('src/gsl_wrap.c') or (not os.path.isfile('src/swigpyrun.h')) or \
False in [os.path.isfile(WRAP_INFO[x][0]) for x in MODULES]) or \
- (max( [os.path.getmtime('simuPOP/' + x) for x in HEADER_FILES] ) > \
+ (max( [os.path.getmtime('src/' + x) for x in HEADER_FILES] ) > \
min( [os.path.getmtime(WRAP_INFO[x][0]) for x in MODULES])):
(v1, v2, v3) = swig_version()
if (v1, v2, v3) < (1, 3, 35):
@@ -558,8 +558,8 @@
print('Swig >= 2.0.4 is required for Python 3.2 or higher')
sys.exit(1)
# generate header file
- print("Generating external runtime header file simuPOP/swigpyrun.h...")
- os.system('%s %s simuPOP/swigpyrun.h' % (SWIG, SWIG_RUNTIME_FLAGS))
+ print("Generating external runtime header file src/swigpyrun.h...")
+ os.system('%s %s src/swigpyrun.h' % (SWIG, SWIG_RUNTIME_FLAGS))
# try the first option set with the first library
for lib in MODULES:
print("Generating wrapper file " + WRAP_INFO[lib][0])
@@ -567,9 +567,9 @@
SWIG_OUTDIR, WRAP_INFO[lib][2], WRAP_INFO[lib][0], WRAP_INFO[lib][1])) != 0:
print("Calling swig failed. Please check your swig version.")
sys.exit(1)
- print("Generating wrapper file simuPOP/gsl_wrap.c")
+ print("Generating wrapper file src/gsl_wrap.c")
if os.system('%s %s -outdir %s %s -o %s %s' % (SWIG, SWIG_CC_FLAGS, \
- SWIG_OUTDIR, '', 'simuPOP/gsl_wrap.c', 'simuPOP/gsl.i')) != 0:
+ SWIG_OUTDIR, '', 'src/gsl_wrap.c', 'src/gsl.i')) != 0:
print("Calling swig failed. Please check your swig version.")
sys.exit(1)
print("\nAll wrap files are generated successfully.\n")
@@ -585,13 +585,13 @@
os.mkdir('build/%s' % modu)
for src in SOURCE_FILES:
mod_src = 'build/%s/%s' % (modu, src)
- if not os.path.isfile(mod_src) or not filecmp.cmp(mod_src,'simuPOP/'+src):
- shutil.copy('simuPOP/'+src, mod_src)
+ if not os.path.isfile(mod_src) or not filecmp.cmp(mod_src,'src/'+src):
+ shutil.copy('src/'+src, mod_src)
# build
# For module simuPOP.gsl
EXT_MODULES = [
Extension('simuPOP._gsl',
- sources = GSL_FILES + ['simuPOP/gsl_wrap.c'],
+ sources = GSL_FILES + ['src/gsl_wrap.c'],
include_dirs = ['gsl', 'gsl/specfunc', 'build', '.'],
)
]
@@ -602,7 +602,7 @@
sources = info['src'],
extra_compile_args = info['extra_compile_args'],
# src for config.h etc, build for swigpyrun.h
- include_dirs = info['include_dirs'] + ['simuPOP', 'build'],
+ include_dirs = info['include_dirs'] + ['src', 'build'],
library_dirs = info['library_dirs'],
libraries = info['libraries'],
define_macros = info['define_macros'],
@@ -642,7 +642,7 @@
],
platforms = ['all'],
#
- package_dir = {'simuPOP': 'simuPOP'},
+ package_dir = {'simuPOP': 'src'},
package_data = {'simuPOP': PACKAGE_DATA},
py_modules = [
'simuOpt',
Property changes on: trunk/src
___________________________________________________________________
Added: svn:eol-stype
+ LF
Deleted: trunk/src/__init__.py
===================================================================
--- trunk/src/__init__.py 2011-06-29 21:43:36 UTC (rev 4243)
+++ trunk/src/__init__.py 2011-07-07 03:05:52 UTC (rev 4253)
@@ -1,1153 +0,0 @@
-#!/usr/bin/env python
-
-#
-# $File: __init__.py $
-# $LastChangedDate$
-# $Rev$
-#
-# This file is part of simuPOP, a forward-time population genetics
-# simulation environment. Please visit http://simupop.sourceforge.net
-# for details.
-#
-# Copyright (C) 2004 - 2010 Bo Peng (bp...@md...)
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program. If not, see <http://www.gnu.org/licenses/>.
-#
-
-"""
-simuPOP core module.
-"""
-
-__all__ = [
- # Constants
- #
- 'MALE',
- 'FEMALE',
- #
- 'CUSTOMIZED',
- 'AUTOSOME',
- 'CHROMOSOME_X',
- 'CHROMOSOME_Y',
- #
- 'CONSTANT',
- 'BINOMIAL_DISTRIBUTION',
- 'EXPONENTIAL_DISTRIBUTION',
- 'GEOMETRIC_DISTRIBUTION',
- 'POISSON_DISTRIBUTION',
- 'UNIFORM_DISTRIBUTION',
- 'NORMAL_DISTRIBUTION',
- 'GAMMA_DISTRIBUTION',
- #
- 'NO_SEX',
- 'RANDOM_SEX',
- 'PROB_OF_MALES',
- 'NUM_OF_MALES',
- 'NUM_OF_FEMALES',
- 'SEQUENCE_OF_SEX',
- 'GLOBAL_SEQUENCE_OF_SEX',
- #
- 'NO_CONVERSION',
- 'NUM_MARKERS',
- 'TRACT_LENGTH',
- #
- 'SPOUSE',
- 'OUTBRED_SPOUSE',
- 'FULLSIBLING',
- 'SIBLING',
- 'OFFSPRING',
- 'COMMON_OFFSPRING',
- #
- 'ANY_SEX',
- 'MALE_ONLY',
- 'FEMALE_ONLY',
- 'SAME_SEX',
- 'OPPOSITE_SEX',
- #
- 'MULTIPLICATIVE',
- 'ADDITIVE',
- 'HETEROGENEITY',
- #
- 'BY_IND_INFO',
- 'BY_PROBABILITY',
- 'BY_PROPORTION',
- 'BY_COUNTS',
- #
- 'PATERNAL',
- 'MATERNAL',
- #
- 'MEAN',
- 'MAXIMUM',
- 'MINIMUM',
- 'SUMMATION',
- 'MULTIPLICATION',
- #
- 'HAPLODIPLOID',
- 'ALL_AVAIL',
- 'UNSPECIFIED',
- #
- # Major simuPOP classes
- 'Population',
- # This is just to make help(Individual) available to users.
- 'Individual',
- 'Simulator',
- 'Pedigree',
- # splitters
- 'SexSplitter',
- 'AffectionSplitter',
- 'CombinedSplitter',
- 'ProductSplitter',
- 'ProportionSplitter',
- 'InfoSplitter',
- 'GenotypeSplitter',
- 'RangeSplitter',
- # mating schemes
- 'MatingScheme',
- 'HomoMating',
- 'HeteroMating',
- 'PedigreeMating',
- 'OffspringGenerator',
- 'ControlledOffspringGenerator',
- 'RandomParentChooser',
- 'PyParentsChooser',
- 'CombinedParentsChooser',
- 'SequentialParentChooser',
- 'RandomParentsChooser',
- 'SequentialParentsChooser',
- 'ParentChooser',
- 'PolyParentsChooser',
- #
- 'RandomMating',
- 'RandomSelection',
- 'MonogamousMating',
- 'SelfMating',
- 'CloneMating',
- 'HaplodiploidMating',
- #'consanguineousMating',
- 'ControlledRandomMating',
- 'PolygamousMating',
- #
- #
- # Operators
- #
- 'InitSex',
- 'InitInfo',
- 'InitGenotype',
- #
- 'PyOutput',
- 'PyEval',
- 'PyExec',
- 'InfoEval',
- 'InfoExec',
- #
- 'Migrator',
- 'MergeSubPops',
- 'SplitSubPops',
- 'ResizeSubPops',
- #
- 'GenoTransmitter',
- 'HaplodiploidGenoTransmitter',
- 'MendelianGenoTransmitter',
- 'MitochondrialGenoTransmitter',
- 'SelfingGenoTransmitter',
- 'CloneGenoTransmitter',
- 'Recombinator',
- #
- 'PointMutator',
- 'MatrixMutator',
- 'MixedMutator',
- 'PyMutator',
- 'StepwiseMutator',
- 'SNPMutator',
- 'AcgtMutator',
- 'AminoAcidMutator',
- 'ContextMutator',
- 'KAlleleMutator',
- #
- 'MapSelector',
- 'MaSelector',
- 'MlSelector',
- 'PySelector',
- #
- 'MaPenetrance',
- 'MapPenetrance',
- 'MlPenetrance',
- 'PyPenetrance',
- #
- 'PyQuanTrait',
- #
- 'Stat',
- #
- 'IdTagger',
- 'InheritTagger',
- 'ParentsTagger',
- 'PedigreeTagger',
- 'PyTagger',
- 'SummaryTagger',
- #
- 'TerminateIf',
- 'DiscardIf',
- 'discardIf',
- #
- 'PyOperator',
- #
- 'NoneOp',
- 'Dumper',
- 'SavePopulation',
- 'IfElse',
- 'Pause',
- 'TicToc',
- #
- # Function form of operators
- 'dump',
- #
- 'initSex',
- 'initInfo',
- 'initGenotype',
- #
- 'pyEval',
- 'pyExec',
- 'infoEval',
- 'infoExec',
- #
- 'tagID',
- #
- 'migrate',
- 'resizeSubPops',
- 'splitSubPops',
- 'mergeSubPops',
- #
- 'matrixMutate',
- 'contextMutate',
- 'kAlleleMutate',
- 'mixedMutate',
- 'pointMutate',
- 'pyMutate',
- 'stepwiseMutate',
- 'snpMutate',
- 'acgtMutate',
- #
- 'stat',
- #
- # Global functions
- 'WithArgs',
- # RNG Related
- 'RNG',
- 'getRNG',
- #
- 'closeOutput',
- 'describeEvolProcess',
- 'loadPopulation',
- 'loadPedigree',
- 'moduleInfo',
- 'turnOffDebug',
- 'turnOnDebug',
- 'setOptions',
- #
- 'maPenetrance',
- 'mapPenetrance',
- 'mlPenetrance',
- 'pyPenetrance',
- #
- 'pyQuanTrait',
- #
- # For testing only
- 'applyDuringMatingOperator',
- 'Bernullitrials',
- 'WeightedSampler',
- #
- # modules are not loaded by default because importing plotter will fail if
- # rpy is not installed, and loading R is slow and perhaps unnecessary if
- # rpy is installed.
- #
- #'utils',
- #'plotter',
- #'sampling',
-]
-
-# get options
-from simuOpt import simuOptions
-import os, sys
-
-if simuOptions['Optimized']:
- if simuOptions['AlleleType'] == 'short':
- from simuPOP.simuPOP_op import *
- elif simuOptions['AlleleType'] == 'long':
- from simuPOP.simuPOP_laop import *
- elif simuOptions['AlleleType'] == 'binary':
- from simuPOP.simuPOP_baop import *
- else:
- from simuPOP.simuPOP_op import *
-else:
- if simuOptions['AlleleType'] == 'short':
- from simuPOP.simuPOP_std import *
- elif simuOptions['AlleleType'] == 'long':
- from simuPOP.simuPOP_la import *
- elif simuOptions['AlleleType'] == 'binary':
- from simuPOP.simuPOP_ba import *
- else:
- from simuPOP.simuPOP_std import *
-
-
-if simuOptions['Version'] is not None:
- expMajor, expMinor, expRelease = [int(x) for x in simuOptions['Version'].rstrip('svn').split('.')]
- myMajor, myMinor, myRelease = [int(x) for x in moduleInfo()['version'].rstrip('svn').split('.')]
- if (expMajor > myMajor) or (expMajor == myMajor and expMinor > myMinor) or \
- (expMajor == myMajor and expMinor == myMinor and expRelease > myRelease):
- raise ImportError('simuPOP version %s is installed but version >= %s is required. ' % \
- (moduleInfo()['version'], simuOptions['Version']) +
- 'Please upgrade your simuPOP installation.')
-
-if simuOptions['Revision'] is not None:
- ver = moduleInfo()['version']
- rev = moduleInfo()['revision']
- if rev < simuOptions['Revision']:
- raise ImportError('simuPOP version %s (revision %d) is installed ' % (ver, rev) +
- 'but simuPOP revision >= %d is required. ' % simuOptions['Revision'] +
- 'Please upgrade your simuPOP installation.')
- if 'DBG_COMPATIBILITY' in simuOptions['Debug']:
- print >> sys.stderr, 'WARNING: parameter revision in simuOpt.setOptions is obsolete and might be removed from a future version of simuPOP.'
-
-# set number of threads in openMP
-if simuOptions['NumThreads'] is not None:
- setOptions(numThreads=simuOptions['NumThreads'])
-
-if not simuOptions['Quiet']:
- info = moduleInfo()
- print "simuPOP Version %s : Copyright (c) 2004-2011 Bo Peng" % (info['version'])
- # compile date, compiler etc are macros that are replaced during compile time.
- print "Revision %d (%s) for Python %s (%dbit, %d%s)" % \
- (info['revision'], info['date'], info['python'], info['wordsize'], info['threads'],
- 'thread' if info['threads'] <= 1 else 'threads')
- print "Random Number Generator is set to %s with random seed 0x%08x." % (getRNG().name(), getRNG().seed())
- # MaxAllele + 1 since 0 is one of the allelic states
- print "This is the %s %s allele version with %d maximum allelic states." % \
- ('optimized' if info['optimized'] else 'standard', info['alleleType'], info['maxAllele']+1)
- print "For more information, please visit http://simupop.sourceforge.net,"
- print "or email sim...@li... (subscription required)."
- # Turn on general debug information when not in 'quiet' mode
- # This will print out error messages when needed.
- turnOnDebug('DBG_GENERAL')
- # only display banner once
- simuOptions['Quiet'] = True
-
-if simuOptions['Debug'] != []:
- for g in simuOptions['Debug']:
- if g not in ['', None]:
- print "Turn on debug '%s'" % g
- turnOnDebug(g)
-
-
-ALL_AVAIL = True
-UNSPECIFIED = False
-
-def evolve_pop(self, initOps=[], preOps=[], matingScheme=MatingScheme(), postOps=[],
- finalOps=[], gen=-1, dryrun=False):
- '''Evolve the current population *gen* generations using mating scheme
- *matingScheme* and operators *initOps* (applied before evolution), *preOps*
- (applied to the parental population at the beginning of each life cycle),
- *postOps* (applied to the offspring population at the end of each life
- cycle) and *finalOps* (applied at the end of evolution). More specifically,
- this function creates a *Simulator* using the current population, call its
- *evolve* function using passed parameters and then replace the current
- population with the evolved population. Please refer to function
- ``Simulator.evolve`` for more details about each parameter.'''
- if dryrun:
- print describeEvolProcess(initOps, preOps, matingScheme, postOps, finalOps, gen, 1)
- return (0,)
- if isinstance(self, Pedigree):
- raise ValueError("Evolving a pedigree object directly is not allowed.")
- # create a simulator with self
- simu = Simulator(self)
- # evolve
- gen = simu.evolve(initOps, preOps, matingScheme, postOps, finalOps, gen)
- # get the evolved population
- self.swap(simu.population(0))
- return gen[0]
-
-Population.evolve = evolve_pop
-
-def all_individuals(self, subPops=ALL_AVAIL, ancGens=ALL_AVAIL):
- '''Return an iterator that iterat through all (virtual) subpopulations in
- all ancestral generations. A list of (virtual) subpopulations (*subPops*)
- and a list of ancestral generations (*ancGens*, can be a single number)
- could be specified to iterate through only selected subpopulation and
- generations. Value ``ALL_AVAIL`` is acceptable in the specification of
- ``sp`` and/or ``vsp`` in specifying a virtual subpopulation ``(sp, vsp)``
- for the iteration through all or specific virtual subpopulation in all or
- specific subpopulations.
- '''
- if ancGens is ALL_AVAIL:
- gens = range(self.ancestralGens() + 1)
- elif hasattr(ancGens, '__iter__'):
- gens = ancGens
- else:
- gens = [ancGens]
- #
- curGen = self.curAncestralGen()
- for gen in gens:
- self.useAncestralGen(gen)
- if subPops is ALL_AVAIL:
- for ind in self.individuals():
- yield ind
- else:
- for subPop in subPops:
- if hasattr(subPop, '__iter__'):
- if len(subPop) != 2:
- raise ValueError('Invalid subpopulation ID %s' % subPop)
- if subPop[0] is ALL_AVAIL:
- # (ALL_AVAIL, ALL_AVAIL)
- if subPop[1] is ALL_AVAIL and self.numVirtualSubPop() > 0:
- for sp in range(self.numSubPop()):
- for vsp in range(self.numVirtualSubPop()):
- for ind in self.individuals([sp, vsp]):
- yield ind
- # (ALL_AVAIL, vsp)
- else:
- for sp in range(self.numSubPop()):
- for ind in self.individuals([sp, subPop[1]]):
- yield ind
- else:
- # (sp, ALL_AVAIL)
- if subPop[1] is ALL_AVAIL and self.numVirtualSubPop() > 0:
- for vsp in range(self.numVirtualSubPop()):
- for ind in self.individuals([subPop[0], vsp]):
- yield ind
- # (sp, vsp)
- else:
- for ind in self.individuals(subPop):
- yield ind
- else:
- for ind in self.individuals(subPop):
- yield ind
- self.useAncestralGen(curGen)
-
-Population.allIndividuals = all_individuals
-
-def as_pedigree(self, idField='ind_id', fatherField='father_id', motherField='mother_id'):
- '''Convert the existing population object to a pedigree. After this function
- pedigree function should magically be usable for this function.
- '''
- if isinstance(self, Pedigree):
- return
- ped = Pedigree(self, loci=ALL_AVAIL, infoFields=ALL_AVAIL, ancGens=ALL_AVAIL,
- idField=idField, fatherField=fatherField, motherField=motherField,
- stealPop=True)
- # swap ped and this object. (I do not know if this is the right thing to do)
- self.__class__, ped.__class__ = ped.__class__, self.__class__
- self.this, ped.this = ped.this, self.this
-
-Population.asPedigree = as_pedigree
-
-def as_population(self):
- '''Convert the existing pedigree object to a population. This function will
- behave like a regular population after this function call.'''
- if isinstance(self, Population):
- return
- pop = population(0)
- # the pedigree data has been swapped to pop
- pop.swap(self)
- # swap ped and this object. (I do not know if this is the right thing to do)
- self.__class__, pop.__class__ = pop.__class__, self.__class__
- self.this, pop.this = pop.this, self.this
-
-Pedigree.asPopulation = as_population
-
-# Other definitions that does not really belong to simuUtil.py
-class _dw(object):
- def __init__(self, var):
- try:
- self.__dict__ = var
- except TypeError:
- raise TypeError("The returned value is not a dictionary.\nNote: simu.vars() is a list so simu.dvars() is not allowed. \n Use simu.dvars(rep) for population namespace.")
- def clear(self):
- self.__dict__.clear()
- def __repr__(self):
- return str(self.__dict__)
-
-def dvars(self, *args, **kwargs):
- return _dw(self.vars(*args, **kwargs))
-
-Population.dvars = dvars
-Simulator.dvars = dvars
-
-# expose the clone() method to Python copy module.
-def _deepcopy(self, memo):
- return self.clone()
-
-Population.__deepcopy__ = _deepcopy
-Simulator.__deepcopy__ = _deepcopy
-BaseOperator.__deepcopy__ = _deepcopy
-
-
-Population.__deepcopy__ = _deepcopy
-Simulator.__deepcopy__ = _deepcopy
-BaseOperator.__deepcopy__ = _deepcopy
-
-def ind_setInfo2(self, field, value):
- self.setInfo(value, field)
-
-def ind_setInfo3(self, field, value):
- if field == 'this':
- self.__dict__['this'] = value
- else:
- self.setInfo(value, field)
-
-def ind_getInfo3(self, field):
- if field == 'this':
- return self.__dict__['this']
- else:
- return self.info(field)
-
-if sys.version_info[0] == 3:
- Individual.__setattr__ = ind_setInfo3
- Individual.__getattr__ = ind_getInfo3
-else:
- Individual.__setattr__ = ind_setInfo2
- Individual.__getattr__ = Individual.info
-
-
-def obj_equal(self, obj):
- return self.__cmp__(obj) == 0
-
-if sys.version_info[0] == 3:
- Population.__eq__ = obj_equal
- Pedigree.__eq__ = obj_equal
- Simulator.__eq__ = obj_equal
-
-##
-## This is the result of an attemp to move describeEvolProcess from the C++
-## level to the Python level so that it can correctly call the 'describe'
-## function of a derived operator or mating scheme if they define a 'describe'
-## function.
-##
-## This change has been temporarily reverted because many simuPOP components
-## such as HomoMating, OffspringGenerator accepts such objects but cannot
-## call the Python level 'describe' function correctly. Because this function
-## can only describe customized pre or post mating operators and homogeneous
-## mating schemes, it does not appear to be a good idea to expose (although
-## still hidden) functions such as BaseOperator.applicability() to the Python
-## interface.
-##
-
-## def describeEvolProcess(initOps = [], preOps = [], matingScheme = None,
-## postOps = [], finalOps = [], gen = -1, numRep = 1):
-## '''This function takes the same parameters as ``Simulator.evolve`` and
-## output a description of how an evolutionary process will be executed. It is
-## recommended that you call this function if you have any doubt on how your
-## simulation will proceed.'''
-## allDesc = [''] * numRep
-##
-## # handle single inputs
-## if not hasattr(initOps, '__iter__'):
-## initOps = [initOps]
-## if not hasattr(preOps, '__iter__'):
-## preOps = [preOps]
-## if not hasattr(postOps, '__iter__'):
-## postOps = [postOps]
-## if not hasattr(finalOps, '__iter__'):
-## finalOps = [finalOps]
-##
-## for curRep in range(numRep):
-## desc = ''
-## if not initOps:
-## desc += 'No operator is used to initialize Population (initOps).\n'
-## else:
-## desc += 'Apply pre-evolution operators to the initial population (initOps).\n<ul>\n'
-## for op in initOps:
-## desc += '<li>' + op.describe(False) + ' ' + op.applicability(True, False) + '\n'
-## desc += '</ul>\n'
-## if gen < 0:
-## desc += '\nEvolve a population indefinitely until an operator determines it.\n'
-## else:
-## desc += '\nEvolve a population for %s generations\n' % gen
-## desc += '<ul>\n'
-## if not preOps:
-## desc += '<li>No operator is applied to the parental generation (preOps).\n'
-## else:
-## desc += '<li>Apply pre-mating operators to the parental generation (preOps)\n<ul>\n'
-## for op in preOps:
-## if op.isActive(curRep, 0):
-## desc += '<li>' + op.describe(False) + ' ' + op.applicability() + '\n'
-## desc += '</ul>\n'
-## #
-## desc += '\n<li>Populate an offspring populaton from the parental population using mating scheme ' \
-## + matingScheme.describe(False) + '\n'
-## #
-## if not postOps:
-## desc += '\n<li>No operator is applied to the offspring population (postOps).\n'
-## else:
-## desc += '\n<li>Apply post-mating operators to the offspring population (postOps).\n<ul>\n'
-## for op in postOps:
-## if op.isActive(curRep, 0):
-## desc += '<li>' + op.describe(False) + ' ' + op.applicability() + '\n'
-## desc += '</ul>\n'
-## desc += '</ul>\n\n'
-## #
-## if not finalOps:
-## desc += 'No operator is applied to the final population (finalOps).\n'
-## else:
-## desc += 'Apply post-evolution operators (finalOps)\n<ul>\n'
-## for op in finalOps:
-## desc += '<li>' + op.describe(False) + ' ' + op.applicability(True, False) + '\n'
-## desc += '</ul>\n'
-## #
-## allDesc[curRep] = desc
-## #
-## reps = []
-## for curRep in range(numRep):
-## if not reps:
-## reps.append(str(curRep))
-## else:
-## if allDesc[curRep] == allDesc[curRep - 1]:
-## reps.append(str(curRep))
-## else:
-## desc += 'Replicate' + ' '.join(reps)
-## desc += ':\n' + allDesc[curRep - 1] + '\n'
-## reps = [str(curRep)]
-## #
-## desc += 'Replicate' + ' '.join(reps) + ':\n' + allDesc[-1]
-## return formatDescription(desc)
-
-class WithArgs:
- '''This class wraps around a user-provided function and provides an
- attribute ``args`` so that simuPOP knows which parameters to send to the
- function. This is only needed if the function can not be defined with
- allowed parameters.
- '''
- def __init__(self, func, args):
- '''Return a callable object that wraps around function ``func``.
- Parameter ``args`` should be a list of parameter names.
- '''
- self.__args__ = args
- self.func = func
-
- def __call__(self, *args, **kwargs):
- return self.func(*args, **kwargs)
-
-
-# mating schemes
-
-class SequentialParentsChooser(CombinedParentsChooser):
- '''This parent chooser chooses two parents (a father and a mother)
- sequentially from their respective sex groups. Selection is not considered.
- If all fathers (or mothers) are exhausted, this parent chooser will choose
- fathers (or mothers) from the beginning of the (virtual) subpopulation
- again.'''
- def __init__(self):
- '''Create a parent chooser that chooses two parents sequentially from a
- parental (virtual) subpopulation.'''
- CombinedParentsChooser.__init__(self,
- SequentialParentChooser(MALE_ONLY),
- SequentialParentChooser(FEMALE_ONLY))
-
-
-class CloneMating(HomoMating):
- '''A homogeneous mating scheme that uses a sequential parent chooser and
- a clone offspring generator.'''
- def __init__(self, numOffspring = 1, sexMode = None, ops = CloneGenoTransmitter(),
- subPopSize = [], subPops = ALL_AVAIL, weight = 0, selectionField = None):
- '''Create a clonal mating scheme that clones parents to offspring using
- a ``CloneGenoTransmitter``. Please refer to class ``OffspringGenerator``
- for parameters *ops* and *numOffspring*, and to class ``HomoMating`` for
- parameters *subPopSize*, *subPops* and *weight*. Parameters *sexMode* and
- *selectionField* are ignored because this mating scheme does not support
- natural selection, and ``CloneGenoTransmitter`` copies sex from parents
- to offspring. Note that ``CloneGenoTransmitter`` by default also copies
- all parental information fields to offspring.
- '''
- HomoMating.__init__(self,
- chooser = SequentialParentChooser(),
- generator = OffspringGenerator(ops, numOffspring, RANDOM_SEX),
- subPopSize = subPopSize,
- subPops = subPops,
- weight = weight)
-
-
-class RandomSelection(HomoMating):
- '''A homogeneous mating scheme that uses a random single-parent parent
- chooser with replacement, and a clone offspring generator. This mating
- scheme is usually used to simulate the basic haploid Wright-Fisher model
- but it can also be applied to diploid populations.'''
- def __init__(self, numOffspring = 1, sexMode = None, ops = CloneGenoTransmitter(),
- subPopSize = [], subPops = ALL_AVAIL, weight = 0, selectionField = 'fitness'):
- '''Create a mating scheme that select a parent randomly and copy him or
- her to the offspring population. Please refer to class
- ``RandomParentChooser`` for parameter *selectionField*, to class
- ``OffspringGenerator`` for parameters *ops* and *numOffspring*, and to
- class ``HomoMating`` for parameters *subPopSize*, *subPops* and *weight*.
- Parameter *sexMode* is ignored because ``cloneOffspringGenerator`` copies
- sex from parents to offspring.
- '''
- HomoMating.__init__(self,
- chooser = RandomParentChooser(True, selectionField),
- generator = OffspringGenerator(ops, numOffspring, RANDOM_SEX),
- subPopSize = subPopSize,
- subPops = subPops,
- weight = weight)
-
-
-class RandomMating(HomoMating):
- '''A homogeneous mating scheme that uses a random parents chooser with
- replacement and a Mendelian offspring generator. This mating scheme is
- widely used to simulate diploid sexual Wright-Fisher random mating.'''
- def __init__(self, numOffspring = 1, sexMode = RANDOM_SEX, ops = MendelianGenoTransmitter(),
- subPopSize = [], subPops = ALL_AVAIL, weight = 0, selectionField = 'fitness'):
- '''Creates a random mating ssheme that selects two parents randomly and
- transmit genotypes according to Mendelian laws. Please refer to class
- ``RandomParentsChooser`` for parameter *selectionField*, to class
- ``OffspringGenerator`` for parameters *ops*, *sexMode* and
- *numOffspring*, and to class ``HomoMating`` for parameters
- *subPopSize*, *subPops* and *weight*.
- '''
- HomoMating.__init__(self,
- chooser = RandomParentsChooser(True, selectionField),
- generator = OffspringGenerator(ops, numOffspring, sexMode),
- subPopSize = subPopSize,
- subPops = subPops,
- weight = weight)
-
-
-class MonogamousMating(HomoMating):
- '''A homogeneous mating scheme that uses a random parents chooser without
- replacement and a Mendelian offspring generator. It differs from the basic
- random mating scheme in that each parent can mate only once so there is no
- half-sibling in the population.'''
- def __init__(self, numOffspring = 1, sexMode = RANDOM_SEX, ops = MendelianGenoTransmitter(),
- subPopSize = [], subPops = ALL_AVAIL, weight = 0, selectionField = None):
- '''Creates a monogamous mating scheme that selects each parent only
- once. Please refer to class ``OffspringGenerator`` for parameters
- *ops*, *sexMode* and *numOffspring*, and to class ``HomoMating`` for
- parameters *subPopSize*, *subPops* and *weight*. Parameter
- *selectionField* is ignored because this mating scheme does not
- support natural selection.
- '''
- HomoMating.__init__(self,
- chooser = RandomParentsChooser(replacement=False),
- generator = OffspringGenerator(ops, numOffspring, sexMode),
- subPopSize = subPopSize,
- subPops = subPops,
- weight = weight)
-
-
-class PolygamousMating(HomoMating):
- '''A homogeneous mating scheme that uses a multi-spouse parents chooser
- and a Mendelian offspring generator. It differs from the basic random
- mating scheme in that each parent of sex *polySex* will have *polyNum*
- spouses.'''
- def __init__(self, polySex=MALE, polyNum=1, numOffspring = 1,
- sexMode = RANDOM_SEX, ops = MendelianGenoTransmitter(), subPopSize = [],
- subPops = ALL_AVAIL, weight = 0, selectionField = 'fitness'):
- '''Creates a polygamous mating scheme that each parent mates with
- multiple spouses. Please refer to class ``PolyParentsChooser`` for
- parameters *polySex*, *polyNum* and *selectionField*, to class
- ``OffspringGenerator`` for parameters *ops*, *sexMode* and
- *numOffspring*, and to class ``HomoMating`` for parameters
- *subPopSize*, *subPops* and *weight*. '''
- HomoMating.__init__(self,
- chooser = PolyParentsChooser(polySex, polyNum),
- generator = OffspringGenerator(ops, numOffspring, sexMode),
- subPopSize = subPopSize,
- subPops = subPops,
- weight = weight)
-
-
-class HaplodiploidMating(HomoMating):
- '''A homogeneous mating scheme that uses a random parents chooser with
- replacement and a haplodiploid offspring generator. It should be used
- in a haplodiploid population where male individuals only have one set
- of homologous chromosomes.'''
- def __init__(self, numOffspring = 1., sexMode = RANDOM_SEX,
- ops = HaplodiploidGenoTransmitter(), subPopSize = [], subPops = ALL_AVAIL,
- weight = 0, selectionField = 'fitness'):
- '''Creates a mating scheme in haplodiploid populations. Please refer
- to class ``RandomParentsChooser`` for parameter *selectionField*, to
- class ``OffspringGenerator`` for parameters *ops*, *sexMode* and
- *numOffspring*, and to class ``HomoMating`` for parameters
- *subPopSize*, *subPops* and *weight*.
- '''
- HomoMating.__init__(self,
- chooser = RandomParentsChooser(True, selectionField),
- generator = OffspringGenerator(ops, numOffspring, sexMode),
- subPopSize = subPopSize,
- subPops = subPops,
- weight = weight)
-
-
-class SelfMating(HomoMating):
- '''A homogeneous mating scheme that uses a random single-parent parent
- chooser with or without replacement (parameter *replacement*) and a
- selfing offspring generator. It is used to mimic self-fertilization
- in certain plant populations.'''
- def __init__(self, replacement=True, numOffspring = 1, sexMode = RANDOM_SEX,
- ops = SelfingGenoTransmitter(), subPopSize = [], subPops = ALL_AVAIL, weight = 0,
- selectionField = 'fitness'):
- '''Creates a selfing mating scheme where two homologous copies of
- parental chromosomes are transmitted to offspring according to
- Mendelian laws. Please refer to class ``RandomParentChooser`` for
- parameter *replacement* and *selectionField*, to class
- ``OffspringGenerator`` for parameters *ops*, *sexMode* and
- *numOffspring*, and to class ``HomoMating`` for parameters
- *subPopSize*, *subPops* and *weight*.
- '''
- HomoMating.__init__(self,
- chooser = RandomParentChooser(replacement, selectionField),
- generator = OffspringGenerator(ops, numOffspring, sexMode),
- subPopSize = subPopSize,
- subPops = subPops,
- weight = weight)
-
-##
-## def consanguineousMating(infoFields = [], func = None, param = None,
-## replacement = False, numOffspring = 1., sexMode = RANDOM_SEX,
-## ops = MendelianGenoTransmitter(), subPopSize = [],
-## subPops = ALL_AVAIL, weight = 0, selectionField = 'fitness'):
-## '''A homogeneous mating scheme that uses an information parents chooser and
-## a Mendelian offspring generator. A function *func* should be defined to
-## locate certain types of relative to each individual and save their indexes
-## to information fields *infoFields*. This mating scheme will then choose a
-## parent randomly and then another parent from his/her relatives using their
-## saved indexes. Please refer to class ``infoParentsChooser`` for parameters
-## *infoFields*, *func*, *param* and *selectionField*, to class
-## ``OffspringGenerator`` for parameters *ops*, *sexMode* and *numOffspring*,
-## and to class ``HomoMating`` for parameters *subPopSize*, *subPops* and
-## *weight*.
-## '''
-## return HomoMating(
-## chooser = infoParentsChooser(infoFields, func, param, selectionField),
-## generator = OffspringGenerator(ops, numOffspring, sexMode),
-## subPopSize = subPopSize,
-## subPops = subPops,
-## weight = weight)
-##
-
-class ControlledRandomMating(HomoMating):
- '''A homogeneous mating scheme that uses a random sexual parents chooser
- with replacement and a controlled offspring generator using Mendelian
- genotype transmitter. It falls back to a regular random mating scheme
- if there is no locus to control or no trajectory is defined.'''
- def __init__(self, loci=[], alleles=[], freqFunc=None,
- numOffspring = 1, sexMode = RANDOM_SEX, ops = MendelianGenoTransmitter(),
- subPopSize = [], subPops = ALL_AVAIL, weight = 0, selectionField = 'fitness'):
- '''Creates a random mating scheme that controls allele frequency at
- loci *loci*. At each generation, function *freqFunc* will be called to
- called to obtain intended frequencies of alleles *alleles* at loci
- *loci*. The controlled offspring generator will control the acceptance
- of offspring so that the generation reaches desired allele frequencies
- at these loci. If *loci* is empty or *freqFunc* is ``None``, this mating
- scheme works identically to a ``RandomMating scheme``. Rationals and
- applications of this mating scheme is described in details in a paper *Peng
- et al, 2007 (PLoS Genetics)*. Please refer to class ``RandomParentsChooser``
- for parameters *selectionField*, to class ``ControlledOffspringGenerator``
- for parameters *loci*, *alleles*, *freqFunc*, to class
- ``OffspringGenerator`` for parameters *ops*, *sexMode* and *numOffspring*,
- and to class ``HomoMating`` for parameters *subPopSize*, *subPops* and
- *weight*.
- '''
- if (type(loci) in [type([]), type(())] and len(loci) == 0) or (freqFunc is None):
- HomoMating.__init__(self,
- chooser = RandomParentsChooser(True, selectionField),
- generator = OffspringGenerator(ops, numOffspring, sexMode),
- subPopSize = subPopSize,
- subPops = subPops,
- weight = weight)
- else:
- HomoMating.__init__(self,
- chooser = RandomParentsChooser(True, selectionField),
- generator = ControlledOffspringGenerator(loci, alleles, freqFunc,
- ops, numOffspring, sexMode),
- subPopSize = subPopSize,
- subPops = subPops,
- weight = weight)
-
-
-class SNPMutator(MatrixMutator):
- '''A mutator model that assumes two alleles 0 and 1 and accepts mutation
- rate from 0 to 1, and from 1 to 0 alleles. '''
- def __init__(self, u=0, v=0, *args, **kwargs):
- '''Return a ``MatrixMutator`` with proper mutate matrix for a two-allele
- mutation model using mutation rate from allele 0 to 1 (parameter ``u``)
- and from 1 to 0 (parameter ``v``)'''
- MatrixMutator.__init__(self, [[1-u, u], [v, 1-v]], *args, **kwargs)
-
-
-class AcgtMutator(MatrixMutator):
- '''This mutation operator assumes alleles 0, 1, 2, 3 as nucleotides ``A``,
- ``C``, ``G`` and ``T`` and use a 4 by 4 mutation rate matrix to mutate them.
- Although a general model needs 12 parameters, less parameters are needed
- for specific nucleotide mutation models (parameter ``model``). The length
- and meaning of parameter ``rate`` is model dependent.'''
- def __init__(self, rate=[], model='general', *args, **kwargs):
- '''Create a mutation model that mutates between nucleotides ``A``,
- ``C``, ``G``, and ``T`` (alleles are coded in that order as 0, 1, 2
- and 3). Currently supported models are Jukes and Cantor 1969 model
- (``JC69``), Kimura's 2-parameter model (``K80``), Felsenstein 1981
- model (``F81``), Hasgawa, Kishino and Yano 1985 model (``HKY85``),
- Tamura 1992 model (``T92``), Tamura and Nei 1993 model (``TN93``),
- Generalized time reversible model (``GTR``), and a general model
- (``general``) with 12 parameters. Please refer to the simuPOP user's
- guide for detailed information about each model.
- '''
- if model == 'JC69':
- if type(rate) in [type(()), type([])]:
- if len(rate) != 1:
- raise ValueError('A Jukes and Cantor 1969 model needs one parameter mu.')
- mu = rate[0]
- else:
- mu = rate
- m = [[0, mu/4., mu/4., mu/4.],
- [mu/4., 0, mu/4., mu/4.],
- [mu/4., mu/4., 0, mu/4.],
- [mu/4., mu/4., mu/4., 0 ]]
- elif model == 'K80':
- if len(rate) != 2:
- raise ValueError('A Kimura 2-parameter model requires two parameters mu and k')
- mu, k = rate
- m = [[0, mu/4., mu*k/4., mu/4. ],
- [mu/4., 0, mu/4., mu*k/4.],
- [mu*k/4., mu/4., 0, mu/4. ],
- [mu/4., mu*k/4., mu/4., 0 ]]
- elif model == 'F81':
- if len(rate) != 4:
- raise ValueError('A Felsenstein 1981 model requires four parameters mu, pi_A, pi_C and pi_G')
- mu, piA, piC, piG = rate
- piT = 1 - piA - piC - piG
- if piA < 0 or piA > 1 or piC < 0 or piC > 1 or \
- piG < 0 or piG > 1 or piT < 0 or piT > 1:
- raise ValueError('Basic frequencies should be between 0 and 1')
- m = [[0, mu*piC, mu*piG, mu*piT],
- [mu*piA, 0, mu*piG, mu*piT],
- [mu*piA, mu*piC, 0, mu*piT],
- [mu*piA, mu*piC, mu*piG, 0 ]]
- elif model == 'HKY85':
- if len(rate) != 5:
- raise ValueError('A Hasegawa, Kishino and Yano 1985 model requires five parameters mu, k, pi_A, pi_C and pi_G')
- mu, k, piA, piC, piG = rate
- piT = 1 - piA - piC - piG
- if piA < 0 or piA > 1 or piC < 0 or piC > 1 or \
- piG < 0 or piG > 1 or piT < 0 or piT > 1:
- raise ValueError('Basic frequencies should be between 0 and 1')
- m = [[0, mu*piC, mu*k*piG, mu*piT ],
- [mu*piA, 0, mu*piG, mu*k*piT],
- [mu*k*piA, mu*piC, 0, mu*piT ],
- [mu*piA, mu*k*piC, mu*piG, 0 ]]
- elif model == 'T92':
- if len(rate) != 2:
- raise ValueError('A Tamura 1992 model requires two parameters mu and pi_GC')
- mu, piGC = rate
- piG = piC = piGC/2.
- piA = piT = (1 - piGC)/2.
- if piA < 0 or piA > 1 or piC < 0 or piC > 1 or \
- piG < 0 or piG > 1 or piT < 0 or piT > 1:
- raise ValueError('B...
[truncated message content] |
|
From: <si...@us...> - 2011-07-07 04:27:17
|
Revision: 4256
http://simupop.svn.sourceforge.net/simupop/?rev=4256&view=rev
Author: simupop
Date: 2011-07-07 04:27:10 +0000 (Thu, 07 Jul 2011)
Log Message:
-----------
Reapply format change
Modified Paths:
--------------
trunk/doc/refManual.lyx
trunk/doc/userGuide.lyx
trunk/simuPOP_version.py
trunk/src/initializer.cpp
trunk/src/simuPOP_doc.i
trunk/src/stator.cpp
trunk/src/transmitter.cpp
trunk/src/transmitter.h
trunk/src/utility.cpp
trunk/src/utility.h
Modified: trunk/doc/refManual.lyx
===================================================================
--- trunk/doc/refManual.lyx 2011-07-07 03:09:56 UTC (rev 4255)
+++ trunk/doc/refManual.lyx 2011-07-07 04:27:10 UTC (rev 4256)
@@ -5,7 +5,7 @@
\textclass manual
\begin_preamble
\renewcommand{\py@ptsize}{12pt}
-\setreleaseinfo{Release 1.0.6 (\mbox{Rev: 4250})}
+\setreleaseinfo{Release 1.0.6 (\mbox{Rev: 4252})}
% file revision $Rev: 3372$
\authoraddress{
{\bf Department of Epidemiology, U.T. M.D. Anderson Cancer Center}\\
Modified: trunk/doc/userGuide.lyx
===================================================================
--- trunk/doc/userGuide.lyx 2011-07-07 03:09:56 UTC (rev 4255)
+++ trunk/doc/userGuide.lyx 2011-07-07 04:27:10 UTC (rev 4256)
@@ -6,7 +6,7 @@
\begin_preamble
\renewcommand{\py@ptsize}{12pt}
-\setreleaseinfo{Release 1.0.6 (\mbox{Rev: 4250})}
+\setreleaseinfo{Release 1.0.6 (\mbox{Rev: 4252})}
% file revision $Rev: 3372$
\authoraddress{
{\bf Department of Epidemiology, U.T. M.D. Anderson Cancer Center}\\
Modified: trunk/simuPOP_version.py
===================================================================
--- trunk/simuPOP_version.py 2011-07-07 03:09:56 UTC (rev 4255)
+++ trunk/simuPOP_version.py 2011-07-07 04:27:10 UTC (rev 4256)
@@ -1,2 +1,2 @@
SIMUPOP_VER = "1.0.6"
-SIMUPOP_REV = "4250"
+SIMUPOP_REV = "4252"
Modified: trunk/src/initializer.cpp
===================================================================
--- trunk/src/initializer.cpp 2011-07-07 03:09:56 UTC (rev 4255)
+++ trunk/src/initializer.cpp 2011-07-07 04:27:10 UTC (rev 4256)
@@ -71,13 +71,13 @@
else {
if (numThreads() > 1) {
#ifdef _OPENMP
-#pragma omp parallel private(ind)
+# pragma omp parallel private(ind)
{
ind = pop.indIterator(sp->subPop(), omp_get_thread_num());
for (; ind.valid(); ++ind)
ind->setSex(ws.draw() == 0 ? MALE : FEMALE);
}
-#endif
+#endif
} else
for (; ind.valid(); ++ind)
ind->setSex(ws.draw() == 0 ? MALE : FEMALE);
Modified: trunk/src/simuPOP_doc.i
===================================================================
--- trunk/src/simuPOP_doc.i 2011-07-07 03:09:56 UTC (rev 4255)
+++ trunk/src/simuPOP_doc.i 2011-07-07 04:27:10 UTC (rev 4256)
@@ -740,13 +740,13 @@
";
-%ignore simuPOP::Bernullitrials::Bernullitrials(RNG &rng);
+%ignore simuPOP::Bernullitrials::Bernullitrials(RNG &);
%feature("docstring") simuPOP::Bernullitrials::Bernullitrials "
Usage:
- Bernullitrials(rng, prob, trials)
+ Bernullitrials(, prob, trials=0)
";
@@ -768,7 +768,7 @@
";
-%ignore simuPOP::Bernullitrials::setParameter(const vectorf &prob, size_t trials);
+%ignore simuPOP::Bernullitrials::setParameter(const vectorf &prob, size_t trials=0);
%feature("docstring") simuPOP::Bernullitrials::doTrial "
@@ -1032,6 +1032,8 @@
%feature("docstring") simuPOP::CombinedParentsChooser::describe "Obsolete or undocumented function."
+%ignore simuPOP::CombinedParentsChooser::parallelizable() const;
+
%ignore simuPOP::CombinedParentsChooser::initialize(Population &pop, size_t sp);
%ignore simuPOP::CombinedParentsChooser::finalize(Population &pop, size_t sp);
@@ -3191,6 +3193,8 @@
%feature("docstring") simuPOP::InheritTagger::clone "Obsolete or undocumented function."
+%ignore simuPOP::InheritTagger::parallelizable() const;
+
%feature("docstring") simuPOP::InitGenotype "
Details:
@@ -3547,6 +3551,8 @@
%feature("docstring") simuPOP::MaPenetrance::describe "Obsolete or undocumented function."
+%ignore simuPOP::MaPenetrance::parallelizable() const;
+
%feature("docstring") simuPOP::MapPenetrance "
Details:
@@ -3595,6 +3601,8 @@
%feature("docstring") simuPOP::MapPenetrance::describe "Obsolete or undocumented function."
+%ignore simuPOP::MapPenetrance::parallelizable() const;
+
%feature("docstring") simuPOP::MapSelector "
Details:
@@ -3644,6 +3652,8 @@
%feature("docstring") simuPOP::MapSelector::describe "Obsolete or undocumented function."
+%ignore simuPOP::MapSelector::parallelizable() const;
+
%feature("docstring") simuPOP::MaSelector "
Details:
@@ -3700,6 +3710,8 @@
%feature("docstring") simuPOP::MaSelector::describe "Obsolete or undocumented function."
+%ignore simuPOP::MaSelector::parallelizable() const;
+
%feature("docstring") simuPOP::MatingScheme "
Details:
@@ -4065,6 +4077,8 @@
%ignore simuPOP::MitochondrialGenoTransmitter::applyDuringMating(Population &pop, Population &offPop, RawIndIterator offspring, Individual *dad=NULL, Individual *mom=NULL) const;
+%ignore simuPOP::MitochondrialGenoTransmitter::parallelizable() const;
+
%feature("docstring") simuPOP::MixedMutator "
Details:
@@ -4158,6 +4172,8 @@
%feature("docstring") simuPOP::MlPenetrance::describe "Obsolete or undocumented function."
+%ignore simuPOP::MlPenetrance::parallelizable() const;
+
%feature("docstring") simuPOP::MlSelector "
Details:
@@ -4208,6 +4224,8 @@
%feature("docstring") simuPOP::MlSelector::describe "Obsolete or undocumented function."
+%ignore simuPOP::MlSelector::parallelizable() const;
+
%feature("docstring") simuPOP::MutSpaceMutator "
Details:
@@ -4838,6 +4856,8 @@
%ignore simuPOP::ParentsTagger::applyDuringMating(Population &pop, Population &offPop, RawIndIterator offspring, Individual *dad=NULL, Individual *mom=NULL) const;
+%ignore simuPOP::ParentsTagger::parallelizable() const;
+
%feature("docstring") simuPOP::Pause "
Details:
@@ -5256,6 +5276,14 @@
%ignore simuPOP::PedigreeMating::mate(Population &pop, Population &scratch);
+%feature("docstring") simuPOP::PedigreeMating::parallelizable "
+
+Usage:
+
+ x.parallelizable()
+
+";
+
%feature("docstring") simuPOP::PedigreeTagger "
Details:
@@ -5330,6 +5358,8 @@
%ignore simuPOP::PedigreeTagger::applyDuringMating(Population &pop, Population &offPop, RawIndIterator offspring, Individual *dad=NULL, Individual *mom=NULL) const;
+%ignore simuPOP::PedigreeTagger::parallelizable() const;
+
%feature("docstring") simuPOP::PointMutator "
Details:
@@ -5445,6 +5475,8 @@
%feature("docstring") simuPOP::PolyParentsChooser::describe "Obsolete or undocumented function."
+%ignore simuPOP::PolyParentsChooser::parallelizable() const;
+
%ignore simuPOP::PolyParentsChooser::initialize(Population &pop, size_t sp);
%ignore simuPOP::PolyParentsChooser::chooseParents(RawIndIterator basePtr);
@@ -7190,6 +7222,8 @@
%feature("docstring") simuPOP::PyParentsChooser::describe "Obsolete or undocumented function."
+%ignore simuPOP::PyParentsChooser::parallelizable() const;
+
%ignore simuPOP::PyParentsChooser::initialize(Population &pop, size_t sp);
%ignore simuPOP::PyParentsChooser::finalize(Population &pop, size_t sp);
@@ -7251,6 +7285,8 @@
%feature("docstring") simuPOP::PyPenetrance::describe "Obsolete or undocumented function."
+%ignore simuPOP::PyPenetrance::parallelizable() const;
+
%feature("docstring") simuPOP::pyPopIterator "
Details:
@@ -7383,6 +7419,8 @@
%feature("docstring") simuPOP::PySelector::describe "Obsolete or undocumented function."
+%ignore simuPOP::PySelector::parallelizable() const;
+
%feature("docstring") simuPOP::PyTagger "
Details:
@@ -7424,6 +7462,8 @@
%ignore simuPOP::PyTagger::applyDuringMating(Population &pop, Population &offPop, RawIndIterator offspring, Individual *dad=NULL, Individual *mom=NULL) const;
+%ignore simuPOP::PyTagger::parallelizable() const;
+
%feature("docstring") simuPOP::RandomParentChooser "
Details:
@@ -7767,6 +7807,8 @@
%ignore simuPOP::Recombinator::applyDuringMating(Population &pop, Population &offPop, RawIndIterator offspring, Individual *dad, Individual *mom) const;
+%ignore simuPOP::Recombinator::parallelizable() const;
+
%feature("docstring") simuPOP::ResizeSubPops "
Details:
@@ -7942,8 +7984,6 @@
";
-%ignore simuPOP::RNG::generateRandomSeed();
-
%feature("docstring") simuPOP::RNG::randUniform "
Usage:
@@ -10378,6 +10418,8 @@
%ignore simuPOP::fetchAndIncrement(ATOMICLONG *val);
+%ignore simuPOP::parallelSort(T1 start, T1 end, T2 cmp);
+
%ignore simuPOP::simuPOPkbhit();
%ignore simuPOP::simuPOPgetch();
Modified: trunk/src/stator.cpp
===================================================================
--- trunk/src/stator.cpp 2011-07-07 03:09:56 UTC (rev 4255)
+++ trunk/src/stator.cpp 2011-07-07 04:27:10 UTC (rev 4256)
@@ -2483,7 +2483,7 @@
}
}
#endif
- } else {
+ } else{
HAPLOLIST::const_iterator it = begin;
for (; it != end; ++it) {
HAPLOLIST::const_iterator it1 = it;
Modified: trunk/src/transmitter.cpp
===================================================================
--- trunk/src/transmitter.cpp 2011-07-07 03:09:56 UTC (rev 4255)
+++ trunk/src/transmitter.cpp 2011-07-07 04:27:10 UTC (rev 4256)
@@ -420,7 +420,7 @@
GenoTransmitter(output, begin, end, step, at, reps, subPops, infoFields),
m_intensity(intensity), m_rates(rates.elems()), m_loci(loci),
m_recBeforeLoci(0), m_convMode(convMode.elems()), m_chromX(-1), m_chromY(-1),
- m_customizedBegin(-1), m_customizedEnd(-1), m_algorithm(0), m_debugOutput(NULL),
+ m_customizedBegin(-1), m_customizedEnd(-1), m_algorithm(0), m_debugOutput(NULL),
#ifdef _OPENMP
m_bt(numThreads(), getRNG())
#else
Modified: trunk/src/transmitter.h
===================================================================
--- trunk/src/transmitter.h 2011-07-07 03:09:56 UTC (rev 4255)
+++ trunk/src/transmitter.h 2011-07-07 04:27:10 UTC (rev 4256)
@@ -638,7 +638,7 @@
#ifdef _OPENMP
mutable vector<Bernullitrials> m_bt;
#else
- mutable Bernullitrials m_bt;
+ mutable Bernullitrials m_bt;
#endif
Modified: trunk/src/utility.cpp
===================================================================
--- trunk/src/utility.cpp 2011-07-07 03:09:56 UTC (rev 4255)
+++ trunk/src/utility.cpp 2011-07-07 04:27:10 UTC (rev 4256)
@@ -495,7 +495,7 @@
ATOMICLONG fetchAndIncrement(ATOMICLONG * val)
{
- if(g_numThreads == 1)
+ if (g_numThreads == 1)
return (*val)++;
else
#ifdef _WIN64
@@ -503,11 +503,11 @@
#elif defined(_WIN32)
return InterlockedIncrement(val) - 1;
#else
- // for Intel C++, see page 164 of
- // http://softwarecommunity.intel.com/isn/downloads/softwareproducts/pdfs/347603.pdf
- //
- // for gcc, see
- // http://gcc.gnu.org/onlinedocs/gcc-4.1.0/gcc/Atomic-Builtins.html
+ // for Intel C++, see page 164 of
+ // http://softwarecommunity.intel.com/isn/downloads/softwareproducts/pdfs/347603.pdf
+ //
+ // for gcc, see
+ // http://gcc.gnu.org/onlinedocs/gcc-4.1.0/gcc/Atomic-Builtins.html
return __sync_fetch_and_add(val, 1);
#endif
}
@@ -2268,9 +2268,9 @@
if (m_stmts != NULL) {
#if PY_VERSION_HEX >= 0x03020000
res = PyEval_EvalCode((PyObject *)m_stmts, m_locals, m_locals);
-#else
+#else
res = PyEval_EvalCode((PyCodeObject *)m_stmts, m_locals, m_locals);
-#endif
+#endif
if (res == NULL) {
#ifndef OPTIMIZED
if (debug(DBG_GENERAL)) {
@@ -2290,7 +2290,7 @@
res = PyEval_EvalCode((PyObject *)m_expr, m_locals, m_locals);
#else
res = PyEval_EvalCode((PyCodeObject *)m_expr, m_locals, m_locals);
-#endif
+#endif
if (res == NULL) {
#ifndef OPTIMIZED
if (debug(DBG_GENERAL)) {
Modified: trunk/src/utility.h
===================================================================
--- trunk/src/utility.h 2011-07-07 03:09:56 UTC (rev 4255)
+++ trunk/src/utility.h 2011-07-07 04:27:10 UTC (rev 4256)
@@ -80,7 +80,7 @@
# include "tbb/parallel_sort.h"
# include "tbb/task_scheduler_init.h"
# elif defined(GCC_VERSION) && GCC_VERSION >= 40300
-# include "parallel/algorithm"
+# include "parallel/algorithm"
# endif
#endif
/// for bernulli trials.
@@ -171,6 +171,7 @@
}
}
+
/// a utility function to check keyboard stroke
/// CPPONLY
int simuPOP_kbhit();
@@ -1228,7 +1229,7 @@
if (expr.empty() && stmts.empty())
return;
- //detect leading spaces from python expressions
+ //detect leading spaces from python expressions
DBG_FAILIF(!expr.empty() && (expr[0] == ' ' || expr[0] == '\t'), ValueError,
"Can not include leading space in python expression '" + expr + "'");
DBG_FAILIF(!stmts.empty() && (stmts[0] == ' ' || stmts[0] == '\t'), ValueError,
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <si...@us...> - 2011-07-11 21:13:49
|
Revision: 4260
http://simupop.svn.sourceforge.net/simupop/?rev=4260&view=rev
Author: simupop
Date: 2011-07-11 21:13:42 +0000 (Mon, 11 Jul 2011)
Log Message:
-----------
automatic checkin on Mon Jul 11 16:13:35 2011
Modified Paths:
--------------
trunk/ChangeLog
trunk/Doxy_web
trunk/doc/refManual.lyx
trunk/doc/userGuide.lyx
trunk/simuPOP_version.py
Modified: trunk/ChangeLog
===================================================================
--- trunk/ChangeLog 2011-07-08 21:48:07 UTC (rev 4259)
+++ trunk/ChangeLog 2011-07-11 21:13:42 UTC (rev 4260)
@@ -6,7 +6,7 @@
version 1.0.7 - Not released, available at https://simupop.svn.sourceforge.net/svnroot/simupop/trunk
-version 1.0.6 - Rev 4250 (July 6, 2011)
+version 1.0.6 - Rev 4260 (July 11, 2011)
Major new feature:
- Multi-thread support that allows simuPOP to take advantage of multi-core CPUs.
Modified: trunk/Doxy_web
===================================================================
--- trunk/Doxy_web 2011-07-08 21:48:07 UTC (rev 4259)
+++ trunk/Doxy_web 2011-07-11 21:13:42 UTC (rev 4260)
@@ -25,7 +25,7 @@
# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
# by quotes) that should identify the project.
-PROJECT_NAME = "simuPOP: a forward-time population genetics simulation framework"
+PROJECT_NAME = "simuPOP: a forward-time population genetics simulation environment"
# The PROJECT_NUMBER tag can be used to enter a project or revision number.
# This could be handy for archiving the generated documentation or
Modified: trunk/doc/refManual.lyx
===================================================================
--- trunk/doc/refManual.lyx 2011-07-08 21:48:07 UTC (rev 4259)
+++ trunk/doc/refManual.lyx 2011-07-11 21:13:42 UTC (rev 4260)
@@ -5,7 +5,7 @@
\textclass manual
\begin_preamble
\renewcommand{\py@ptsize}{12pt}
-\setreleaseinfo{Release 1.0.6 (\mbox{Rev: 4252})}
+\setreleaseinfo{Release 1.0.6 (\mbox{Rev: 4259})}
% file revision $Rev: 3372$
\authoraddress{
{\bf Department of Epidemiology, U.T. M.D. Anderson Cancer Center}\\
Modified: trunk/doc/userGuide.lyx
===================================================================
--- trunk/doc/userGuide.lyx 2011-07-08 21:48:07 UTC (rev 4259)
+++ trunk/doc/userGuide.lyx 2011-07-11 21:13:42 UTC (rev 4260)
@@ -6,7 +6,7 @@
\begin_preamble
\renewcommand{\py@ptsize}{12pt}
-\setreleaseinfo{Release 1.0.6 (\mbox{Rev: 4252})}
+\setreleaseinfo{Release 1.0.6 (\mbox{Rev: 4259})}
% file revision $Rev: 3372$
\authoraddress{
{\bf Department of Epidemiology, U.T. M.D. Anderson Cancer Center}\\
Modified: trunk/simuPOP_version.py
===================================================================
--- trunk/simuPOP_version.py 2011-07-08 21:48:07 UTC (rev 4259)
+++ trunk/simuPOP_version.py 2011-07-11 21:13:42 UTC (rev 4260)
@@ -1,2 +1,2 @@
SIMUPOP_VER = "1.0.6"
-SIMUPOP_REV = "4252"
+SIMUPOP_REV = "4259"
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <si...@us...> - 2011-12-25 20:15:29
|
Revision: 4354
http://simupop.svn.sourceforge.net/simupop/?rev=4354&view=rev
Author: simupop
Date: 2011-12-25 20:15:22 +0000 (Sun, 25 Dec 2011)
Log Message:
-----------
Merge the bug fixes to trunk
Modified Paths:
--------------
trunk/ChangeLog
trunk/src/genoStru.h
trunk/src/population.cpp
trunk/src/sandbox.cpp
trunk/src/sandbox.h
Property Changed:
----------------
trunk/
trunk/SConstruct
trunk/simuOpt.py
trunk/src/__init__.py
trunk/src/main.cpp
trunk/src/qtrait.h
trunk/src/sandbox.py
trunk/test/performance.csv
trunk/test/performance.log
trunk/test/performance.py
trunk/test/run_tests.py
trunk/test/test_00_genoStru.py
trunk/test/test_01_individual.py
trunk/test/test_02_population.py
trunk/test/test_03_operator.py
trunk/test/test_04_simulator.py
trunk/test/test_05_matings.py
trunk/test/test_06_initialization.py
trunk/test/test_07_tagging.py
trunk/test/test_08_stat.py
trunk/test/test_09_selection.py
trunk/test/test_10_qtrait.py
trunk/test/test_11_terminator.py
trunk/test/test_12_migration.py
trunk/test/test_13_mutation.py
trunk/test/test_14_transmitter.py
trunk/test/test_15_penetrance.py
trunk/test/test_16_sampling.py
trunk/test/test_17_utils.py
trunk/test/test_18_plotter.py
Property changes on: trunk
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/openMP:3999-4241
+ /branches/mutant_new:4352-4353
/branches/openMP:3999-4241
Modified: trunk/ChangeLog
===================================================================
--- trunk/ChangeLog 2011-12-25 19:53:08 UTC (rev 4353)
+++ trunk/ChangeLog 2011-12-25 20:15:22 UTC (rev 4354)
@@ -6,6 +6,10 @@
version 1.0.7 - Not released, available at https://simupop.svn.sourceforge.net/svnroot/simupop/trunk
+BUG:
+ - Fix a bug that prevents the correct handling of population structure when evolving
+ populations with changing population structure.
+
version 1.0.6 - Rev 4260 (July 11, 2011)
Major new feature:
- Multi-thread support that allows simuPOP to take advantage of multi-core CPUs.
Property changes on: trunk/SConstruct
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/SConstruct:4262-4317
/branches/mutant_new/SConstruct:4318-4337
/branches/openMP/SConstruct:3999-4241
+ /branches/mutant/SConstruct:4262-4317
/branches/mutant_new/SConstruct:4318-4337,4352-4353
/branches/openMP/SConstruct:3999-4241
Property changes on: trunk/simuOpt.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/simuOpt.py:4262-4317
/branches/mutant_new/simuOpt.py:4318-4337
/branches/openMP/simuOpt.py:3999-4241
+ /branches/mutant/simuOpt.py:4262-4317
/branches/mutant_new/simuOpt.py:4318-4337,4352-4353
/branches/openMP/simuOpt.py:3999-4241
Property changes on: trunk/src/__init__.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/src/__init__.py:4262-4317
/branches/mutant_new/src/__init__.py:4318-4337
/branches/openMP/src/__init__.py:3999-4241
+ /branches/mutant/src/__init__.py:4262-4317
/branches/mutant_new/src/__init__.py:4318-4337,4352-4353
/branches/openMP/src/__init__.py:3999-4241
Modified: trunk/src/genoStru.h
===================================================================
--- trunk/src/genoStru.h 2011-12-25 19:53:08 UTC (rev 4353)
+++ trunk/src/genoStru.h 2011-12-25 20:15:22 UTC (rev 4354)
@@ -305,7 +305,13 @@
m_genoStruIdx = static_cast<TraitIndexType>(idx);
}
+ /// CPPONLY set geno stru
+ void swapGenoStru(GenoStruTrait & rhs)
+ {
+ std::swap(m_genoStruIdx, rhs.m_genoStruIdx);
+ }
+
/** Return the distance between loci \e locus1 and \e locus2 on the
* same chromosome. A negative value will be returned if \e locus1 is
* after \e locus2.
Property changes on: trunk/src/main.cpp
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/src/main.cpp:4262-4317
/branches/mutant_new/src/main.cpp:4318-4337
/branches/openMP/src/main.cpp:3999-4241
+ /branches/mutant/src/main.cpp:4262-4317
/branches/mutant_new/src/main.cpp:4318-4337,4352-4353
/branches/openMP/src/main.cpp:3999-4241
Modified: trunk/src/population.cpp
===================================================================
--- trunk/src/population.cpp 2011-12-25 19:53:08 UTC (rev 4353)
+++ trunk/src/population.cpp 2011-12-25 20:15:22 UTC (rev 4354)
@@ -2359,9 +2359,11 @@
void Population::push(Population & rhs)
{
- DBG_ASSERT(rhs.genoStruIdx() == genoStruIdx(), ValueError,
- "Evolution can not continue because the new generation has different \n"
- "genotypic structure.\n");
+ if (rhs.genoStruIdx() != genoStruIdx()) {
+ if (m_ancestralGens > 0)
+ throw ValueError("Cannot save a population with different structure as an ancestral population to the existing population");
+ swapGenoStru(rhs);
+ }
DBG_FAILIF(this == &rhs, ValueError,
"Passed population is a reference of current population, population.push failed.");
Property changes on: trunk/src/qtrait.h
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/src/qtrait.h:4262-4317
/branches/mutant_new/src/qtrait.h:4318-4337
/branches/openMP/src/qtrait.h:3999-4241
+ /branches/mutant/src/qtrait.h:4262-4317
/branches/mutant_new/src/qtrait.h:4318-4337,4352-4353
/branches/openMP/src/qtrait.h:3999-4241
Modified: trunk/src/sandbox.cpp
===================================================================
--- trunk/src/sandbox.cpp 2011-12-25 19:53:08 UTC (rev 4353)
+++ trunk/src/sandbox.cpp 2011-12-25 20:15:22 UTC (rev 4354)
@@ -564,6 +564,7 @@
added[j] = static_cast<double>(offPop.numLoci(ch) + j + 1);
vectoru addedChrom(sz, ch);
offPop.addLoci(addedChrom, added);
+ pop.addLoci(addedChrom, added);
}
//
GenoIterator it = offPop.individual(offIndex).genoBegin(ploidy, ch);
@@ -577,7 +578,7 @@
}
-void MutSpaceRecombinator::transmitGenotype1(Population & offPop, const Individual & parent,
+void MutSpaceRecombinator::transmitGenotype1(Population & pop, Population & offPop, const Individual & parent,
size_t offIndex, int ploidy) const
{
#ifdef BINARYALLELE
@@ -677,6 +678,7 @@
added[j] = static_cast<double>(offPop.numLoci(ch) + j + 1);
vectoru addedChrom(sz, ch);
offPop.addLoci(addedChrom, added);
+ pop.addLoci(addedChrom, added);
}
//
it = offPop.individual(offIndex).genoBegin(ploidy, ch);
@@ -707,11 +709,11 @@
copyChromosome(*dad, getRNG().randBit(), *offspring, 1, ch);
}
} else if (m_rate == 0.5) {
- transmitGenotype0(offPop, *mom, offspring - offPop.rawIndBegin(), 0);
- transmitGenotype0(offPop, *dad, offspring - offPop.rawIndBegin(), 1);
+ transmitGenotype0(pop, offPop, *mom, offspring - offPop.rawIndBegin(), 0);
+ transmitGenotype0(pop, offPop, *dad, offspring - offPop.rawIndBegin(), 1);
} else {
- transmitGenotype1(offPop, *mom, offspring - offPop.rawIndBegin(), 0);
- transmitGenotype1(offPop, *dad, offspring - offPop.rawIndBegin(), 1);
+ transmitGenotype1(pop, offPop, *mom, offspring - offPop.rawIndBegin(), 0);
+ transmitGenotype1(pop, offPop, *dad, offspring - offPop.rawIndBegin(), 1);
}
return true;
}
Modified: trunk/src/sandbox.h
===================================================================
--- trunk/src/sandbox.h 2011-12-25 19:53:08 UTC (rev 4353)
+++ trunk/src/sandbox.h 2011-12-25 20:15:22 UTC (rev 4354)
@@ -232,6 +232,349 @@
* mutation rates are low, these two mutation models should yield
* similar results.
*/
+ MutSpaceMutator(double rate,
+ // FIXME: we should not have ranges, because ranges are just
+ // chromosomes, so, ranges=[1, 63000], [5000, 50000] shouldbe
+ // loci=[63000, 450000], lociPos=range(63000) + range(5000, 500000)
+ //
+ // The problem is that you need to optimize the storage of loci positions
+ // by saving ranges, not every locations in genoStru.h/cpp.
+ //
+ const intMatrix & ranges,
+ int model = 1,
+ const stringFunc & output = "",
+ int begin = 0, int end = -1, int step = 1, const intList & at = vectori(),
+ const intList & reps = intList(), const subPopList & subPops = subPopList(),
+ const stringList & infoFields = vectorstr()) :
+ BaseOperator(output, begin, end, step, at, reps, subPops, infoFields),
+ m_rate(rate), m_ranges(ranges), m_model(model)
+ {
+ const matrixi & rngs = m_ranges.elems();
+
+ for (size_t i = 0; i < rngs.size(); ++i) {
+ DBG_FAILIF(rngs[i].size() != 2, ValueError, "Ranges should have two elements");
+ for (size_t j = i + 1; j < rngs.size(); ++j) {
+ DBG_FAILIF(rngs[j].size() != 2, ValueError, "Ranges should have two elements");
+ if (i == j)
+ continue;
+ if (rngs[i][0] >= rngs[j][0] && rngs[i][0] <= rngs[j][1])
+ throw ValueError("Overlapping ranges are currently not supported because of potential conflict of mutant locations on different chromosomes.");
+ if (rngs[i][1] >= rngs[j][0] && rngs[i][1] <= rngs[j][1])
+ throw ValueError("Overlapping ranges are currently not supported because of potential conflict of mutant locations on different chromosomes.");
+ }
+ }
+#ifdef BINARYALLELE
+ DBG_FAILIF(true, ValueError, "This operator does not work in binary allele type.");
+#endif
+ }
+
+
+ /// destructor.
+ ~MutSpaceMutator()
+ {
+ }
+
+
+ virtual bool apply(Population & pop) const;
+
+ /// HIDDEN Deep copy of a \c MutSpaceMutator
+ virtual BaseOperator * clone() const
+ {
+ return new MutSpaceMutator(*this);
+ }
+
+
+ /// HIDDEN
+ string describe(bool format = true) const
+ {
+ (void)format; // avoid warning about unused parameter
+ return "<simuPOP.MutSpaceMutator>";
+ }
+
+
+private:
+ size_t locateVacantLocus(Population & pop, size_t beg, size_t end, std::set<size_t> & mutants) const;
+
+private:
+ const double m_rate;
+
+ const intMatrix m_ranges;
+
+ const int m_model;
+};
+
+
+/** This during mating operator recombine chromosomes, which records mutant
+ * locations, using a fixed recombination rate (per base pair).
+ */
+ // FIXME:
+ // This should jsut be the usual recombinator that is implemented for
+ // mutational model. so this should be removed and be replaced with regular
+ // recombinator.
+ //
+class MutSpaceRecombinator : public GenoTransmitter
+{
+public:
+ /** Create a Recombinator (a mendelian genotype transmitter with
+ * recombination and gene conversion) that passes genotypes from parents
+ * (or a parent in case of self-fertilization) to offspring. A
+ * recombination \e rate in the unit of base pair is needed.
+ */
+ MutSpaceRecombinator(double rate, const intMatrix & ranges,
+ const stringFunc & output = "", int begin = 0, int end = -1, int step = 1,
+ const intList & at = vectori(),
+ const intList & reps = intList(), const subPopList & subPops = subPopList(),
+ const stringList & infoFields = vectorstr())
+ : GenoTransmitter(output, begin, end, step, at, reps, subPops, infoFields),
+ m_rate(rate), m_ranges(ranges)
+ {
+ DBG_FAILIF(rate > 0.5 || rate < 0, ValueError, "Recombination rate should be between 0 and 0.5");
+#ifdef BINARYALLELE
+ DBG_FAILIF(true, ValueError, "This operator does not work in binary allele type.");
+#endif
+ }
+
+
+ /// HIDDEN Deep copy of a Recombinator
+ virtual BaseOperator * clone() const
+ {
+ return new MutSpaceRecombinator(*this);
+ }
+
+
+ virtual ~MutSpaceRecombinator()
+ {
+ }
+
+
+ /// HIDDEN
+ string describe(bool format = true) const
+ {
+ (void)format; // avoid warning about unused parameter
+ return "<simuPOP.MutSpaceRecombinator>";
+ }
+
+
+ /** CPPONLY
+ * Apply the Recombinator during mating
+ */
+ virtual bool applyDuringMating(Population & pop, Population & offPop,
+ RawIndIterator offspring,
+ Individual * dad, Individual * mom) const;
+
+private:
+#if TR1_SUPPORT == 0
+ typedef std::map<unsigned int, int> MutCounter;
+#else
+ // this is faster than std::map
+ typedef std::tr1::unordered_map<unsigned int, int> MutCounter;
+#endif
+ // use when m_rate = 0.5
+ void transmitGenotype0(Population & pop, Population & offPop, const Individual & parent,
+ size_t offIndex, int ploidy) const;
+
+ // use when m_rate < 1e-4
+ void transmitGenotype1(Population & pop, Population & offPop, const Individual & parent,
+ size_t offIndex, int ploidy) const;
+
+private:
+ /// recombination rate
+ const double m_rate;
+ const intMatrix m_ranges;
+};
+
+
+/// ######################################
+#else
+
+/** This operator looks into a population in mutational space and revert a mutant
+ * to wildtype allele if it is fixed in the population. If a valid output is
+ * specifieid, fixed alleles will be outputed with a leading generation number.
+ */
+class RevertFixedSites : public BaseOperator
+{
+public:
+ /** Create an operator to revert alleles at fixed loci from value 1 to 0.
+ * Parameter \e subPops is ignored.
+ */
+ RevertFixedSites(const stringFunc & output = "", int begin = 0, int end = -1, int step = 1,
+ const intList & at = vectori(),
+ const intList & reps = intList(), const subPopList & subPops = subPopList(),
+ const stringList & infoFields = vectorstr())
+ : BaseOperator(output, begin, end, step, at, reps, subPops, infoFields)
+ {
+ }
+
+
+ /// destructor
+ virtual ~RevertFixedSites()
+ {
+ }
+
+
+ /// HIDDEN Deep copy of a Migrator
+ virtual BaseOperator * clone() const
+ {
+ return new RevertFixedSites(*this);
+ }
+
+
+ /// HIDDEN apply the Migrator to populaiton \e pop.
+ virtual bool apply(Population & pop) const;
+
+ /// HIDDEN
+ string describe(bool format = true) const
+ {
+ (void)format; // avoid warning about unused parameter
+ return "Revert fixed alleles to wildtype allele if it is fixed in the population.";
+ }
+
+
+};
+
+/** This selector assumes that alleles are mutant locations in the mutational
+ * space and assign fitness values to them according to a random distribution.
+ * The overall individual fitness is determined by either an additive, an
+ * multiplicative or an exponential model.
+ */
+class MutSpaceSelector : public BaseSelector
+{
+public:
+ /** Create a selector that assigns individual fitness values according to
+ * random fitness effects. \e selDist can be
+ * \li <tt>(CONSTANT, s, h)</tt> where s will be used for all mutants. The
+ * fitness value for genotypes AA, Aa and aa will be (1, 1-hs, 1-s).
+ * If h is unspecified, a default value h=0.5 (additive model) will
+ * be used.
+ * \li <tt>(GAMMA_DISTRIBUTION, theta, k, h</tt> where s follows a gamma
+ * distribution with scale parameter theta and shape parameter k.
+ * Fitness values for genotypes AA, Aa and aa will be 1, 1-hs and 1-s.
+ * A default value h=0.5 will be used if h is unspecified.
+ * \li a Python function, which will be called when selection coefficient
+ * of a new mutant is needed. This function should return a single
+ * value s (with default value h=0.5) or a sequence of (h, s). Mutant
+ * location will be passed to this function if it accepts a parameter
+ * \c loc. This allows the definition of site-specific selection
+ * coefficients.
+ * Individual fitness will be combined in \c ADDITIVE,
+ * \c MULTIPLICATIVE or \c EXPONENTIAL mode. (See \c MlSelector for
+ * details).
+ * If an output is given, mutants and their fitness values will be written
+ * to the output, in the form of 'mutant s h'.
+ */
+ MutSpaceSelector(const floatListFunc & selDist, int mode = EXPONENTIAL,
+ const stringFunc & output = "",
+ int begin = 0, int end = -1, int step = 1, const intList & at = vectori(),
+ const intList & reps = intList(), const subPopList & subPops = subPopList(),
+ const stringList & infoFields = stringList("fitness")) :
+ BaseSelector(output, begin, end, step, at, reps, subPops, infoFields),
+ m_selDist(selDist), m_mode(mode), m_selFactory(), m_additive(true)
+ {
+ if (m_selDist.size() == 0) {
+ DBG_FAILIF(!m_selDist.func().isValid(), ValueError,
+ "Please specify either a distribution with parameter or a function.");
+ } else if (static_cast<int>(m_selDist[0]) == CONSTANT) {
+ DBG_FAILIF(m_selDist.size() < 2, ValueError, "At least one parameter is needed for constant selection coefficient.");
+ } else if (static_cast<int>(m_selDist[0]) == GAMMA_DISTRIBUTION) {
+ DBG_FAILIF(m_selDist.size() < 3, ValueError, "At least two parameters are needed for gamma distribution.");
+ }
+ }
+
+
+ virtual ~MutSpaceSelector()
+ {
+ }
+
+
+ /// HIDDEN Deep copy of a map selector
+ virtual BaseOperator * clone() const
+ {
+ return new MutSpaceSelector(*this);
+ }
+
+
+ /** CPPONLY
+ * calculate/return the fitness value, currently assuming diploid
+ */
+ virtual double indFitness(Population & pop, Individual * ind) const;
+
+ /// HIDDEN
+ string describe(bool format = true) const
+ {
+ (void)format; // avoid warning about unused parameter
+ return "<simuPOP.MutSpaceSelector>" ;
+ }
+
+
+ /// CPPONLY
+ bool apply(Population & pop) const;
+
+ typedef std::pair<double, double> SelCoef;
+
+private:
+ SelCoef getFitnessValue(size_t mutant) const;
+
+
+ double randomSelAddFitness(GenoIterator it, GenoIterator it_end) const;
+
+ double randomSelExpFitness(GenoIterator it, GenoIterator it_end) const;
+
+ // extended models does not assume additivity (h != 0.5)
+ double randomSelMulFitnessExt(GenoIterator it, GenoIterator it_end) const;
+
+ double randomSelAddFitnessExt(GenoIterator it, GenoIterator it_end) const;
+
+ double randomSelExpFitnessExt(GenoIterator it, GenoIterator it_end) const;
+
+private:
+ ///
+ floatListFunc m_selDist;
+
+ int m_mode;
+ ///
+#if TR1_SUPPORT == 0
+ typedef std::map<unsigned int, SelCoef> SelMap;
+ typedef std::map<unsigned int, int> MutCounter;
+#else
+ // this is faster than std::map
+ typedef std::tr1::unordered_map<size_t, SelCoef> SelMap;
+ typedef std::tr1::unordered_map<size_t, size_t> MutCounter;
+#endif
+ mutable SelMap m_selFactory;
+ mutable vectoru m_newMutants;
+ // whether or not all markers are additive.
+ mutable bool m_additive;
+};
+
+
+/** This is an infite site mutation model in mutational space. The alleles
+ * in the population is assumed to be locations of mutants. A mutation
+ * rate is given that mutate alleles in 'regions'. If number of mutants
+ * for an individual exceed the number of loci, 10 loci will be added
+ * to everyone in the population.
+ */
+class MutSpaceMutator : public BaseOperator
+{
+public:
+ /** This operator accepts a list of ranges which is the 'real range' of
+ * each chromosome. Mutation happens with muation rate \e rate and mutants
+ * will be recorded to the population (instead of alleles). By default,
+ * this mutator assumes an finite-allele model where all mutations are
+ * allowed and if a mutant (allele 1) is mutated, it will be mutated to
+ * allele 0 (back mutation). Alternatively (\e model = 2), an
+ * infinite-sites mutation model can be used where mutations can happen
+ * only at a new locus. Mutations happen at a locus with existing mutants
+ * will be moved to a random locus without existing mutant. A warning
+ * message will be printed if there is no vacant locus available. If a
+ * valid \e output is given, mutants will be outputted in the format of
+ * "gen mutant ind type" where type is 0 for forward (0->1), 1 for
+ * backward (1->0), 2 for relocated mutations, and 3 for ignored mutation
+ * because no vacent locus is available. The second mode has the
+ * advantage that all mutants in the simulated population can be traced
+ * to a single mutation event. If the regions are reasonably wide and
+ * mutation rates are low, these two mutation models should yield
+ * similar results.
+ */
MutSpaceMutator(double rate, const intMatrix & ranges, int model = 1,
const stringFunc & output = "",
int begin = 0, int end = -1, int step = 1, const intList & at = vectori(),
@@ -356,11 +699,11 @@
typedef std::tr1::unordered_map<unsigned int, int> MutCounter;
#endif
// use when m_rate = 0.5
- void transmitGenotype0(Population & offPop, const Individual & parent,
+ void transmitGenotype0(Population & pop, Population & offPop, const Individual & parent,
size_t offIndex, int ploidy) const;
// use when m_rate < 1e-4
- void transmitGenotype1(Population & offPop, const Individual & parent,
+ void transmitGenotype1(Population & pop, Population & offPop, const Individual & parent,
size_t offIndex, int ploidy) const;
private:
Property changes on: trunk/src/sandbox.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/src/sandbox.py:4262-4317
/branches/mutant_new/src/sandbox.py:4318-4337
/branches/openMP/src/sandbox.py:3999-4241
+ /branches/mutant/src/sandbox.py:4262-4317
/branches/mutant_new/src/sandbox.py:4318-4337,4352-4353
/branches/openMP/src/sandbox.py:3999-4241
Property changes on: trunk/test/performance.csv
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/performance.csv:4262-4317
/branches/mutant_new/test/performance.csv:4318-4337
/branches/openMP/test/performance.csv:3999-4241
+ /branches/mutant/test/performance.csv:4262-4317
/branches/mutant_new/test/performance.csv:4318-4337,4352-4353
/branches/openMP/test/performance.csv:3999-4241
Property changes on: trunk/test/performance.log
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/performance.log:4262-4317
/branches/mutant_new/test/performance.log:4318-4337
/branches/openMP/test/performance.log:3999-4241
+ /branches/mutant/test/performance.log:4262-4317
/branches/mutant_new/test/performance.log:4318-4337,4352-4353
/branches/openMP/test/performance.log:3999-4241
Property changes on: trunk/test/performance.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/performance.py:4262-4317
/branches/mutant_new/test/performance.py:4318-4337
/branches/openMP/test/performance.py:3999-4241
+ /branches/mutant/test/performance.py:4262-4317
/branches/mutant_new/test/performance.py:4318-4337,4352-4353
/branches/openMP/test/performance.py:3999-4241
Property changes on: trunk/test/run_tests.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/run_tests.py:4262-4317
/branches/mutant_new/test/run_tests.py:4318-4337
/branches/openMP/test/run_tests.py:3999-4241
+ /branches/mutant/test/run_tests.py:4262-4317
/branches/mutant_new/test/run_tests.py:4318-4337,4352-4353
/branches/openMP/test/run_tests.py:3999-4241
Property changes on: trunk/test/test_00_genoStru.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_00_genoStru.py:4262-4317
/branches/mutant_new/test/test_00_genoStru.py:4318-4337
/branches/openMP/test/test_00_genoStru.py:3999-4241
+ /branches/mutant/test/test_00_genoStru.py:4262-4317
/branches/mutant_new/test/test_00_genoStru.py:4318-4337,4352-4353
/branches/openMP/test/test_00_genoStru.py:3999-4241
Property changes on: trunk/test/test_01_individual.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_01_individual.py:4262-4317
/branches/mutant_new/test/test_01_individual.py:4318-4337
/branches/openMP/test/test_01_individual.py:3999-4241
+ /branches/mutant/test/test_01_individual.py:4262-4317
/branches/mutant_new/test/test_01_individual.py:4318-4337,4352-4353
/branches/openMP/test/test_01_individual.py:3999-4241
Property changes on: trunk/test/test_02_population.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_02_population.py:4262-4317
/branches/mutant_new/test/test_02_population.py:4318-4337
/branches/openMP/test/test_02_population.py:3999-4241
+ /branches/mutant/test/test_02_population.py:4262-4317
/branches/mutant_new/test/test_02_population.py:4318-4337,4352-4353
/branches/openMP/test/test_02_population.py:3999-4241
Property changes on: trunk/test/test_03_operator.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_03_operator.py:4262-4317
/branches/mutant_new/test/test_03_operator.py:4318-4337
/branches/openMP/test/test_03_operator.py:3999-4241
+ /branches/mutant/test/test_03_operator.py:4262-4317
/branches/mutant_new/test/test_03_operator.py:4318-4337,4352-4353
/branches/openMP/test/test_03_operator.py:3999-4241
Property changes on: trunk/test/test_04_simulator.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_04_simulator.py:4262-4317
/branches/mutant_new/test/test_04_simulator.py:4318-4337
/branches/openMP/test/test_04_simulator.py:3999-4241
+ /branches/mutant/test/test_04_simulator.py:4262-4317
/branches/mutant_new/test/test_04_simulator.py:4318-4337,4352-4353
/branches/openMP/test/test_04_simulator.py:3999-4241
Property changes on: trunk/test/test_05_matings.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_05_matings.py:4262-4317
/branches/mutant_new/test/test_05_matings.py:4318-4337
/branches/openMP/test/test_05_matings.py:3999-4241
+ /branches/mutant/test/test_05_matings.py:4262-4317
/branches/mutant_new/test/test_05_matings.py:4318-4337,4352-4353
/branches/openMP/test/test_05_matings.py:3999-4241
Property changes on: trunk/test/test_06_initialization.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_06_initialization.py:4262-4317
/branches/mutant_new/test/test_06_initialization.py:4318-4337
/branches/openMP/test/test_06_initialization.py:3999-4241
+ /branches/mutant/test/test_06_initialization.py:4262-4317
/branches/mutant_new/test/test_06_initialization.py:4318-4337,4352-4353
/branches/openMP/test/test_06_initialization.py:3999-4241
Property changes on: trunk/test/test_07_tagging.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_07_tagging.py:4262-4317
/branches/mutant_new/test/test_07_tagging.py:4318-4337
/branches/openMP/test/test_07_tagging.py:3999-4241
+ /branches/mutant/test/test_07_tagging.py:4262-4317
/branches/mutant_new/test/test_07_tagging.py:4318-4337,4352-4353
/branches/openMP/test/test_07_tagging.py:3999-4241
Property changes on: trunk/test/test_08_stat.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_08_stat.py:4262-4317
/branches/mutant_new/test/test_08_stat.py:4318-4337
/branches/openMP/test/test_08_stat.py:3999-4241
+ /branches/mutant/test/test_08_stat.py:4262-4317
/branches/mutant_new/test/test_08_stat.py:4318-4337,4352-4353
/branches/openMP/test/test_08_stat.py:3999-4241
Property changes on: trunk/test/test_09_selection.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_09_selection.py:4262-4317
/branches/mutant_new/test/test_09_selection.py:4318-4337
/branches/openMP/test/test_09_selection.py:3999-4241
+ /branches/mutant/test/test_09_selection.py:4262-4317
/branches/mutant_new/test/test_09_selection.py:4318-4337,4352-4353
/branches/openMP/test/test_09_selection.py:3999-4241
Property changes on: trunk/test/test_10_qtrait.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_10_qtrait.py:4262-4317
/branches/mutant_new/test/test_10_qtrait.py:4318-4337
/branches/openMP/test/test_10_qtrait.py:3999-4241
+ /branches/mutant/test/test_10_qtrait.py:4262-4317
/branches/mutant_new/test/test_10_qtrait.py:4318-4337,4352-4353
/branches/openMP/test/test_10_qtrait.py:3999-4241
Property changes on: trunk/test/test_11_terminator.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_11_terminator.py:4262-4317
/branches/mutant_new/test/test_11_terminator.py:4318-4337
/branches/openMP/test/test_11_terminator.py:3999-4241
+ /branches/mutant/test/test_11_terminator.py:4262-4317
/branches/mutant_new/test/test_11_terminator.py:4318-4337,4352-4353
/branches/openMP/test/test_11_terminator.py:3999-4241
Property changes on: trunk/test/test_12_migration.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_12_migration.py:4262-4317
/branches/mutant_new/test/test_12_migration.py:4318-4337
/branches/openMP/test/test_12_migration.py:3999-4241
+ /branches/mutant/test/test_12_migration.py:4262-4317
/branches/mutant_new/test/test_12_migration.py:4318-4337,4352-4353
/branches/openMP/test/test_12_migration.py:3999-4241
Property changes on: trunk/test/test_13_mutation.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_13_mutation.py:4262-4317
/branches/mutant_new/test/test_13_mutation.py:4318-4337
/branches/openMP/test/test_13_mutation.py:3999-4241
+ /branches/mutant/test/test_13_mutation.py:4262-4317
/branches/mutant_new/test/test_13_mutation.py:4318-4337,4352-4353
/branches/openMP/test/test_13_mutation.py:3999-4241
Property changes on: trunk/test/test_14_transmitter.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_14_transmitter.py:4262-4317
/branches/mutant_new/test/test_14_transmitter.py:4318-4337
/branches/openMP/test/test_14_transmitter.py:3999-4241
+ /branches/mutant/test/test_14_transmitter.py:4262-4317
/branches/mutant_new/test/test_14_transmitter.py:4318-4337,4352-4353
/branches/openMP/test/test_14_transmitter.py:3999-4241
Property changes on: trunk/test/test_15_penetrance.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_15_penetrance.py:4262-4317
/branches/mutant_new/test/test_15_penetrance.py:4318-4337
/branches/openMP/test/test_15_penetrance.py:3999-4241
+ /branches/mutant/test/test_15_penetrance.py:4262-4317
/branches/mutant_new/test/test_15_penetrance.py:4318-4337,4352-4353
/branches/openMP/test/test_15_penetrance.py:3999-4241
Property changes on: trunk/test/test_16_sampling.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_16_sampling.py:4262-4317
/branches/mutant_new/test/test_16_sampling.py:4318-4337
/branches/openMP/test/test_16_sampling.py:3999-4241
+ /branches/mutant/test/test_16_sampling.py:4262-4317
/branches/mutant_new/test/test_16_sampling.py:4318-4337,4352-4353
/branches/openMP/test/test_16_sampling.py:3999-4241
Property changes on: trunk/test/test_17_utils.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_17_utils.py:4262-4317
/branches/mutant_new/test/test_17_utils.py:4318-4337
/branches/openMP/test/test_17_utils.py:3999-4241
+ /branches/mutant/test/test_17_utils.py:4262-4317
/branches/mutant_new/test/test_17_utils.py:4318-4337,4352-4353
/branches/openMP/test/test_17_utils.py:3999-4241
Property changes on: trunk/test/test_18_plotter.py
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant/test/test_18_plotter.py:4262-4317
/branches/mutant_new/test/test_18_plotter.py:4318-4337
/branches/openMP/test/test_18_plotter.py:3999-4241
+ /branches/mutant/test/test_18_plotter.py:4262-4317
/branches/mutant_new/test/test_18_plotter.py:4318-4337,4352-4353
/branches/openMP/test/test_18_plotter.py:3999-4241
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <si...@us...> - 2011-12-25 20:26:18
|
Revision: 4355
http://simupop.svn.sourceforge.net/simupop/?rev=4355&view=rev
Author: simupop
Date: 2011-12-25 20:26:08 +0000 (Sun, 25 Dec 2011)
Log Message:
-----------
Merge mutant_new to trunk in order to make trunk compile
Modified Paths:
--------------
trunk/ChangeLog
trunk/setup.py
trunk/simuPOP_version.py
trunk/src/customizedTypes.c
trunk/src/individual.cpp
trunk/src/individual.h
trunk/src/mating.cpp
trunk/src/mutator.cpp
trunk/src/population.cpp
trunk/src/population.h
trunk/src/sandbox.cpp
trunk/src/sandbox.h
trunk/src/simuPOP_cfg.h
trunk/src/simuPOP_common.i
trunk/src/simuPOP_doc.i
trunk/src/stator.cpp
trunk/src/stator.h
trunk/src/transmitter.cpp
trunk/src/utility.cpp
trunk/src/virtualSubPop.cpp
trunk/test/performance.csv
trunk/test/performance.log
trunk/test/performance.py
trunk/test/test_08_stat.py
Added Paths:
-----------
trunk/src/mutant_vector.h
trunk/src/simuPOP_mu.i
trunk/src/simuPOP_muop.i
Property Changed:
----------------
trunk/
trunk/SConstruct
trunk/simuOpt.py
trunk/src/__init__.py
trunk/src/main.cpp
trunk/src/qtrait.h
trunk/src/sandbox.py
trunk/test/performance.csv
trunk/test/performance.log
trunk/test/performance.py
trunk/test/run_tests.py
trunk/test/test_00_genoStru.py
trunk/test/test_01_individual.py
trunk/test/test_02_population.py
trunk/test/test_03_operator.py
trunk/test/test_04_simulator.py
trunk/test/test_05_matings.py
trunk/test/test_06_initialization.py
trunk/test/test_07_tagging.py
trunk/test/test_08_stat.py
trunk/test/test_09_selection.py
trunk/test/test_10_qtrait.py
trunk/test/test_11_terminator.py
trunk/test/test_12_migration.py
trunk/test/test_13_mutation.py
trunk/test/test_14_transmitter.py
trunk/test/test_15_penetrance.py
trunk/test/test_16_sampling.py
trunk/test/test_17_utils.py
trunk/test/test_18_plotter.py
Property changes on: trunk
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant_new:4352-4353
/branches/openMP:3999-4241
+ /branches/mutant:4262-4317
/branches/mutant_new:4318-4354
/branches/openMP:3999-4241
Modified: trunk/ChangeLog
===================================================================
--- trunk/ChangeLog 2011-12-25 20:15:22 UTC (rev 4354)
+++ trunk/ChangeLog 2011-12-25 20:26:08 UTC (rev 4355)
@@ -6,6 +6,10 @@
version 1.0.7 - Not released, available at https://simupop.svn.sourceforge.net/svnroot/simupop/trunk
+New features:
+ - New option numOfSegSites to operator Stat to calculate the number of segragating
+ sites.
+
BUG:
- Fix a bug that prevents the correct handling of population structure when evolving
populations with changing population structure.
Property changes on: trunk/SConstruct
___________________________________________________________________
Deleted: svn:mergeinfo
- /branches/mutant/SConstruct:4262-4317
/branches/mutant_new/SConstruct:4318-4337,4352-4353
/branches/openMP/SConstruct:3999-4241
Modified: trunk/setup.py
===================================================================
--- trunk/setup.py 2011-12-25 20:15:22 UTC (rev 4354)
+++ trunk/setup.py 2011-12-25 20:26:08 UTC (rev 4355)
@@ -70,10 +70,11 @@
output = ferr.readlines()[-1].decode('utf8')
try:
version = re.match('.*gcc version\s*(\d+).(\d+).(\d+).*', output).groups()
+ if int(version[0]) < 4 or int(version[1]) < 2:
+ print('Support for openMP is turned off because version %s.%s.%s of gcc does not support this feature' % version)
+ USE_OPENMP = False
except:
- print('Can not obtain version of gcc.')
- if int(version[0]) < 4 or int(version[1]) < 2:
- print('Support for openMP is turned off because version %s.%s.%s of gcc does not support this feature' % version)
+ print('Can not obtain version of gcc, and openMP is disable')
USE_OPENMP = False
USE_ICC = False
@@ -192,6 +193,7 @@
#
HEADER_FILES = [
+ 'mutant_vector.h',
'simuPOP_cfg.h',
'utility.h',
'genoStru.h',
@@ -236,7 +238,7 @@
'pedigree.cpp',
'virtualSubPop.cpp',
'sandbox.cpp',
- 'main.cpp',
+# 'main.cpp',
]
# since it is troublesome to link to external gsl library,
@@ -418,6 +420,11 @@
('_SECURE_SCL', 1), ('_HAS_ITERATOR_DEBUGGING', 0)],
'baop': [('SIMUPOP_MODULE', 'simuPOP_baop'), ('BINARYALLELE', None), ('OPTIMIZED', None),
('_SECURE_SCL', 0), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ 'mu': [('SIMUPOP_MODULE', 'simuPOP_mu'), ('MUTANTALLELE', None),
+ ('_SECURE_SCL', 1), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ 'muop': [('SIMUPOP_MODULE', 'simuPOP_muop'), ('MUTANTALLELE', None), ('OPTIMIZED', None),
+ ('_SECURE_SCL', 0), ('_HAS_ITERATOR_DEBUGGING', 0)],
+
}
WRAP_INFO = {
@@ -427,6 +434,8 @@
'laop': ['src/simuPOP_laop_wrap.cpp', 'src/simuPOP_laop.i', '-DLONGALLELE -DOPTIMIZED'],
'ba': ['src/simuPOP_ba_wrap.cpp', 'src/simuPOP_ba.i', '-DBINARYALLELE'],
'baop': ['src/simuPOP_baop_wrap.cpp', 'src/simuPOP_baop.i', '-DBINARYALLELE -DOPTIMIZED'],
+ 'mu': ['src/simuPOP_mu_wrap.cpp', 'src/simuPOP_mu.i', '-DMUTANTALLELE'],
+ 'muop': ['src/simuPOP_muop_wrap.cpp', 'src/simuPOP_muop.i', '-DMUTANTALLELE -DOPTIMIZED'],
}
if os.name == 'nt':
@@ -501,7 +510,7 @@
if USE_OPENMP:
res['extra_compile_args'].append('/Qopenmp' if USE_ICC else '/openmp')
else:
- res['extra_compile_args'] = ['-O3', '-Wall', '-Wno-unknown-pragmas']
+ res['extra_compile_args'] = ['-O3', '-Wall', '-Wno-unknown-pragmas', '-Wno-unused-parameter']
if not USE_ICC: # for gcc, turn on extra warning message
res['extra_compile_args'].append('-Wextra')
if USE_OPENMP:
@@ -544,7 +553,7 @@
if __name__ == '__main__':
SIMUPOP_VER, SIMUPOP_REV = simuPOP_version()
# create source file for each module
- MODULES = ['std', 'op', 'la', 'laop', 'ba', 'baop']
+ MODULES = ['std', 'op', 'la', 'laop', 'ba', 'baop', 'mu', 'muop']
#
# Generate Wrapping files
#
Property changes on: trunk/simuOpt.py
___________________________________________________________________
Deleted: svn:mergeinfo
- /branches/mutant/simuOpt.py:4262-4317
/branches/mutant_new/simuOpt.py:4318-4337,4352-4353
/branches/openMP/simuOpt.py:3999-4241
Modified: trunk/simuPOP_version.py
===================================================================
--- trunk/simuPOP_version.py 2011-12-25 20:15:22 UTC (rev 4354)
+++ trunk/simuPOP_version.py 2011-12-25 20:26:08 UTC (rev 4355)
@@ -1,2 +1,2 @@
-SIMUPOP_VER = "1.0.6"
+SIMUPOP_VER = "1.0.7svn"
SIMUPOP_REV = "4259"
Property changes on: trunk/src/__init__.py
___________________________________________________________________
Deleted: svn:mergeinfo
- /branches/mutant/src/__init__.py:4262-4317
/branches/mutant_new/src/__init__.py:4318-4337,4352-4353
/branches/openMP/src/__init__.py:3999-4241
Modified: trunk/src/customizedTypes.c
===================================================================
--- trunk/src/customizedTypes.c 2011-12-25 20:15:22 UTC (rev 4354)
+++ trunk/src/customizedTypes.c 2011-12-25 20:26:08 UTC (rev 4355)
@@ -715,7 +715,11 @@
}
//
op->ob_iter = begin;
+#ifdef MUTANTALLELE
+ Py_SIZE(op) = end.getIndex() - begin.getIndex();
+#else
Py_SIZE(op) = end - begin;
+#endif
return (PyObject *)op;
}
Modified: trunk/src/individual.cpp
===================================================================
--- trunk/src/individual.cpp 2011-12-25 20:15:22 UTC (rev 4354)
+++ trunk/src/individual.cpp 2011-12-25 20:26:08 UTC (rev 4355)
@@ -49,7 +49,11 @@
Individual & Individual::copyFrom(const Individual & rhs)
{
m_flags = rhs.m_flags;
+#ifdef MUTANTALLELE
+ simuPOP::copy(rhs.genoBegin(), rhs.genoEnd(), genoBegin());
+#else
copy(rhs.genoBegin(), rhs.genoEnd(), genoBegin());
+#endif
copy(rhs.infoBegin(), rhs.infoEnd(), infoBegin());
// also copy genoStru pointer...
this->setGenoStruIdx(rhs.genoStruIdx());
@@ -234,6 +238,7 @@
}
+
PyObject * Individual::genoAtLoci(const lociList & lociList)
{
ssize_t ply = ploidy();
@@ -295,16 +300,28 @@
"A valid ploidy index has to be specified if chrom is non-positive");
if (p < 0) {
CHECKRANGEGENOSIZE(idx);
+#ifdef MUTANTALLELE
+ (m_genoPtr + idx).assign(allele);
+#else
*(m_genoPtr + idx) = allele;
+#endif
} else if (chrom < 0) {
CHECKRANGEABSLOCUS(idx);
CHECKRANGEPLOIDY(static_cast<size_t>(p));
+#ifdef MUTANTALLELE
+ (m_genoPtr + idx + p * totNumLoci()).assign(allele);
+#else
*(m_genoPtr + idx + p * totNumLoci()) = allele;
+#endif
} else {
CHECKRANGELOCUS(static_cast<size_t>(chrom), idx);
CHECKRANGEPLOIDY(static_cast<size_t>(p));
CHECKRANGECHROM(static_cast<size_t>(chrom));
- *(m_genoPtr + idx + p * totNumLoci() + chromBegin(chrom)) = allele;
+#ifdef MUTANTALLELE
+ (m_genoPtr + idx + p * totNumLoci() + chromBegin(chrom)).assign(allele);
+#else
+ *(m_genoPtr + idx + p * totNumLoci() + chromBegin(chrom)) = allele;
+#endif
}
}
@@ -344,9 +361,8 @@
for (size_t j = 0; j < chroms.size(); ++j) {
size_t chrom = chroms[j];
GenoIterator ptr = m_genoPtr + p * totNumLoci() + chromBegin(chrom);
-
for (size_t i = 0; i < numLoci(chrom); i++, ++idx)
- *(ptr + i) = ToAllele(geno[idx % sz]);
+ *(ptr + i) = ToAllele(geno[idx % sz]);
}
}
}
Modified: trunk/src/individual.h
===================================================================
--- trunk/src/individual.h 2011-12-25 20:15:22 UTC (rev 4354)
+++ trunk/src/individual.h 2011-12-25 20:26:08 UTC (rev 4355)
@@ -343,7 +343,6 @@
m_infoPtr[idx] = value;
}
-
/// CPPONLY start of alleles
GenoIterator genoBegin() const
{
@@ -363,7 +362,6 @@
{
CHECKRANGEPLOIDY(p);
return m_genoPtr + p * totNumLoci();
-
}
@@ -394,7 +392,6 @@
}
-
/// CPPONLY start of info
InfoIterator infoBegin() const
{
@@ -903,13 +900,12 @@
typedef Allele value_type;
typedef long int difference_type;
typedef AlleleRef reference;
- typedef GenoIterator pointer;
+ //typedef GenoIterator pointer;
CombinedAlleleIterator()
{
}
-
CombinedAlleleIterator(size_t shift, GenoIterator ptr, GenoIterator ptrEnd, size_t size)
: m_useGappedIterator(true), m_valid(true), m_shift(shift),
m_ptr(ptr), m_ptrEnd(ptrEnd), m_size(size),
Property changes on: trunk/src/main.cpp
___________________________________________________________________
Deleted: svn:mergeinfo
- /branches/mutant/src/main.cpp:4262-4317
/branches/mutant_new/src/main.cpp:4318-4337,4352-4353
/branches/openMP/src/main.cpp:3999-4241
Modified: trunk/src/mating.cpp
===================================================================
--- trunk/src/mating.cpp 2011-12-25 20:15:22 UTC (rev 4354)
+++ trunk/src/mating.cpp 2011-12-25 20:26:08 UTC (rev 4355)
@@ -1599,8 +1599,6 @@
// scrtach will have the right structure.
if (!prepareScratchPop(pop, scratch))
return false;
- vectormating::const_iterator it = m_matingSchemes.begin();
- vectormating::const_iterator it_end = m_matingSchemes.end();
for (size_t sp = 0; sp < static_cast<size_t>(pop.numSubPop()); ++sp) {
vectormating m;
Added: trunk/src/mutant_vector.h
===================================================================
--- trunk/src/mutant_vector.h (rev 0)
+++ trunk/src/mutant_vector.h 2011-12-25 20:26:08 UTC (rev 4355)
@@ -0,0 +1,527 @@
+#include "boost/numeric/ublas/vector_sparse.hpp"
+using boost::numeric::ublas::compressed_vector;
+using boost::numeric::ublas::sparse_vector_element;
+
+#ifndef _MUTANT_VECTOR_H
+#define _MUTANT_VECTOR_H
+
+
+namespace simuPOP {
+
+/// CPPONLY
+template <class T>
+class mutant_vector
+{
+ public:
+
+ class iterator;
+ typedef const iterator const_iterator;
+
+ mutant_vector()
+ {
+ }
+
+ mutant_vector(size_t size)
+ {
+ m_container.resize(size);
+ }
+
+ mutant_vector(size_t size, const T& value)
+ {
+ if (value == 0)
+ m_container.resize(size);
+ else {
+ m_container.resize(size);
+ m_container.reserve(size);
+ for ( size_t i = 0; i < size; i++)
+ m_container.push_back(i, value);
+ }
+ }
+
+ void resize (size_t size)
+ {
+ m_container.resize(size);
+ }
+
+ void reserve (size_t size)
+ {
+ m_container.reserve(size);
+ }
+
+ size_t size() const {
+ return m_container.size();
+ }
+
+ typename mutant_vector<T>::iterator begin()
+ {
+ return typename mutant_vector<T>::iterator(&m_container, 0);
+ }
+
+ const typename mutant_vector<T>::iterator begin() const
+ {
+ return typename mutant_vector<T>::iterator(const_cast<compressed_vector<T> *>(&m_container), 0);
+ }
+
+ typename mutant_vector<T>::iterator end()
+ {
+ return typename mutant_vector<T>::iterator(&m_container, m_container.size());
+ }
+
+ const typename mutant_vector<T>::iterator end() const
+ {
+ return typename mutant_vector<T>::iterator(const_cast<compressed_vector<T> *>(&m_container), m_container.size());
+ }
+
+ typename compressed_vector<T>::reference operator [] (size_t i)
+ {
+ return m_container[i];
+ }
+
+ void push_back (typename compressed_vector<T>::size_type i, typename compressed_vector<T>::const_reference t)
+ {
+ m_container.push_back(i, t);
+ }
+
+ void swap(mutant_vector<T> & vec)
+ {
+ m_container.swap(vec.getContainer());
+
+ }
+
+
+ compressed_vector<T> & getContainer()
+ {
+ return m_container;
+ }
+
+ const compressed_vector<T> & getContainer() const
+ {
+ return m_container;
+ }
+
+ class iterator
+ {
+ protected:
+ compressed_vector<T> * m_container;
+ mutable size_t m_index;
+ mutable ssize_t m_com_index;
+
+ public:
+
+ iterator (compressed_vector<T> * c) : m_container(c), m_index(0), m_com_index(-1)
+ {
+ // m_com_index is the smallest index of mutants (or -1 is nothing is there)
+ }
+
+ iterator (const compressed_vector<T> * c) : m_container(c), m_index(0), m_com_index(-1)
+ {
+ }
+
+ iterator (compressed_vector<T> * c, size_t index) : m_container(c), m_index(index)
+ {
+ typename compressed_vector<size_t>::index_array_type::iterator lower =
+ std::lower_bound(m_container->index_data().begin(), m_container->index_data().begin() + m_container->filled(), index);
+ m_com_index = lower - m_container->index_data().begin();
+ // find the smallest m_com_index that is larger than index
+ }
+
+ iterator (const compressed_vector<T> * c, size_t index) : m_container(c), m_index(index)
+ {
+ typename compressed_vector<size_t>::index_array_type::iterator lower =
+ std::lower_bound(m_container->index_data().begin(), m_container->index_data().begin() + m_container->filled(), index);
+ m_com_index = lower - m_container->index_data().begin();
+ }
+
+ iterator () : m_container(NULL), m_index(0), m_com_index(-1)
+ {
+ }
+
+ iterator & operator = (const iterator & iter)
+ {
+ m_container = iter.m_container;
+ m_index = iter.m_index;
+ return *this;
+ }
+
+ bool operator == (const iterator & iter) const
+ {
+ if (m_index == iter.m_index)
+ return true;
+ return false;
+ }
+
+ bool operator != (const iterator & iter) const
+ {
+ if (m_index != iter.m_index)
+ return true;
+ return false;
+ }
+ bool operator >= (const iterator & iter) const
+ {
+ if (m_index >= iter.m_index)
+ return true;
+ return false;
+ }
+
+ bool operator <= (const iterator & iter) const {
+ if (m_index <= iter.m_index)
+ return true;
+ return false;
+ }
+
+ bool operator > (const iterator & iter) const
+ {
+ if (m_index > iter.m_index)
+ return true;
+ return false;
+ }
+
+ bool operator < (const iterator & iter) const
+ {
+ if (m_index < iter.m_index)
+ return true;
+ return false;
+ }
+
+ typename compressed_vector<T>::const_reference operator* () const
+ {
+ static const T zero = 0;
+ if (m_index < m_container->index_data()[m_com_index])
+ return zero;
+ else
+ return m_container->value_data()[m_com_index];
+
+ }
+
+ typename compressed_vector<T>::reference operator* ()
+ {
+ return (*m_container)[m_index];
+ }
+
+
+
+ typename compressed_vector<T>::reference operator [] (const size_t i)
+ {
+ return (*m_container)[m_index + i];
+ }
+
+ typename compressed_vector<T>::const_reference operator [] (const size_t i) const
+ {
+ return (*m_container)[m_index + i];
+ }
+
+ /// CPPONLY pre-incrment return by-reference
+ iterator & operator++ ()
+ {
+ ++m_index;
+ if (m_index >= m_container->index_data()[m_com_index])
+ ++m_com_index;
+ return *this;
+ }
+
+ const iterator & operator++ () const
+ {
+ ++m_index;
+ if (m_index >= m_container->index_data()[m_com_index])
+ ++m_com_index;
+ return *this;
+ }
+
+ /// CPPONLY post-incrment return by-value
+ iterator operator++ ( int )
+ {
+ iterator orig = *this;
+ ++(*this);
+ return orig;
+ }
+
+ const iterator operator++ ( int ) const
+ {
+ const iterator orig = *this;
+ ++(*this);
+ return orig;
+ }
+
+ iterator & operator+= (const iterator & iter)
+ {
+ m_index+=iter.m_index;
+ if (m_index > m_container->size())
+ m_index = m_container->size();
+ while (true) {
+ if (m_com_index < (int)m_container->filled())
+ if (m_index < m_container->index_data()[m_com_index]) {
+ break;
+ }
+ else if (m_index == m_container->index_data()[m_com_index]) {
+ ++m_com_index;
+ break;
+ } else {
+ ++m_com_index;
+ }
+ else
+ break;
+ }
+ return *this;
+ }
+
+ const iterator & operator+= (const iterator & iter) const
+ {
+ m_index+=iter.m_index;
+ if (m_index > m_container->size())
+ m_index = m_container->size();
+ while (true) {
+ if (m_com_index < (int)m_container->filled())
+ if (m_index < m_container->index_data()[m_com_index]) {
+ break;
+ }
+ else if (m_index == m_container->index_data()[m_com_index]) {
+ ++m_com_index;
+ break;
+ } else {
+ ++m_com_index;
+ }
+ else
+ break;
+ }
+
+ return *this;
+ }
+
+ iterator & operator+= (const size_t size)
+ {
+ m_index+=size;
+ if (m_index > m_container->size())
+ m_index = m_container->size();
+ while (true) {
+ if (m_com_index < (int)m_container->filled())
+ if (m_index < m_container->index_data()[m_com_index]) {
+ break;
+ }
+ else if (m_index == m_container->index_data()[m_com_index]) {
+ ++m_com_index;
+ break;
+ } else {
+ ++m_com_index;
+ }
+ else
+ break;
+ }
+
+ return *this;
+ }
+
+ const iterator & operator+= (const size_t size) const
+ {
+ m_index+=size;
+ if (m_index > m_container->size())
+ m_index = m_container->size();
+ while (true) {
+ if (m_com_index < (int)m_container->filled())
+ if (m_index < m_container->index_data()[m_com_index]) {
+ break;
+ }
+ else if (m_index == m_container->index_data()[m_com_index]) {
+ ++m_com_index;
+ break;
+ } else {
+ ++m_com_index;
+ }
+ else
+ break;
+ }
+
+ return *this;
+ }
+
+ /*size_t operator + (iterator & iter)
+ {
+ return (*this).m_index + iter.m_index;
+ }
+ */
+
+ iterator operator + (const iterator & iter) const
+ {
+ iterator result = *this;
+ result.m_index += iter.m_index;
+ return result;
+ }
+
+ iterator operator + (const size_t size) const
+ {
+ iterator result = *this;
+ result.m_index += size;
+ return result;
+ }
+
+ /*
+ size_t operator - (iterator & iter)
+ {
+ return (*this).m_index - iter.m_index;
+ }
+ */
+
+
+ iterator operator - (const iterator & iter) const
+ {
+ iterator result = *this;
+ result.m_index -= iter.m_index;
+ return result;
+ }
+
+ iterator operator - (const size_t size) const
+ {
+ iterator result = *this;
+ result.m_index -= size;
+ return result;
+ }
+
+ size_t findPositionIndexData () {
+ for (size_t i = 0; i < m_container->filled(); i++) {
+ if (i < m_container->filled() - 1 && m_index > m_container->index_data()[i]) {
+ continue;
+ } else if (i == m_container->filled() - 1 && m_index > m_container->index_data()[i]) {
+ return i + 1;
+ }
+ else {
+ return i;
+ }
+ }
+ return 0;
+ }
+
+
+ typename compressed_vector<T>::index_array_type::iterator getIndexIterator () {
+ //return m_container->index_data().begin() + findPositionIndexData();
+ return std::lower_bound(m_container->index_data().begin(), m_container->index_data().begin() + m_container->filled(), m_index);
+ }
+
+ typename compressed_vector<T>::value_array_type::iterator getValueIterator () {
+ return m_container->value_data().begin() + findPositionIndexData();
+ //return m_container->value_data().begin() + (getIndexIterator() - m_container->index_data().begin());
+ }
+
+ typename compressed_vector<T>::iterator getCompressedVectorIterator()
+ {
+ return m_container->find(m_index);
+ }
+
+ size_t getIndex ()
+ {
+ return m_index;
+ }
+
+ compressed_vector<T> * getContainer()
+ {
+ return m_container;
+ }
+
+ void deleted ()
+ {
+ m_container->erase_element(m_index);
+ }
+
+ void assign (typename compressed_vector<T>::const_reference value)
+ {
+ if (value == 0u && (*m_container)[m_index] == 0u)
+ return;
+ else
+ (*m_container)[m_index] = value;
+ }
+
+
+ };
+
+ void erase (typename mutant_vector<T>::iterator begin,typename mutant_vector<T>::iterator end)
+ {
+ typename mutant_vector<T>::iterator it = begin;
+ typename mutant_vector<T>::iterator it2 = end;
+ for(;it != end; ++it) {
+ it.deleted();
+ }
+ it = begin;
+ if (end != this->end())
+ for(it2 = end; it2 != this->end(); ++it2, ++it) {
+ *it = *it2;
+ }
+ // compressed vector doesn't decrease the size when it is erased.
+ // we have to resize it.
+ m_container.resize(m_container.size() - (end.getIndex() - begin.getIndex()));
+ }
+
+ void insert(typename mutant_vector<T>::iterator it, typename mutant_vector<T>::iterator begin, typename mutant_vector<T>::iterator end)
+ {
+ compressed_vector<size_t>::index_array_type::iterator it_src_begin = begin.getIndexIterator();
+ compressed_vector<size_t>::index_array_type::iterator iend = end.getIndexIterator();
+ size_t src_begin = *it_src_begin;
+ size_t src_index = *it_src_begin != begin.getIndex() ? *it_src_begin - begin.getIndex() : 0;
+ size_t dest_begin = it.getIndex();
+
+ m_container.resize(m_container.size() + (end.getIndex() - begin.getIndex()));
+
+ for (;it_src_begin != iend; ++it_src_begin) {
+ m_container.push_back(((*it_src_begin + src_index) - src_begin) + dest_begin, (*begin.getContainer())[*it_src_begin]);
+ }
+
+ }
+
+ template<class Archive>
+ void serialize(Archive & ar, const unsigned int /*file_version*/)
+ {
+ ar & m_container;
+ }
+
+
+ private:
+ compressed_vector<T> m_container;
+};
+
+}
+
+# ifdef MUTANTALLELE
+typedef unsigned int Allele;
+typedef compressed_vector<Allele>::reference AlleleRef;
+typedef simuPOP::mutant_vector<Allele> mutant_vectora;
+
+namespace simuPOP
+{
+
+inline void copy(mutant_vectora::iterator begin, mutant_vectora::iterator end, mutant_vectora::iterator it)
+{
+ mutant_vectora::iterator itt = begin;
+ for (;itt != end; ++itt, ++it) {
+ if (*it == 0u && *itt == 0u)
+ continue;
+ else
+ *it = *itt;
+ }
+}
+
+inline void fill (mutant_vectora::iterator begin, mutant_vectora::iterator end, Allele value)
+{
+ if (value == 0)
+ for (mutant_vectora::iterator it = begin; it != end; ++it)
+ it.deleted();
+ else
+ for (mutant_vectora::iterator it = begin; it != end; ++it)
+ *it = value;
+
+
+
+}
+
+inline mutant_vectora::iterator find (mutant_vectora::iterator begin, mutant_vectora::iterator end, Allele value)
+{
+ mutant_vectora::iterator it = begin;
+ for(; it != end; ++it)
+ {
+ if(*it == value)
+ return it;
+ }
+ return end;
+
+}
+
+}
+# endif
+
+#endif
Modified: trunk/src/mutator.cpp
===================================================================
--- trunk/src/mutator.cpp 2011-12-25 20:15:22 UTC (rev 4354)
+++ trunk/src/mutator.cpp 2011-12-25 20:26:08 UTC (rev 4355)
@@ -232,7 +232,6 @@
}
}
-
void MatrixMutator::mutate(AlleleRef allele, size_t) const
{
if (static_cast<size_t>(allele) >= m_sampler.size()) {
@@ -254,15 +253,15 @@
+ toStr(m_k - 1));
return;
}
-#ifdef BINARYALLELE
+# ifdef BINARYALLELE
allele = !allele;
-#else
+# else
Allele new_allele = static_cast<Allele>(getRNG().randInt(m_k - 1));
if (new_allele >= allele)
allele = new_allele + 1;
else
allele = new_allele;
-#endif
+# endif
}
@@ -297,6 +296,13 @@
void StepwiseMutator::mutate(AlleleRef allele, size_t) const
{
+#ifdef BINARYALLELE
+ if (getRNG().randUniform() < m_incProb)
+ allele = 1;
+ // decrease
+ else
+ allele = 0;
+#else
UINT step = 1;
if (m_mutStep.size() == 1)
@@ -310,29 +316,21 @@
"Invalid Python function for StepwiseMutator");
step = m_mutStep.func() (PyObj_As_Int, "(i)", static_cast<int>(allele));
}
-
// increase
if (getRNG().randUniform() < m_incProb) {
-#ifdef BINARYALLELE
- allele = 1;
-#else
if (static_cast<UINT>(allele + step) < m_maxAllele)
AlleleAdd(allele, step);
else
allele = ToAllele(m_maxAllele);
-#endif
}
// decrease
else {
-#ifdef BINARYALLELE
- allele = 0;
-#else
if (allele > step)
AlleleMinus(allele, step);
else
allele = 0;
-#endif
}
+#endif
}
Modified: trunk/src/population.cpp
===================================================================
--- trunk/src/population.cpp 2011-12-25 20:15:22 UTC (rev 4354)
+++ trunk/src/population.cpp 2011-12-25 20:26:08 UTC (rev 4355)
@@ -13,8 +13,7 @@
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
+ * * This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
@@ -144,10 +143,10 @@
// copy genotype one by one so Individual genoPtr will not
// point outside of subpopulation region.
- GenoIterator ptr = m_genotype.begin();
InfoIterator infoPtr = m_info.begin();
+ size_t infoStep = infoSize();
size_t step = genoSize();
- size_t infoStep = infoSize();
+ GenoIterator ptr = m_genotype.begin();
for (size_t i = 0; i < m_popSize; ++i, ptr += step, infoPtr += infoStep) {
m_inds[i].setGenoPtr(ptr);
m_inds[i].setInfoPtr(infoPtr);
@@ -165,10 +164,8 @@
vector<Individual> & linds = lp.m_inds;
const vector<Individual> & rinds = rp.m_inds;
-
GenoIterator lg = lp.m_genotype.begin();
ConstGenoIterator rg = rp.m_genotype.begin();
-
InfoIterator li = lp.m_info.begin();
ConstInfoIterator ri = rp.m_info.begin();
@@ -194,12 +191,27 @@
void Population::popData::swap(Population & pop)
{
+#ifdef MUTANTALLELE
+ size_t genoSize = 0;
+ if (m_inds.size() != 0)
+ genoSize = m_genotype.size() / m_inds.size();
+#endif
+
pop.m_subPopSize.swap(m_subPopSize);
pop.m_subPopNames.swap(m_subPopNames);
pop.m_genotype.swap(m_genotype);
pop.m_info.swap(m_info);
pop.m_inds.swap(m_inds);
std::swap(pop.m_indOrdered, m_indOrdered);
+#ifdef MUTANTALLELE
+ // compressed_vectora must be setGenoPtr after swap
+ GenoIterator ptr = pop.m_genotype.begin();
+ for (size_t i = 0; i < pop.m_inds.size(); ++i, ptr += genoSize)
+ pop.m_inds[i].setGenoPtr(ptr);
+ ptr = m_genotype.begin();
+ for (size_t i = 0; i < m_inds.size(); ++i, ptr += pop.genoSize())
+ m_inds[i].setGenoPtr(ptr);
+#endif
}
@@ -511,7 +523,6 @@
totNumLoci());
}
-
/// CPPONLY allele begin, for given subPop
IndAlleleIterator Population::alleleIterator(size_t locus, size_t subPop)
{
@@ -655,13 +666,17 @@
#ifdef BINARYALLELE
+ toStr((m_popSize * step / 8 + m_popSize * is * sizeof(double) + m_popSize * sizeof(Individual)) / 1024)
#else
+# ifdef MUTANTALLELE
+ + toStr((m_popSize * is * sizeof(double) + m_popSize * sizeof(Individual)) / 1024)
+# else
+ toStr((m_popSize * step * sizeof(Allele) + m_popSize * is * sizeof(double) + m_popSize * sizeof(Individual)) / 1024)
+# endif
#endif
+ "k bytes)");
}
// reset individual pointers
+ InfoIterator infoPtr = m_info.begin();
GenoIterator ptr = m_genotype.begin();
- InfoIterator infoPtr = m_info.begin();
for (size_t i = 0; i < m_popSize; ++i, ptr += step, infoPtr += is) {
m_inds[i].setGenoPtr(ptr);
m_inds[i].setInfoPtr(infoPtr);
@@ -702,8 +717,8 @@
if (oldInfoSize != newInfoSize)
m_info.resize(newInfoSize * popSize());
// reset structure
+ InfoIterator infoPtr = m_info.begin();
GenoIterator ptr = m_genotype.begin();
- InfoIterator infoPtr = m_info.begin();
for (size_t i = 0; i < m_popSize; ++i, ptr += newSize, infoPtr += newInfoSize) {
m_inds[i].setGenoStruIdx(stru);
m_inds[i].setGenoPtr(ptr);
@@ -739,6 +754,7 @@
}
+
size_t Population::subPopSize(vspID subPopID, int ancGen) const
{
vspID subPop = subPopID.resolve(*this);
@@ -792,6 +808,7 @@
}
+
void Population::setSubPopByIndInfo(const string & field)
{
DBG_FAILIF(hasActivatedVirtualSubPop(), ValueError,
@@ -820,15 +837,19 @@
DBG_DO(DBG_POPULATION, cerr << "New pop size" << newPopSize << endl);
// allocate new genotype and inds
+#ifdef MUTANTALLELE
+ mutant_vectora newGenotype(genoSize() * newPopSize);
+#else
vectora newGenotype(genoSize() * newPopSize);
+#endif
vectorf newInfo(newPopSize * infoSize());
vector<Individual> newInds(newPopSize);
// assign genotype location and set structure information for individuals
- GenoIterator ptr = newGenotype.begin();
InfoIterator infoPtr = newInfo.begin();
size_t step = genoSize();
size_t infoStep = infoSize();
+ GenoIterator ptr = newGenotype.begin();
for (size_t i = 0; i < newPopSize; ++i, ptr += step, ++it, infoPtr += infoStep) {
newInds[i].setGenoStruIdx(genoStruIdx());
newInds[i].setGenoPtr(ptr);
@@ -840,9 +861,15 @@
m_genotype.swap(newGenotype);
m_info.swap(newInfo);
m_inds.swap(newInds);
-
m_popSize = newPopSize;
setIndOrdered(true);
+#ifdef MUTANTALLELE
+ // compressed_vectora must be setGenoPtr after swap
+ ptr = m_genotype.begin();
+ for (size_t i = 0; i < m_popSize; ++i, ptr += genoSize())
+ m_inds[i].setGenoPtr(ptr);
+
+#endif
}
if (m_inds.empty()) {
@@ -968,7 +995,11 @@
++newSize;
if (oldInd != newInd) {
*newInd = *oldInd;
+#ifdef MUTANTALLELE
+ simuPOP::copy(oldPtr, oldPtr + step, newPtr);
+#else
copy(oldPtr, oldPtr + step, newPtr);
+#endif
copy(oldInfoPtr, oldInfoPtr + infoStep, newInfoPtr);
}
++newInd;
@@ -990,8 +1021,12 @@
new_spNames.push_back(m_subPopNames[sp]);
// do not remove.
if (oldPtr != newPtr) {
+#ifdef MUTANTALLELE
+ simuPOP::copy(oldPtr, oldPtr + step * spSize, newPtr);
+#else
+ copy(oldPtr, oldPtr + step * spSize, newPtr);
+#endif
copy(oldInd, oldInd + spSize, newInd);
- copy(oldPtr, oldPtr + step * spSize, newPtr);
copy(oldInfoPtr, oldInfoPtr + infoStep * spSize, newInfoPtr);
}
newInd += spSize;
@@ -1009,8 +1044,8 @@
m_popSize = std::accumulate(new_size.begin(), new_size.end(), size_t(0));
setSubPopStru(new_size, new_spNames);
//
+ InfoIterator infoPtr = m_info.begin();
GenoIterator ptr = m_genotype.begin();
- InfoIterator infoPtr = m_info.begin();
for (size_t i = 0; i < m_popSize; ++i, ptr += step, infoPtr += infoStep) {
m_inds[i].setGenoPtr(ptr);
m_inds[i].setInfoPtr(infoPtr);
@@ -1027,10 +1062,10 @@
size_t infoStep = infoSize();
RawIndIterator oldInd = m_inds.begin();
RawIndIterator newInd = m_inds.begin();
+ InfoIterator oldInfoPtr = m_info.begin();
+ InfoIterator newInfoPtr = m_info.begin();
GenoIterator oldPtr = m_genotype.begin();
- InfoIterator oldInfoPtr = m_info.begin();
GenoIterator newPtr = m_genotype.begin();
- InfoIterator newInfoPtr = m_info.begin();
//
for (size_t sp = 0; sp < numSubPop(); ++sp) {
size_t newSize = 0;
@@ -1041,7 +1076,11 @@
++newSize;
if (oldInd != newInd) {
*newInd = *oldInd;
+#ifdef MUTANTALLELE
+ simuPOP::copy(oldPtr, oldPtr + step, newPtr);
+#else
copy(oldPtr, oldPtr + step, newPtr);
+#endif
copy(oldInfoPtr, oldInfoPtr + infoStep, newInfoPtr);
}
++newInd;
@@ -1061,8 +1100,8 @@
m_popSize = std::accumulate(new_size.begin(), new_size.end(), size_t(0));
setSubPopStru(new_size, m_subPopNames);
//
+ InfoIterator infoPtr = m_info.begin();
GenoIterator ptr = m_genotype.begin();
- InfoIterator infoPtr = m_info.begin();
for (size_t i = 0; i < m_popSize; ++i, ptr += step, infoPtr += infoStep) {
m_inds[i].setGenoPtr(ptr);
m_inds[i].setInfoPtr(infoPtr);
@@ -1223,10 +1262,14 @@
size_t step = genoSize();
size_t infoStep = infoSize();
vector<Individual> new_inds;
+ vectorf new_info;
+#ifdef MUTANTALLELE
+ mutant_vectora new_genotype;
+#else
vectora new_genotype;
- vectorf new_info;
+ new_genotype.reserve(step * popSize());
+#endif
new_inds.reserve(popSize());
- new_genotype.reserve(step * popSize());
new_info.reserve(infoStep * popSize());
for (size_t sp = 0; sp < numSubPop(); ++sp) {
@@ -1236,6 +1279,7 @@
// do not remove.
new_inds.insert(new_inds.end(), rawIndBegin(src), rawIndEnd(src));
new_genotype.insert(new_genotype.end(), genoBegin(src, true), genoEnd(src, true));
+
if (infoStep > 0)
new_info.insert(new_info.end(),
m_info.begin() + subPopBegin(src) * infoStep,
@@ -1251,8 +1295,8 @@
m_info.swap(new_info);
setSubPopStru(new_size, new_names);
//
+ InfoIterator infoPtr = m_info.begin();
GenoIterator ptr = m_genotype.begin();
- InfoIterator infoPtr = m_info.begin();
for (size_t i = 0; i < m_popSize; ++i, ptr += step, infoPtr += infoStep) {
m_inds[i].setGenoPtr(ptr);
m_inds[i].setInfoPtr(infoPtr);
@@ -1278,11 +1322,14 @@
//
DBG_FAILIF(m_subPopSize != pop.m_subPopSize, ValueError,
"Can not add chromosomes from a population with different subpopulation sizes");
-
+#ifdef MUTANTALLELE
+ mutant_vectora newGenotype(genoSize() * m_popSize);
+#else
vectora newGenotype(genoSize() * m_popSize);
-
+#endif
// append pop2 chromosomes to the first one
GenoIterator ptr = newGenotype.begin();
+
size_t pEnd = ploidy();
for (size_t i = 0; i < m_popSize; ++i) {
// set new geno structure
@@ -1294,10 +1341,17 @@
for (size_t j = 0; j < numLoci1; ++j)
*(ptr++) = *(ptr1++);
for (size_t j = 0; j < numLoci2; ++j)
- *(ptr++) = *(ptr2++);
+ *(ptr++) = *(ptr2++);
}
+
}
m_genotype.swap(newGenotype);
+#ifdef MUTANTALLELE
+ // compressed_vectora must be setGenoPtr after swap
+ ptr = m_genotype.begin();
+ for (size_t i = 0; i < m_popSize; ++i, ptr += genoSize())
+ m_inds[i].setGenoPtr(ptr);
+#endif
}
if (!indOrdered())
// sort information only
@@ -1305,6 +1359,7 @@
}
+
void Population::addIndFrom(const Population & pop)
{
DBG_FAILIF(genoStruIdx() != pop.genoStruIdx(), ValueError,
@@ -1327,10 +1382,10 @@
m_genotype.insert(m_genotype.end(), pop.m_genotype.begin(), pop.m_genotype.end());
m_info.insert(m_info.end(), pop.m_info.begin(), pop.m_info.end());
// iterators ready
- GenoIterator ptr = m_genotype.begin();
InfoIterator infoPtr = m_info.begin();
size_t step = genoSize();
size_t infoStep = infoSize();
+ GenoIterator ptr = m_genotype.begin();
// set pointers
for (size_t i = 0; i < m_popSize; ++i, ptr += step, infoPtr += infoStep) {
m_inds[i].setGenoStruIdx(genoStruIdx());
@@ -1379,8 +1434,11 @@
DBG_FAILIF(m_subPopSize != pop.m_subPopSize, ValueError,
"Can not add chromosomes from a population with different subpopulation sizes");
//
+#ifdef MUTANTALLELE
+ mutant_vectora newGenotype(genoSize() * m_popSize);
+#else
vectora newGenotype(genoSize() * m_popSize);
-
+#endif
// merge chromosome by chromosome
GenoIterator ptr = newGenotype.begin();
size_t pEnd = ploidy();
@@ -1402,6 +1460,12 @@
}
}
m_genotype.swap(newGenotype);
+#ifdef MUTANTALLELE
+ // compressed_vectora must be setGenoPtr after swap
+ ptr = m_genotype.begin();
+ for (size_t i = 0; i < m_popSize; ++i, ptr += genoSize())
+ m_inds[i].setGenoPtr(ptr);
+#endif
}
// sort information only
@@ -1428,17 +1492,22 @@
for (int depth = ancestralGens(); depth >= 0; --depth) {
useAncestralGen(depth);
- //
size_t newPopGenoSize = genoSize() * m_popSize;
+#ifdef MUTANTALLELE
+ mutant_vectora newGenotype(newPopGenoSize, 0);
+#else
vectora newGenotype(newPopGenoSize, 0);
+#endif
// copy data over
GenoIterator newPtr = newGenotype.begin();
+
size_t pEnd = ploidy();
size_t gap = totNumLoci() - oldNumLoci;
for (size_t i = 0; i < m_popSize; ++i) {
// set new geno structure
m_inds[i].setGenoStruIdx(genoStruIdx());
+
GenoIterator oldPtr = m_inds[i].genoPtr();
// new genotype
m_inds[i].setGenoPtr(newPtr);
@@ -1448,8 +1517,16 @@
*(newPtr++) = *(oldPtr++);
newPtr += gap;
}
+
}
m_genotype.swap(newGenotype);
+#ifdef MUTANTALLELE
+ // compressed_vectora must be setGenoPtr after swap
+ GenoIterator ptr = m_genotype.begin();
+ for (size_t i = 0; i < m_popSize; ++i, ptr += genoSize())
+ m_inds[i].setGenoPtr(ptr);
+#endif
+
}
// if indOrdered is false:
// individual genotype is now sorted. If we do not do
@@ -1489,8 +1566,11 @@
useAncestralGen(depth);
//
size_t newPopGenoSize = genoSize() * m_popSize;
+#ifdef MUTANTALLELE
+ mutant_vectora newGenotype(newPopGenoSize, 0);
+#else
vectora newGenotype(newPopGenoSize, 0);
-
+#endif
// copy data over
GenoIterator newPtr = newGenotype.begin();
size_t pEnd = ploidy();
@@ -1509,6 +1589,12 @@
}
}
m_genotype.swap(newGenotype);
+#ifdef MUTANTALLELE
+ // compressed_vectora must be setGenoPtr after swap
+ GenoIterator ptr = m_genotype.begin();
+ for (size_t i = 0; i < m_popSize; ++i, ptr += genoSize())
+ m_inds[i].setGenoPtr(ptr);
+#endif
}
// if indOrdered is false:
// individual genotype is now sorted. If we do not do
@@ -1530,17 +1616,21 @@
// prepare new Population
vector<Individual> newInds(newPopSize);
- vectora newGenotype(genoSize() * newPopSize);
vectorf newInfo(newPopSize * infoSize());
// iterators ready
- GenoIterator ptr = newGenotype.begin();
InfoIterator infoPtr = newInfo.begin();
size_t step = genoSize();
size_t infoStep = infoSize();
- // set pointers
+#ifdef MUTANTALLELE
+ mutant_vectora newGenotype(genoSize() * newPopSize);
+#else
+ vectora newGenotype(genoSize() * newPopSize);
+#endif
+ GenoIterator ptr = newGenotype.begin();
for (size_t i = 0; i < newPopSize; ++i, ptr += step, infoPtr += infoStep) {
newInds[i].setGenoStruIdx(genoStruIdx());
newInds[i].setGenoPtr(ptr);
+ // set pointers
newInds[i].setInfoPtr(infoPtr);
}
// copy stuff over
@@ -1563,6 +1653,13 @@
m_popSize = newPopSize;
setIndOrdered(true);
m_subPopSize = newSubPopSizes;
+
+#ifdef MUTANTALLELE
+ // compressed_vectora must be setGenoPtr after swap
+ ptr = m_genotype.begin();
+ for (size_t i = 0; i < m_popSize; ++i, ptr += genoSize())
+ m_inds[i].setGenoPtr(ptr);
+#endif
// rebuild index
size_t idx = 1;
for (m_subPopIndex[0] = 0; idx <= numSubPop(); ++idx)
@@ -1594,7 +1691,11 @@
size_t infoStep = infoSize();
vector<Individual> new_inds;
+#ifdef MUTANTALLELE
+ mutant_vectora new_genotype;
+#else
vectora new_genotype;
+#endif
vectorf new_info;
if (rearrange) {
@@ -1622,7 +1723,11 @@
ConstIndIterator oldInd = indIterator(it->subPop());
for (; oldInd.valid(); ++oldInd) {
*newInd = *oldInd;
+#ifdef MUTANTALLELE
+ simuPOP::copy(oldInd->genoBegin(), oldInd->genoEnd(), newPtr);
+#else
copy(oldInd->genoBegin(), oldInd->genoEnd(), newPtr);
+#endif
copy(oldInd->infoBegin(), oldInd->infoEnd(), newInfoPtr);
++newInd;
newPtr += step;
@@ -1658,7 +1763,11 @@
new_spNames.push_back(m_subPopNames[sp]);
//
copy(oldInd, oldInd + spSize, newInd);
+#ifdef MUTANTALLELE
+ simuPOP::copy(oldPtr, oldPtr + step * spSize, newPtr);
+#else
copy(oldPtr, oldPtr + step * spSize, newPtr);
+#endif
copy(oldInfoPtr, oldInfoPtr + infoStep * spSize, newInfoPtr);
oldInd += spSize;
@@ -1668,8 +1777,8 @@
newPtr += step * spSize;
newInfoPtr += infoStep * spSize;
} else if (subPops.overlap(sp)) {
- // partial copy
- //
+ // partial copy
+ //
// mark for copy
markIndividuals(sp, false);
subPopList::const_iterator it = subPops.begin();
@@ -1684,7 +1793,11 @@
if (oldInd->marked()) {
++newSize;
*newInd = *oldInd;
+#ifdef MUTANTALLELE
+ simuPOP::copy(oldPtr, oldPtr + step, newPtr);
+#else
copy(oldPtr, oldPtr + step, newPtr);
+#endif
copy(oldInfoPtr, oldInfoPtr + infoStep, newInfoPtr);
++newInd;
newPtr += step;
@@ -1717,8 +1830,8 @@
pop.m_popSize = sz;
pop.setSubPopStru(new_size, new_spNames);
//
+ InfoIterator infoPtr = pop.m_info.begin();
GenoIterator ptr = pop.m_genotype.begin();
- InfoIterator infoPtr = pop.m_info.begin();
for (size_t i = 0; i < pop.m_popSize; ++i, ptr += step, infoPtr += infoStep) {
pop.m_inds[i].setGenoPtr(ptr);
pop.m_inds[i].setInfoPtr(infoPtr);
@@ -1753,7 +1866,11 @@
++sz;
vector<Individual> new_inds(sz);
+#ifdef MUTANTALLELE
+ mutant_vectora new_genotype(sz * step);
+#else
vectora new_genotype(sz * step);
+#endif
vectorf new_info(sz * infoStep);
RawIndIterator newInd = new_inds.begin();
@@ -1768,7 +1885,11 @@
if (oldInd->marked()) {
++newSize;
*newInd = *oldInd;
+#ifdef MUTANTALLELE
+ simuPOP::copy(oldPtr, oldPtr + step, newPtr);
+#else
copy(oldPtr, oldPtr + step, newPtr);
+#endif
copy(oldInfoPtr, oldInfoPtr + infoStep, newInfoPtr);
++newInd;
newPtr += step;
@@ -1787,8 +1908,8 @@
pop.m_popSize = std::accumulate(new_size.begin(), new_size.end(), size_t(0));
pop.setSubPopStru(new_size, m_subPopNames);
//
+ InfoIterator infoPtr = pop.m_info.begin();
GenoIterator ptr = pop.m_genotype.begin();
- InfoIterator infoPtr = pop.m_info.begin();
for (size_t i = 0; i < pop.m_popSize; ++i, ptr += step, infoPtr += infoStep) {
pop.m_inds[i].setGenoPtr(ptr);
pop.m_inds[i].setInfoPtr(infoPtr);
@@ -2031,11 +2152,19 @@
}
vector<Individual> new_inds;
+#ifdef MUTANTALLELE
+ size_t newIdx = 0;
+ mutant_vectora new_genotype;
+ if (removeLoci)
+ new_genotype.resize(size * step);
+ new_genotype.reserve(m_genotype.getContainer().index_data().end() - m_genotype.getContainer().index_data().begin());
+#else
vectora new_genotype;
+ new_genotype.reserve(size * step);
+#endif
vectorf new_info;
new_inds.reserve(size);
- new_genotype.reserve(size * step);
new_info.reserve(size * infoStep);
// copy genotype and info...
if (!removeInd) {
@@ -2050,7 +2179,12 @@
GenoIterator ptr = it->genoBegin();
for (size_t p = 0; p < pEnd; p += pStep) {
for (lociPtr = new_loci.begin(); lociPtr != lociEnd; ++lociPtr)
+#ifdef MUTANTALLELE
+ new_genotype.push_back(newIdx++, *(ptr + *lociPtr + p));
+#else
new_genotype.push_back(*(ptr + *lociPtr + p));
+#endif
+
}
}
}
@@ -2083,7 +2217,11 @@
GenoIterator ptr = indGenoBegin(*it);
for (size_t p = 0; p < pEnd; p += pStep) {
for (lociPtr = new_loci.begin(); lociPtr != lociEnd; ++lociPtr)
+#ifdef MUTANTALLELE
+ new_genotype.push_back(newIdx++, *(ptr + *lociPtr + p));
+#else
new_genotype.push_back(*(ptr + *lociPtr + p));
+#endif
}
}
if (!removeInfo)
@@ -2103,8 +2241,12 @@
else
pop.setSubPopStru(spSizes, m_subPopNames);
// set pointer
+ vectorf::iterator infoPtr = new_info.begin();
+#ifdef MUTANTALLELE
+ mutant_vectora::iterator ptr = new_genotype.begin();
+#else
vectora::iterator ptr = new_genotype.begin();
- vectorf::iterator infoPtr = new_info.begin();
+#endif
for (size_t i = 0; i < size; ++i, ptr += step, infoPtr += infoStep) {
new_inds[i].setGenoStruIdx(pop.genoStruIdx());
new_inds[i].setGenoPtr(ptr);
@@ -2122,6 +2264,13 @@
pop.m_inds.swap(new_inds);
pop.m_genotype.swap(new_genotype);
pop.m_info.swap(new_info);
+#ifdef MUTANTALLELE
+ // compressed_vectora must be setGenoPtr after swap
+ GenoIterator ptr = pop.m_genotype.begin();
+ for (size_t i = 0; i < pop.m_inds.size(); ++i, ptr += step)
+ pop.m_inds[i].setGenoPtr(ptr);
+
+#endif
} else {
pop.m_ancestralPops.push_front(popData());
popData & pd = pop.m_ancestralPops.front();
@@ -2129,6 +2278,12 @@
pd.m_genotype.swap(new_genotype);
pd.m_info.swap(new_info);
pd.m_inds.swap(new_inds);
+#ifdef MUTANTALLELE
+ // compressed_vectora must be setGenoPtr after swap
+ GenoIterator ptr = pd.m_genotype.begin();
+ for (size_t i = 0; i < pd.m_inds.size(); ++i, ptr += step)
+ pd.m_inds[i].setGenoPtr(ptr);
+#endif
}
}
pop.m_curAncestralGen = 0;
@@ -2178,7 +2333,11 @@
for (int depth = ancestralGens(); depth >= 0; --depth) {
useAncestralGen(depth);
//
+#ifdef MUTANTALLELE
+ mutant_vectora newGenotype(genoSize() * m_popSize);
+#else
vectora newGenotype(genoSize() * m_popSize);
+#endif
// copy data over
GenoIterator newPtr = newGenotype.begin();
size_t pEnd = ploidy();
@@ -2192,11 +2351,17 @@
vectoru::iterator loc = kept.begin();
for (; loc != kept.end(); ++loc)
// this line needs ordered kept array
- *(newPtr++) = oldPtr[*loc];
+ *(newPtr++) = oldPtr[*loc]; //assginGenotype
oldPtr += oldTotNumLoci;
}
}
m_genotype.swap(newGenotype);
+#ifdef MUTANTALLELE
+ // compressed_vectora must be setGenoPtr after swap
+ GenoIterator ptr = m_genotype.begin();
+ for (size_t i = 0; i < m_popSize; ++i, ptr += genoSize())
+ m_inds[i].setGenoPtr(ptr);
+#endif
}
setIndOrdered(true);
}
@@ -2252,6 +2417,7 @@
GenoIterator ptr = m_genotype.begin();
GenoIterator ptrEnd = m_genotype.end();
+
if (!newAlleles.empty()) {
const vectoru & map = newAlleles.elems();
if (loci_.allAvail()) {
@@ -2396,6 +2562,17 @@
m_info.swap(rhs.m_info);
m_inds.swap(rhs.m_inds);
std::swap(m_indOrdered, rhs.m_indOrdered);
+
+#ifdef MUTANTALLELE
+ // compressed_vectora must be setGenoPtr after swap
+ GenoIterator ptr = m_genotype.begin();
+ for (size_t i = 0; i < m_inds.size(); ++i, ptr += genoSize())
+ m_inds[i].setGenoPtr(ptr);
+ ptr = rhs.m_genotype.begin();
+ for (size_t i = 0; i < rhs.m_inds.size(); ++i, ptr += genoSize())
+ rhs.m_inds[i].setGenoPtr(ptr);
+#endif
+
// current population should be working well
// (with all datamember copied form rhs
// rhs may not be working well since m_genotype etc
@@ -2655,6 +2832,14 @@
pd1.m_info.swap(pd.m_info);
pd1.m_inds.swap(pd.m_inds);
std::swap(pd1.m_indOrdered, pd.m_indOrdered);
+#ifdef MUTANTALLELE
+ GenoIterator ptr = pd1.m_genotype.begin();
+ for (size_t i = 0; i < pd1.m_inds.size(); ++i, ptr += pd1.m_genotype.size() / pd1.m_inds.size())
+ pd1.m_inds[i].setGenoPtr(ptr);
+ ptr = pd.m_genotype.begin();
+ for (size_t i = 0; i < pd.m_inds.size(); ++i, ptr += pd.m_genotype.size() / pd.m_inds.size())
+ pd.m_inds[i].setGenoPtr(ptr);
+#endif
}
}
}
@@ -2700,6 +2885,7 @@
}
+
//template<class Archive>
void Population::save(boost::archive::text_oarchive & ar, const unsigned int /* version */) const
{
@@ -2732,6 +2918,15 @@
data = 0;
}
}
+#elif defined MUTANTALLELE
+ size_t size = m_genotype.size();
+ ar & size;
+ ConstGenoIterator ptr = m_genotype.begin();
+ unsigned int data = 0;
+ for (size_t i = 0; i < size; ++i, ++ptr) {
+ data = *ptr;
+ ar & data;
+ }
#else
ar & m_genotype;
#endif
@@ -2763,6 +2958,15 @@
data = 0;
}
}
+#elif defined MUTANTALLELE
+ size_t size = m_genotype.size();
+ ar & size;
+ ConstGenoIterator ptr = m_genotype.begin();
+ unsigned int data = 0;
+ for (size_t i = 0; i < size; ++i, ++ptr) {
+ data = *ptr;
+ ar & data;
+ }
#else
ar & m_genotype;
#endif
@@ -2809,9 +3013,20 @@
ar & data;
*ptr++ = (data & (1UL << (i % 32))) != 0;
}
- }
+ // binary from mutant
+ } else if (ma == 256) {
+ DBG_DO(DBG_POPULATION, cerr << "Load bin from mutant. " << endl);
+ size_t size;
+ ar & size;
+ m_genotype.resize(size);
+ GenoIterator ptr = m_genotype.begin();
+ unsigned int data = 0;
+ for (size_t i = 0; i < size; ++i, ++ptr) {
+ ar & data;
+ *ptr = ToAllele(data);
+ }
// binary from others (long types)
- else {
+ } else {
DBG_DO(DBG_POPULATION, cerr << "Load bin from long. " << endl);
vectoru tmpgeno;
ar & tmpgeno;
@@ -2820,7 +3035,7 @@
m_genotype[i] = ToAllele(tmpgeno[i]);
}
#else
- // long from binary
+ // long or mutant from binary
if (ma == 1) {
// for version 2 and higher, archive in 32bit blocks.
size_t size;
@@ -2835,9 +3050,49 @@
}
} // if ma == 1
else { // for non-binary types, ...
- DBG_DO(DBG_POPULATION, cerr << "Load long from long. " << endl);
+# ifdef MUTANTALLELE
+ // mutant from mutant
+ if (ma == 256) {
+ DBG_DO(DBG_POPULATION, cerr << "Load mutant from mutant. " << endl);
+ size_t size;
+ ar & size;
+ m_genotype.resize(size);
+ GenoIterator ptr = m_genotype.begin();
+ unsigned int data = 0;
+ for (size_t i = 0; i < size; ++i, ++ptr) {
+ ar & data;
+ *ptr = data;
+ }
+ }
+ // mutant from long
+ else {
+ DBG_DO(DBG_POPULATION, cerr << "Load mutant from long. " << endl);
+ vectora data;
+ ar & data;
+ m_genotype.resize(data.size());
+ for (size_t i = 0; i < data.size(); ++i) {
+ m_genotype[i] = data[i];
+ }
+ }
+# else
+ // long from mutant
+ if (ma == 256) {
+ DBG_DO(DBG_POPULATION, cerr << "Load long from mutant. " << endl);
+ size_t size;
+ ar & size;
+ m_genotype.resize(size);
+ GenoIterator ptr = m_genotype.begin();
+ unsigned int data = 0;
+ for (size_t i = 0; i < size; ++i, ++ptr) {
+ ar & data;
+ *ptr = data;
+ }
// long from long
- ar & m_genotype;
+ } else {
+ DBG_DO(DBG_POPULATION, cerr << "Load long from long. " << endl);
+ ar & m_genotype;
+ }
+# endif
}
#endif
@@ -2867,10 +3122,11 @@
m_subPopIndex[i] = m_subPopIndex[i - 1] + m_subPopSize[i - 1];
// assign genotype location and set structure information for individuals
- GenoIterator ptr = m_genotype.begin();
- size_t step = genoSize();
+
InfoIterator infoPtr = m_info.begin();
size_t infoStep = infoSize();
+ size_t step = genoSize();
+ GenoIterator ptr = m_genotype.begin();
for (size_t i = 0; i < m_popSize; ++i, ptr += step, infoPtr += infoStep) {
m_inds[i].setGenoStruIdx(genoStruIdx());
m_inds[i].setGenoPtr(ptr);
@@ -2902,6 +3158,19 @@
ar & data;
*ptr++ = (data & (1UL << i % 32)) != 0;
}
+ // binary from mutant
+ } else if (ma == 256) {
+ DBG_DO(DBG_POPULATION, cerr << "Load bin from mutant. " << endl);
+ size_t size;
+ ar & size;
+ pd.m_genotype.resize(size);
+ GenoIterator ptr = pd.m_genotype.begin();
+ unsigned int data = 0;
+ for (size_t i = 0; i < size; ++i, ++ptr) {
+ ar & data;
+ *ptr = ToAllele(data);
+ }
+ // binary from others (long types)
} else {
DBG_DO(DBG_POPULATION, cerr << "Load bin from long. " << endl);
// binary from long types
@@ -2925,9 +3194,49 @@
*ptr++ = (data & (1UL << i % 32)) != 0;
}
} else {
- DBG_DO(DBG_POPULATION, cerr << "Load long from long. " << endl);
- // long type from long type.
- ar & pd.m_genotype;
+# ifdef MUTANTALLELE
+ // mutant from mutant
+ if (ma == 256) {
+ DBG_DO(DBG_POPULATION, cerr << "Load mutant from mutant. " << endl);
+ size_t size;
+ ar & size;
+ pd.m_genotype.resize(size);
+ GenoIterator ptr = pd.m_genotype.begin();
+ unsigned int data = 0;
+ for (size_t i = 0; i < size; ++i, ++ptr) {
+ ar & data;
+ *ptr = data;
+ }
+ }
+ // mutant from long
+ else {
+ DBG_DO(DBG_POPULATION, cerr << "Load mutant from long. " << endl);
+ vectora data;
+ ar & data;
+ pd.m_genotype.resize(data.size());
+ for (size_t i = 0; i < data.size(); ++i) {
+ pd.m_genotype[i] = data[i];
+ }
+ }
+# else
+ // long from mutant
+ if (ma == 256) {
+ DBG_DO(DBG_POPULATION, cerr << "Load long from mutant. " << endl);
+ size_t size;
+ ar & size;
+ pd.m_genotype.resize(size);
+ GenoIterator ptr = pd.m_genotype.begin();
+ unsigned int data = 0;
+ for (size_t i = 0; i < size; ++i, ++ptr) {
+ ar & data;
+ *ptr = data;
+ }
+ // long from long
+ } else {
+ DBG_DO(DBG_POPULATION, cerr << "Load long from long. " << endl);
+ ar & pd.m_genotype;
+ }
+# endif
}
#endif
ar & pd.m_info;
@@ -2939,9 +3248,8 @@
// set pointers
vector<Individual> & inds = p.m_inds;
size_t ps = inds.size();
+ infoPtr = p.m_info.begin();
ptr = p.m_genotype.begin();
- infoPtr = p.m_info.begin();
-
for (size_t i = 0; i < ps; ++i, ptr += step, infoPtr += infoStep) {
inds[i].setGenoPtr(ptr);
inds[i].setInfoPtr(infoPtr);
@@ -3001,7 +3309,6 @@
Py_INCREF(m_vars.dict());
return m_vars.dict();
}
-
DBG_ASSERT(static_cast<size_t>(vsp.subPop()) < numSubPop(),
IndexError, "Subpop index out of range of 0 ~ " + toStr(numSubPop() - 1));
@@ -3085,11 +3392,16 @@
} else {
DBG_DO(DBG_POPULATION, cerr << "Adjust geno and info position " << endl);
+ size_t is = infoSize();
size_t sz = genoSize();
- size_t is = infoSize();
+#ifdef MUTANTALLELE
+ mutant_vectora tmpGenotype(m_popSize * genoSize());
+ mutant_vectora::iterator it = tmpGenotype.begin();
+#else
vectora tmpGenotype(m_popSize * genoSize());
+ vectora::iterator it = tmpGenotype.begin();
+#endif
vectorf tmpInfo(m_popSize * infoSize());
- vectora::iterator it = tmpGenotype.begin();
vectorf::iterator infoPtr = tmpInfo.begin();
IndIterator ind = const_cast<Population *>(this)->indIterator();
@@ -3097,11 +3409,15 @@
#ifdef BINARYALLELE
copyGenotype(ind->genoBegin(), it, sz);
#else
+# ifdef MUTANTALLELE
+ simuPOP::copy(ind->genoBegin(), ind->genoEnd(), it);
+# else
copy(ind->genoBegin(), ind->genoEnd(), it);
+# endif
#endif
+
ind->setGenoPtr(it);
it += sz;
-
copy(ind->infoBegin(), ind->infoEnd(), infoPtr);
ind->setInfoPtr(infoPtr);
infoPtr += is;
@@ -3123,6 +3439,7 @@
}
+
}
Modified: trunk/src/population.h
===================================================================
--- trunk/src/population.h 2011-12-25 20:15:22 UTC (rev 4354)
+++ trunk/src/population.h 2011-12-25 20:26:08 UTC (rev 4355)
@@ -295,9 +295,17 @@
std::swap(m_vspSplitter, rhs.m_vspSplitter);
std::swap(rhs.m_gen, m_gen);
std::swap(rhs.m_rep, m_rep);
+#ifdef MUTANTALLELE
+ // compressed_vectora must be setGenoPtr after swap
+ GenoIterator ptr = m_genotype.begin();
+ for (size_t i = 0; i < m_inds.size(); ++i, ptr += genoSize())
+ m_inds[i].setGenoPtr(ptr);
+ ptr = rhs.m_genotype.begin();
+ for (size_t i = 0; i < rhs.m_inds.size(); ++i, ptr += rhs.genoSize())
+ rhs.m_inds[i].setGenoPtr(ptr);
+#endif
}
-
/// destroy a population
~Population();
@@ -824,6 +832,7 @@
IndAlleleIterator alleleIterator(size_t locus, size_t subPop);
+
/// CPPONLY allele iterator, go through all allels one by one, without subPop info
/**
if order, in order
@@ -1461,9 +1470,8 @@
void execute(const string & stmts = string())
{
Expression("", stmts, m_vars.dict()).evaluate();
- }
+ }
-
private:
friend class boost::serialization::access;
@@ -1490,7 +1498,11 @@
BaseVspSplitter * m_vspSplitter;
/// pool of genotypic information
+#ifdef MUTANTALLELE
+ mutant_vectora m_genotype;
+#else
vectora m_genotype;
+#endif
/// information
/// only in head node
@@ -1511,7 +1523,11 @@
{
vectoru m_subPopSize;
vectorstr m_subPopNames;
+#ifdef MUTANTALLELE
+ mutant_vectora m_genotype;
+#else
vectora m_genotype;
+#endif
vectorf m_info;
vector<Individual> m_inds;
bool m_indOrdered;
Property changes on: trunk/src/qtrait.h
___________________________________________________________________
Deleted: svn:mergeinfo
- /branches/mutant/src/qtrait.h:4262-4317
/branches/mutant_new/src/qtrait.h:4318-4337,4352-4353
/branches/openMP/src/qtrait.h:3999-4241
Modified: trunk/src/sandbox.cpp
===================================================================
--- trunk/src/sandbox.cpp 2011-12-25 20:15:22 UTC (rev 4354)
+++ trunk/src/sandbox.cpp 2011-12-25 20:26:08 UTC (rev 4355)
@@ -28,6 +28,7 @@
namespace simuPOP {
+#ifdef MUTANTALLELE
bool RevertFixedSites::apply(Population & pop) const
{
@@ -36,6 +37,702 @@
RawIndIterator it = pop.rawIndBegin();
RawIndIterator it_end = pop.rawIndEnd();
+ std::set<Allele> commonAlleles(it->genoBegin(0).getIndexIterator(), it->genoEnd(0).getIndexIterator());
+
+ if (commonAlleles.size() == 0)
+ return true;
+
+ for (; it != it_end; ++it) {
+ // common = commonAlleles & geno0
+ std::set<Allele> common;
+ std::set<Allele> alleles1(it->genoBegin(0).getIndexIterator(), it->genoEnd(0).getIndexIterator());
+ set_intersection(commonAlleles.begin(),
+ commonAlleles.end(), alleles1.begin(), alleles1.end(),
+ std::inserter(common, common.begin()));
+ // commonAlleles = common & geno1
+ commonAlleles.clear();
+ // ALl mutants in the second ploidy
+ std::set<Allele> alleles2(it->genoBegin(1).getIndexIterator(), it->genoEnd(1).getIndexIterator());
+ set_intersection(common.begin(),
+ common.end(), alleles2.begin(), alleles2.end(),
+ std::inserter(commonAlleles, commonAlleles.begin()));
+ if (commonAlleles.size() == 0)
+ return true;
+ }
+ if (!noOutput()) {
+ ostream & out = getOstream(pop.dict());
+ out << pop.gen();
+ std::set<Allele>::iterator beg = commonAlleles.begin();
+ std::set<Allele>::iterator end = commonAlleles.end();
+ for (; beg != end ; ++beg)
+ out << '\t' << *beg;
+ out << endl;
+ }
+ it = pop.rawIndBegin();
+ vectora new_alleles(pop.totNumLoci());
+ for (; it != it_end; ++it) {
+ for (size_t p = 0; p < 2; ++p) {
+ // FIXME: get old alleles
+ std::set<Allele> old_alleles(it->genoBegin(p).getIndexIterator(), it->genoEnd(p).getIndexIterator());
+ //old_alleles.erase(0);
+ // FIXME: fill with all zero, do not have to do that for mutant type
+ //std::fill(new_alleles.begin(), new_alleles.end(), Allele(0));
+ set_difference(old_alleles.begin(), old_alleles.end(),
+ commonAlleles.begin(), commonAlleles.end(), new_alleles.begin());
+ GenoIterator ptr = it->genoBegin(p);
+ // FIXME: basically, you need to remove those mutants.
+ for (vectora::iterator new_it = new_alleles.begin(); new_it != new_alleles.end(); ++new_it, ++ptr) {
+ if (*new_it == 0u && *ptr == 0u)
+ continue;
+ else if (*new_it == 0u && *ptr != 0u)
+ ptr.deleted();
+ else
+ *ptr = *new_it;
+ }
+
+ //std::copy(new_alleles.begin(), new_alleles.end(),
+ // it->genoBegin(p));
+ }
+ }
+ return true;
+}
+
+
+double MutSpaceSelector::indFitness(Population & /* pop */, Individual * ind) const
+{
+ if (m_mode == MULTIPLICATIVE) {
+ return randomSelMulFitnessExt(ind->genoBegin(), ind->genoEnd());
+ } else if (m_mode == ADDITIVE) {
+ if (m_additive)
+ return randomSelAddFitness(ind->genoBegin(), ind->genoEnd());
+ else
+ return randomSelAddFitnessExt(ind->genoBegin(), ind->genoEnd());
+ } else if (m_mode == EXPONENTIAL) {
+ if (m_additive)
+ retur...
[truncated message content] |
|
From: <ti...@us...> - 2012-01-31 20:31:53
|
Revision: 4366
http://simupop.svn.sourceforge.net/simupop/?rev=4366&view=rev
Author: tiwcpe8
Date: 2012-01-31 20:31:46 +0000 (Tue, 31 Jan 2012)
Log Message:
-----------
Merge mutant_new branch to trunk
Modified Paths:
--------------
trunk/src/mutant_vector.h
trunk/src/sandbox.cpp
trunk/src/stator.cpp
Added Paths:
-----------
trunk/test/sample_32_mu.pop
trunk/test/sample_64_mu.pop
Property Changed:
----------------
trunk/
Property changes on: trunk
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/mutant:4262-4317
/branches/mutant_new:4318-4354
/branches/openMP:3999-4241
+ /branches/mutant:4262-4317
/branches/mutant_new:4318-4365
/branches/openMP:3999-4241
Modified: trunk/src/mutant_vector.h
===================================================================
--- trunk/src/mutant_vector.h 2012-01-31 18:12:21 UTC (rev 4365)
+++ trunk/src/mutant_vector.h 2012-01-31 20:31:46 UTC (rev 4366)
@@ -107,6 +107,22 @@
mutable ssize_t m_com_index;
public:
+ iterator (const iterator& iter)
+ {
+ m_container = iter.m_container;
+ m_index = iter.m_index;
+ m_com_index = iter.m_com_index;
+ if (m_index == 0) {
+ m_com_index = -1;
+ } else {
+ typename compressed_vector<size_t>::index_array_type::iterator lower =
+ std::lower_bound(m_container->index_data().begin(), m_container->index_data().begin() + m_container->filled(), m_index);
+ m_com_index = lower - m_container->index_data().begin();
+ }
+
+
+
+ }
iterator (compressed_vector<T> * c) : m_container(c), m_index(0), m_com_index(-1)
{
@@ -119,17 +135,25 @@
iterator (compressed_vector<T> * c, size_t index) : m_container(c), m_index(index)
{
- typename compressed_vector<size_t>::index_array_type::iterator lower =
- std::lower_bound(m_container->index_data().begin(), m_container->index_data().begin() + m_container->filled(), index);
- m_com_index = lower - m_container->index_data().begin();
+ if (index == 0) {
+ m_com_index = -1;
+ } else {
+ typename compressed_vector<size_t>::index_array_type::iterator lower =
+ std::lower_bound(m_container->index_data().begin(), m_container->index_data().begin() + m_container->filled(), index);
+ m_com_index = lower - m_container->index_data().begin();
+ }
// find the smallest m_com_index that is larger than index
}
iterator (const compressed_vector<T> * c, size_t index) : m_container(c), m_index(index)
{
- typename compressed_vector<size_t>::index_array_type::iterator lower =
- std::lower_bound(m_container->index_data().begin(), m_container->index_data().begin() + m_container->filled(), index);
- m_com_index = lower - m_container->index_data().begin();
+ if (index == 0) {
+ m_com_index = -1;
+ } else {
+ typename compressed_vector<size_t>::index_array_type::iterator lower =
+ std::lower_bound(m_container->index_data().begin(), m_container->index_data().begin() + m_container->filled(), index);
+ m_com_index = lower - m_container->index_data().begin();
+ }
}
iterator () : m_container(NULL), m_index(0), m_com_index(-1)
@@ -140,6 +164,7 @@
{
m_container = iter.m_container;
m_index = iter.m_index;
+ m_com_index = iter.m_com_index;
return *this;
}
@@ -186,10 +211,15 @@
typename compressed_vector<T>::const_reference operator* () const
{
static const T zero = 0;
- if (m_index < m_container->index_data()[m_com_index])
+ if (m_com_index < (int)m_container->index_data().size()) {
+ if (m_com_index == -1)
+ return zero;
+ else if (m_index < m_container->index_data()[m_com_index])
+ return zero;
+ else
+ return m_container->value_data()[m_com_index];
+ } else
return zero;
- else
- return m_container->value_data()[m_com_index];
}
@@ -214,7 +244,11 @@
iterator & operator++ ()
{
++m_index;
- if (m_index >= m_container->index_data()[m_com_index])
+ if (m_container->index_data().size() == 0)
+ return *this;
+ if (m_com_index == -1)
+ m_com_index = 0;
+ if (m_com_index < (int)m_container->index_data().size() && m_index > m_container->index_data()[m_com_index])
++m_com_index;
return *this;
}
@@ -222,7 +256,11 @@
const iterator & operator++ () const
{
++m_index;
- if (m_index >= m_container->index_data()[m_com_index])
+ if (m_container->index_data().size() == 0)
+ return *this;
+ if (m_com_index == -1)
+ m_com_index = 0;
+ if (m_com_index < (int)m_container->index_data().size() && m_index > m_container->index_data()[m_com_index])
++m_com_index;
return *this;
}
@@ -247,6 +285,10 @@
m_index+=iter.m_index;
if (m_index > m_container->size())
m_index = m_container->size();
+ if (m_container->index_data().size() == 0)
+ return *this;
+ if (m_com_index == -1)
+ m_com_index = 0;
while (true) {
if (m_com_index < (int)m_container->filled())
if (m_index < m_container->index_data()[m_com_index]) {
@@ -269,6 +311,10 @@
m_index+=iter.m_index;
if (m_index > m_container->size())
m_index = m_container->size();
+ if (m_container->index_data().size() == 0)
+ return *this;
+ if (m_com_index == -1)
+ m_com_index = 0;
while (true) {
if (m_com_index < (int)m_container->filled())
if (m_index < m_container->index_data()[m_com_index]) {
@@ -292,6 +338,10 @@
m_index+=size;
if (m_index > m_container->size())
m_index = m_container->size();
+ if (m_container->index_data().size() == 0)
+ return *this;
+ if (m_com_index == -1)
+ m_com_index = 0;
while (true) {
if (m_com_index < (int)m_container->filled())
if (m_index < m_container->index_data()[m_com_index]) {
@@ -315,6 +365,10 @@
m_index+=size;
if (m_index > m_container->size())
m_index = m_container->size();
+ if (m_container->index_data().size() == 0)
+ return *this;
+ if (m_com_index == -1)
+ m_com_index = 0;
while (true) {
if (m_com_index < (int)m_container->filled())
if (m_index < m_container->index_data()[m_com_index]) {
@@ -353,12 +407,10 @@
return result;
}
- /*
size_t operator - (iterator & iter)
{
return (*this).m_index - iter.m_index;
}
- */
iterator operator - (const iterator & iter) const
@@ -386,13 +438,13 @@
return i;
}
}
+
return 0;
}
-
typename compressed_vector<T>::index_array_type::iterator getIndexIterator () {
- //return m_container->index_data().begin() + findPositionIndexData();
- return std::lower_bound(m_container->index_data().begin(), m_container->index_data().begin() + m_container->filled(), m_index);
+ return m_container->index_data().begin() + findPositionIndexData();
+ //return std::lower_bound(m_container->index_data().begin(), m_container->index_data().begin() + m_container->filled(), m_index);
}
typename compressed_vector<T>::value_array_type::iterator getValueIterator () {
@@ -405,7 +457,7 @@
return m_container->find(m_index);
}
- size_t getIndex ()
+ size_t getIndex () const
{
return m_index;
}
@@ -433,18 +485,16 @@
void erase (typename mutant_vector<T>::iterator begin,typename mutant_vector<T>::iterator end)
{
- typename mutant_vector<T>::iterator it = begin;
- typename mutant_vector<T>::iterator it2 = end;
- for(;it != end; ++it) {
- it.deleted();
+
+ if (end != this->end()) {
+ std::copy(end.getValueIterator(), this->end().getValueIterator(), begin.getValueIterator());
+ typename compressed_vector<T>::index_array_type::iterator it = end.getIndexIterator();
+ typename compressed_vector<T>::index_array_type::iterator index_end = end.getIndexIterator();
+ for (; it != this->end().getIndexIterator(); ++it) {
+ *it -= (end - begin);
+ }
+ std::copy(index_end, this->end().getIndexIterator(), begin.getIndexIterator());
}
- it = begin;
- if (end != this->end())
- for(it2 = end; it2 != this->end(); ++it2, ++it) {
- *it = *it2;
- }
- // compressed vector doesn't decrease the size when it is erased.
- // we have to resize it.
m_container.resize(m_container.size() - (end.getIndex() - begin.getIndex()));
}
@@ -487,12 +537,59 @@
inline void copy(mutant_vectora::iterator begin, mutant_vectora::iterator end, mutant_vectora::iterator it)
{
- mutant_vectora::iterator itt = begin;
- for (;itt != end; ++itt, ++it) {
- if (*it == 0u && *itt == 0u)
- continue;
- else
- *it = *itt;
+
+ size_t size = end - begin;
+ mutant_vectora::iterator it_end = it + size;
+ if (it_end.getIndex() <= it_end.getContainer()->size()) {
+ compressed_vector<Allele>::value_array_type::iterator src_value_begin = begin.getValueIterator();
+ compressed_vector<Allele>::value_array_type::iterator src_value_end = end.getValueIterator();
+ compressed_vector<Allele>::value_array_type::iterator dest_value_begin = it.getValueIterator();
+ compressed_vector<Allele>::value_array_type::iterator dest_value_end = it_end.getValueIterator();
+ compressed_vector<Allele>::index_array_type::iterator src_index_begin = begin.getIndexIterator();
+ compressed_vector<Allele>::index_array_type::iterator dest_index_begin = it.getIndexIterator();
+ size_t src_size = src_value_end - src_value_begin;
+ size_t dest_size = dest_value_end - dest_value_begin;
+ size_t src_idx_num_begin = begin.getIndex();
+ size_t dest_idx_num_begin = it.getIndex();
+ if (src_size > dest_size) {
+ size_t diff_size = src_size - dest_size;
+ size_t filled_size = it.getContainer()->filled();
+ if (filled_size + diff_size >= it.getContainer()->nnz_capacity()) {
+ it.getContainer()->reserve(it.getContainer()->filled() + diff_size, true);
+ }
+ dest_index_begin = it.getIndexIterator();
+ dest_value_begin = it.getValueIterator();
+ std::copy_backward(dest_index_begin, it.getContainer()->index_data().begin() + filled_size, it.getContainer()->index_data().begin() + filled_size + diff_size);
+ for (size_t i = 0; i < src_size; i++) {
+ size_t range = *(src_index_begin + i) - src_idx_num_begin;
+ *(dest_index_begin+i) = dest_idx_num_begin + range;
+ }
+ std::copy_backward(dest_value_begin, it.getContainer()->value_data().begin() + filled_size, it.getContainer()->value_data().begin() + filled_size + diff_size);
+ std::copy(src_value_begin, src_value_end, dest_value_begin);
+ it.getContainer()->set_filled(filled_size + diff_size);
+ } else if (src_size < dest_size) {
+ size_t diff_size = dest_size - src_size;
+ size_t filled_size = it.getContainer()->filled();
+ dest_index_begin = it.getIndexIterator();
+ dest_value_begin = it.getValueIterator();
+ std::copy(dest_index_begin + diff_size, it.getContainer()->index_data().begin() + filled_size, dest_index_begin);
+ for (size_t i = 0; i < src_size; i++) {
+ size_t range = *(src_index_begin + i) - src_idx_num_begin;
+ *(dest_index_begin + i) = dest_idx_num_begin + range;
+ }
+ std::copy(dest_value_begin + diff_size, it.getContainer()->value_data().begin() + filled_size, dest_value_begin);
+ std::copy(src_value_begin, src_value_end, dest_value_begin);
+ it.getContainer()->set_filled(filled_size - diff_size);
+
+ } else {
+ dest_index_begin = it.getIndexIterator();
+ dest_value_begin = it.getValueIterator();
+ for (size_t i = 0; i < src_size; i++) {
+ size_t range = *(src_index_begin + i) - src_idx_num_begin;
+ *(dest_index_begin + i) = dest_idx_num_begin + range;
+ }
+ std::copy(src_value_begin, src_value_end, dest_value_begin);
+ }
}
}
@@ -511,7 +608,7 @@
inline mutant_vectora::iterator find (mutant_vectora::iterator begin, mutant_vectora::iterator end, Allele value)
{
- mutant_vectora::iterator it = begin;
+ mutant_vectora::const_iterator it = begin;
for(; it != end; ++it)
{
if(*it == value)
Modified: trunk/src/sandbox.cpp
===================================================================
--- trunk/src/sandbox.cpp 2012-01-31 18:12:21 UTC (rev 4365)
+++ trunk/src/sandbox.cpp 2012-01-31 20:31:46 UTC (rev 4366)
@@ -497,12 +497,6 @@
void MutSpaceRecombinator::transmitGenotype0(Population & pop, Population & offPop, const Individual & parent,
size_t offIndex, int ploidy) const
{
-#ifdef BINARYALLELE
- (void)offPop; // avoid warning about unused parameter
- (void)parent; // avoid warning about unused parameter
- (void)offIndex; // avoid warning about unused parameter
- (void)ploidy; // avoid warning about unused parameter
-#else
size_t nCh = parent.numChrom();
// count duplicates...
@@ -580,19 +574,12 @@
// fill the rest with 0.
std::fill(it, it_end, 0);
}
-#endif
}
void MutSpaceRecombinator::transmitGenotype1(Population & pop, Population & offPop, const Individual & parent,
size_t offIndex, int ploidy) const
{
-#ifdef BINARYALLELE
- (void)offPop; // avoid warning about unused parameter
- (void)parent; // avoid warning about unused parameter
- (void)offIndex; // avoid warning about unused parameter
- (void)ploidy; // avoid warning about unused parameter
-#else
const matrixi & ranges = m_ranges.elems();
for (size_t ch = 0; ch < parent.numChrom(); ++ch) {
@@ -693,7 +680,6 @@
// fill the rest with 0.
std::fill(it, it_end, 0);
}
-#endif
}
@@ -772,14 +758,8 @@
std::fill(new_alleles.begin(), new_alleles.end(), Allele(0));
set_difference(old_alleles.begin(), old_alleles.end(),
commonAlleles.begin(), commonAlleles.end(), new_alleles.begin());
-#ifdef MUTANTALLELE
- GenoIterator ptr = it->genoBegin(p);
- for (vectora::iterator new_it = new_alleles.begin(); new_it != new_alleles.end(); ++new_it, ++ptr)
- *ptr = *new_it;
-#else
std::copy(new_alleles.begin(), new_alleles.end(),
it->genoBegin(p));
-#endif
}
}
return true;
@@ -1050,9 +1030,9 @@
bool MutSpaceMutator::apply(Population & pop) const
{
-#ifdef BINARYALLELE
+ #ifdef BINARYALLELE
(void)pop; // avoid warning about unused parameter
-#else
+ #else
const matrixi & ranges = m_ranges.elems();
vectoru width(ranges.size());
@@ -1185,7 +1165,7 @@
} // each subpopulation
if (out)
closeOstream();
-#endif
+ #endif
return true;
}
@@ -1193,12 +1173,12 @@
void MutSpaceRecombinator::transmitGenotype0(Population & pop, Population & offPop, const Individual & parent,
size_t offIndex, int ploidy) const
{
-#ifdef BINARYALLELE
+ #ifdef BINARYALLELE
(void)offPop; // avoid warning about unused parameter
(void)parent; // avoid warning about unused parameter
(void)offIndex; // avoid warning about unused parameter
(void)ploidy; // avoid warning about unused parameter
-#else
+ #else
size_t nCh = parent.numChrom();
// count duplicates...
@@ -1277,19 +1257,19 @@
// fill the rest with 0.
std::fill(it, it_end, 0);
}
-#endif
+ #endif
}
void MutSpaceRecombinator::transmitGenotype1(Population & pop, Population & offPop, const Individual & parent,
size_t offIndex, int ploidy) const
{
-#ifdef BINARYALLELE
+ #ifdef BINARYALLELE
(void)offPop; // avoid warning about unused parameter
(void)parent; // avoid warning about unused parameter
(void)offIndex; // avoid warning about unused parameter
(void)ploidy; // avoid warning about unused parameter
-#else
+ #else
const matrixi & ranges = m_ranges.elems();
for (size_t ch = 0; ch < parent.numChrom(); ++ch) {
@@ -1391,7 +1371,7 @@
// fill the rest with 0.
std::fill(it, it_end, 0);
}
-#endif
+ #endif
}
Modified: trunk/src/stator.cpp
===================================================================
--- trunk/src/stator.cpp 2012-01-31 18:12:21 UTC (rev 4365)
+++ trunk/src/stator.cpp 2012-01-31 20:31:46 UTC (rev 4366)
@@ -707,15 +707,43 @@
pop.activateVirtualSubPop(*sp);
// go through all loci
+#ifdef MUTANTALLELE
+ IndIterator ind = pop.indIterator(sp->subPop());
+ for (; ind.valid(); ++ind) {
+ GenoIterator it = ind->genoBegin();
+ GenoIterator it_end = ind->genoEnd();
+ compressed_vector<Allele>::index_array_type::iterator index_it = it.getIndexIterator();
+ compressed_vector<Allele>::index_array_type::iterator index_it_end = it_end.getIndexIterator();
+ compressed_vector<Allele>::value_array_type::iterator value_it = it.getValueIterator();
+ size_t indIndex = it.getIndex();
+ for (;index_it != index_it_end; ++index_it, ++value_it) {
+ if (m_loci.allAvail()) {
+ if (*value_it != 0) {
+ segSites.insert(*index_it - indIndex);
+ }
+ } else {
+ for (size_t idx = 0; idx < loci.size(); ++idx) {
+ if (*index_it == indIndex + loci[idx] && *value_it != 0) {
+ segSites.insert(loci[idx]);
+ break;
+ }
+ }
+ }
+ }
+
+ }
+
+#else
for (ssize_t idx = 0; idx < static_cast<ssize_t>(loci.size()); ++idx) {
size_t loc = loci[idx];
IndAlleleIterator a = pop.alleleIterator(loc, sp->subPop());
for (; a.valid(); ++a)
- if (*a != 0u) {
- segSites.insert(loc);
+ if (*a != 0) {
+ segSites.insert((ULONG)loc);
break;
}
}
+#endif
pop.deactivateVirtualSubPop(sp->subPop());
if (m_vars.contains(numOfSegSites_sp_String))
@@ -766,33 +794,44 @@
subPopList subPops = m_subPops.expandFrom(pop);
subPopList::const_iterator sp = subPops.begin();
subPopList::const_iterator spEnd = subPops.end();
-
for ( ; sp != spEnd; ++sp) {
size_t mutantCount = 0;
pop.activateVirtualSubPop(*sp);
IndIterator ind = pop.indIterator(sp->subPop());
for (; ind.valid(); ++ind) {
GenoIterator it = ind->genoBegin();
+ GenoIterator it_end = ind->genoEnd();
#ifdef MUTANTALLELE
- GenoIterator it_end = ind->genoEnd();
compressed_vector<Allele>::index_array_type::iterator index_it = it.getIndexIterator();
compressed_vector<Allele>::index_array_type::iterator index_it_end = it_end.getIndexIterator();
compressed_vector<Allele>::value_array_type::iterator value_it = it.getValueIterator();
size_t indIndex = it.getIndex();
for (;index_it != index_it_end; ++index_it, ++value_it) {
- for (size_t idx = 0; idx < loci.size(); ++idx) {
- size_t loc = indIndex + loci[idx];
- if (*index_it == loc && *value_it != 0) {
+ if (m_loci.allAvail()) {
+ if (*value_it != 0)
mutantCount++;
- break;
+ } else {
+ for (size_t idx = 0; idx < loci.size(); ++idx) {
+ size_t loc = indIndex + loci[idx];
+ if (*index_it == loc && *value_it != 0) {
+ mutantCount++;
+ break;
+ }
}
}
}
#else
- for (size_t idx = 0; idx < loci.size(); ++idx) {
- size_t loc = loci[idx];
- if (*(it + loc) != 0)
- mutantCount++;
+ if (m_loci.allAvail()) {
+ for (;it != it_end; ++it) {
+ if (*it != 0)
+ mutantCount++;
+ }
+ } else {
+ for (size_t idx = 0; idx < loci.size(); ++idx) {
+ size_t loc = loci[idx];
+ if (*(it + loc) != 0)
+ mutantCount++;
+ }
}
#endif
}
Added: trunk/test/sample_32_mu.pop
===================================================================
(Binary files differ)
Property changes on: trunk/test/sample_32_mu.pop
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/test/sample_64_mu.pop
===================================================================
(Binary files differ)
Property changes on: trunk/test/sample_64_mu.pop
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <ti...@us...> - 2012-02-10 21:02:51
|
Revision: 4372
http://simupop.svn.sourceforge.net/simupop/?rev=4372&view=rev
Author: tiwcpe8
Date: 2012-02-10 21:02:45 +0000 (Fri, 10 Feb 2012)
Log Message:
-----------
Fixed performance problem in load and save Population function
Modified Paths:
--------------
trunk/src/individual.cpp
trunk/src/individual.h
trunk/src/initializer.cpp
trunk/src/population.cpp
trunk/test/sample_32_mu.pop
trunk/test/sample_64_mu.pop
Modified: trunk/src/individual.cpp
===================================================================
--- trunk/src/individual.cpp 2012-02-07 22:17:08 UTC (rev 4371)
+++ trunk/src/individual.cpp 2012-02-10 21:02:45 UTC (rev 4372)
@@ -238,7 +238,7 @@
}
-
+// Fix me: This one has to optimize
PyObject * Individual::genoAtLoci(const lociList & lociList)
{
ssize_t ply = ploidy();
Modified: trunk/src/individual.h
===================================================================
--- trunk/src/individual.h 2012-02-07 22:17:08 UTC (rev 4371)
+++ trunk/src/individual.h 2012-02-10 21:02:45 UTC (rev 4372)
@@ -346,7 +346,13 @@
/// CPPONLY start of alleles
GenoIterator genoBegin() const
{
+#ifdef MUTANTALLELE
+ // Call + operator in order to find the correct m_com_index;
+ // more information see operator+ function in mutant_vector.h
+ return m_genoPtr + 0;
+#else
return m_genoPtr;
+#endif
}
Modified: trunk/src/initializer.cpp
===================================================================
--- trunk/src/initializer.cpp 2012-02-07 22:17:08 UTC (rev 4371)
+++ trunk/src/initializer.cpp 2012-02-10 21:02:45 UTC (rev 4372)
@@ -241,10 +241,12 @@
#else
IndIterator it = pop.indIterator(sp->subPop());
#endif
- for (; it.valid(); ++it)
+ std::cout << "Start init!!!!!!!\n";
+ for (size_t ii=0; it.valid(); ++it,++ii )
for (vectoru::iterator p = ploidy.begin(); p != ploidy.end(); ++p)
for (vectoru::const_iterator loc = loci.begin(); loc != loci.end(); ++loc, ++idx)
it->setAllele(ToAllele(m_genotype[idx % sz]), *loc, static_cast<int>(*p));
+ std::cout << "End init!!!!!!!\n";
}
#ifdef _OPENMP
Modified: trunk/src/population.cpp
===================================================================
--- trunk/src/population.cpp 2012-02-07 22:17:08 UTC (rev 4371)
+++ trunk/src/population.cpp 2012-02-10 21:02:45 UTC (rev 4372)
@@ -104,7 +104,6 @@
decGenoStruRef();
}
-
Population::Population(const Population & rhs) :
GenoStruTrait(rhs),
m_popSize(rhs.m_popSize),
@@ -2918,15 +2917,6 @@
data = 0;
}
}
-#elif defined MUTANTALLELE
- size_t size = m_genotype.size();
- ar & size;
- ConstGenoIterator ptr = m_genotype.begin();
- unsigned int data = 0;
- for (size_t i = 0; i < size; ++i, ++ptr) {
- data = *ptr;
- ar & data;
- }
#else
ar & m_genotype;
#endif
@@ -2958,15 +2948,6 @@
data = 0;
}
}
-#elif defined MUTANTALLELE
- size_t size = m_genotype.size();
- ar & size;
- ConstGenoIterator ptr = m_genotype.begin();
- unsigned int data = 0;
- for (size_t i = 0; i < size; ++i, ++ptr) {
- data = *ptr;
- ar & data;
- }
#else
ar & m_genotype;
#endif
@@ -3015,15 +2996,12 @@
}
// binary from mutant
} else if (ma == 256) {
- DBG_DO(DBG_POPULATION, cerr << "Load bin from mutant. " << endl);
- size_t size;
- ar & size;
- m_genotype.resize(size);
- GenoIterator ptr = m_genotype.begin();
- unsigned int data = 0;
- for (size_t i = 0; i < size; ++i, ++ptr) {
- ar & data;
- *ptr = ToAllele(data);
+ mutant_vector<unsigned int> tmpgeno;
+ ar & tmpgeno;
+ m_genotype.resize(tmpgeno.size());
+ for (size_t i = 0; i < tmpgeno.size(); ++i) {
+ unsigned int data = tmpgeno[i];
+ m_genotype[i] = ToAllele(data);
}
// binary from others (long types)
} else {
@@ -3054,15 +3032,7 @@
// mutant from mutant
if (ma == 256) {
DBG_DO(DBG_POPULATION, cerr << "Load mutant from mutant. " << endl);
- size_t size;
- ar & size;
- m_genotype.resize(size);
- GenoIterator ptr = m_genotype.begin();
- unsigned int data = 0;
- for (size_t i = 0; i < size; ++i, ++ptr) {
- ar & data;
- *ptr = data;
- }
+ ar & m_genotype;
}
// mutant from long
else {
@@ -3071,22 +3041,19 @@
ar & data;
m_genotype.resize(data.size());
for (size_t i = 0; i < data.size(); ++i) {
- m_genotype[i] = data[i];
+ if (data[i] != 0)
+ m_genotype[i] = data[i];
}
}
# else
// long from mutant
if (ma == 256) {
DBG_DO(DBG_POPULATION, cerr << "Load long from mutant. " << endl);
- size_t size;
- ar & size;
- m_genotype.resize(size);
- GenoIterator ptr = m_genotype.begin();
- unsigned int data = 0;
- for (size_t i = 0; i < size; ++i, ++ptr) {
- ar & data;
- *ptr = data;
- }
+ mutant_vector<unsigned int> tmpgeno;
+ ar & tmpgeno;
+ m_genotype.resize(tmpgeno.size());
+ for (size_t i = 0; i < tmpgeno.size(); ++i)
+ m_genotype[i] = tmpgeno[i];
// long from long
} else {
DBG_DO(DBG_POPULATION, cerr << "Load long from long. " << endl);
@@ -3160,15 +3127,12 @@
}
// binary from mutant
} else if (ma == 256) {
- DBG_DO(DBG_POPULATION, cerr << "Load bin from mutant. " << endl);
- size_t size;
- ar & size;
- pd.m_genotype.resize(size);
- GenoIterator ptr = pd.m_genotype.begin();
- unsigned int data = 0;
- for (size_t i = 0; i < size; ++i, ++ptr) {
- ar & data;
- *ptr = ToAllele(data);
+ mutant_vector<unsigned int> tmpgeno;
+ ar & tmpgeno;
+ pd.m_genotype.resize(tmpgeno.size());
+ for (size_t i = 0; i < tmpgeno.size(); ++i) {
+ unsigned int data = tmpgeno[i];
+ pd.m_genotype[i] = ToAllele(data);
}
// binary from others (long types)
} else {
@@ -3197,16 +3161,7 @@
# ifdef MUTANTALLELE
// mutant from mutant
if (ma == 256) {
- DBG_DO(DBG_POPULATION, cerr << "Load mutant from mutant. " << endl);
- size_t size;
- ar & size;
- pd.m_genotype.resize(size);
- GenoIterator ptr = pd.m_genotype.begin();
- unsigned int data = 0;
- for (size_t i = 0; i < size; ++i, ++ptr) {
- ar & data;
- *ptr = data;
- }
+ ar & pd.m_genotype;
}
// mutant from long
else {
@@ -3215,22 +3170,19 @@
ar & data;
pd.m_genotype.resize(data.size());
for (size_t i = 0; i < data.size(); ++i) {
- pd.m_genotype[i] = data[i];
+ if (data[i] != 0)
+ pd.m_genotype[i] = data[i];
}
}
# else
// long from mutant
if (ma == 256) {
DBG_DO(DBG_POPULATION, cerr << "Load long from mutant. " << endl);
- size_t size;
- ar & size;
- pd.m_genotype.resize(size);
- GenoIterator ptr = pd.m_genotype.begin();
- unsigned int data = 0;
- for (size_t i = 0; i < size; ++i, ++ptr) {
- ar & data;
- *ptr = data;
- }
+ mutant_vector<unsigned int> tmpgeno;
+ ar & tmpgeno;
+ pd.m_genotype.resize(tmpgeno.size());
+ for (size_t i = 0; i < tmpgeno.size(); ++i)
+ pd.m_genotype[i] = tmpgeno[i];
// long from long
} else {
DBG_DO(DBG_POPULATION, cerr << "Load long from long. " << endl);
Modified: trunk/test/sample_32_mu.pop
===================================================================
(Binary files differ)
Modified: trunk/test/sample_64_mu.pop
===================================================================
(Binary files differ)
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <si...@us...> - 2012-02-22 22:24:14
|
Revision: 4378
http://simupop.svn.sourceforge.net/simupop/?rev=4378&view=rev
Author: simupop
Date: 2012-02-22 22:24:07 +0000 (Wed, 22 Feb 2012)
Log Message:
-----------
Preliminary support for a dedicated Mitochondrial chromosome type
Modified Paths:
--------------
trunk/ChangeLog
trunk/src/genoStru.cpp
trunk/src/genoStru.h
trunk/src/individual.cpp
trunk/src/individual.h
trunk/src/outputer.cpp
trunk/src/penetrance.cpp
trunk/src/selector.cpp
trunk/src/simuPOP_cfg.h
trunk/src/simuPOP_doc.i
trunk/src/stator.cpp
trunk/src/transmitter.cpp
trunk/src/transmitter.h
Modified: trunk/ChangeLog
===================================================================
--- trunk/ChangeLog 2012-02-22 19:03:33 UTC (rev 4377)
+++ trunk/ChangeLog 2012-02-22 22:24:07 UTC (rev 4378)
@@ -9,6 +9,8 @@
New features:
- New option numOfSegSites to operator Stat to calculate the number of segragating
sites.
+ - Add MITOCHONDRIAL as a natural chromosome type so that operators such as
+ Stat can handle them correctly.
BUG:
- Fix a bug that prevents the correct handling of population structure when evolving
Modified: trunk/src/genoStru.cpp
===================================================================
--- trunk/src/genoStru.cpp 2012-02-22 19:03:33 UTC (rev 4377)
+++ trunk/src/genoStru.cpp 2012-02-22 22:24:07 UTC (rev 4378)
@@ -230,7 +230,7 @@
#ifndef OPTIMIZED
for (size_t i = 0; i < m_chromTypes.size(); ++i) {
size_t type = m_chromTypes[i];
- DBG_ASSERT(type == AUTOSOME || type == CHROMOSOME_X || type == CHROMOSOME_Y || type == CUSTOMIZED,
+ DBG_ASSERT(type == AUTOSOME || type == CHROMOSOME_X || type == CHROMOSOME_Y || type == CUSTOMIZED || type == MITOCHONDRIAL,
ValueError, "Chromsome type can only be one of AUTOSOME, CHROMOSOME_X, CHROMOSOME_Y and CUSTOMIZED.");
}
#endif
@@ -256,6 +256,16 @@
DBG_WARNIF(m_chromX * m_chromY < 0,
"Chromosome X and Y should be both present for sexual transmission to work.");
//
+ m_mitochondrial.clear();
+ for (size_t i = 0; i < m_chromTypes.size(); ++i) {
+ if (m_chromTypes[i] == MITOCHONDRIAL) {
+ DBG_FAILIF(!m_mitochondrial.empty() && m_mitochondrial.back() != i - 1,
+ ValueError,
+ "There can be several mitochondrial chromosmes, but they need to be adjacent to each other.");
+ m_mitochondrial.push_back(static_cast<ULONG>(i));
+ }
+ }
+ //
m_customized.clear();
for (size_t i = 0; i < m_chromTypes.size(); ++i) {
if (m_chromTypes[i] == CUSTOMIZED) {
Modified: trunk/src/genoStru.h
===================================================================
--- trunk/src/genoStru.h 2012-02-22 19:03:33 UTC (rev 4377)
+++ trunk/src/genoStru.h 2012-02-22 22:24:07 UTC (rev 4378)
@@ -73,7 +73,7 @@
public:
/// CPPONLY serialization library requires a default constructor
GenoStructure() : m_ploidy(2), m_totNumLoci(0),
- m_numLoci(0), m_chromTypes(), m_chromX(-1), m_chromY(-1), m_customized(),
+ m_numLoci(0), m_chromTypes(), m_chromX(-1), m_chromY(-1), m_mitochondrial(), m_customized(),
m_haplodiploid(false), m_lociPos(0), m_chromIndex(0),
m_chromNames(), m_alleleNames(), m_lociNames(), m_lociNameMap(), m_infoFields(0),
m_refCount(0)
@@ -207,6 +207,9 @@
/// index of chromosome Y, -1 if not exist
int m_chromY;
+ /// indexes of mitochondrial chromosomes
+ vectoru m_mitochondrial;
+
/// indexes of customized chromosomes
vectoru m_customized;
@@ -475,7 +478,20 @@
return s_genoStruRepository[m_genoStruIdx].m_customized;
}
+ /** CPPONLY
+ * Return the indexes of mitochondrial chromosomes.
+ * <group>2-chromosome</group>
+ */
+ vectoru mitochondrialChroms() const
+ {
+ DBG_FAILIF(m_genoStruIdx == MaxTraitIndex, SystemError,
+ "totNumLoci: You have not set genoStructure. Please use setGenoStrucutre to set such info.");
+ return s_genoStruRepository[m_genoStruIdx].m_mitochondrial;
+ }
+
+
+
/// HIDDEN
bool sexChrom() const
{
@@ -636,7 +652,7 @@
/** return the type of a chromosome \e chrom (\c CUSTOMIZED, \c AUTOSOME,
- * \c CHROMOSOME_X, or \c CHROMOSOME_Y).
+ * \c CHROMOSOME_X, \c CHROMOSOME_Y or \c MITOCHONDRIAL.
* <group>2-chromosome</group>
*/
size_t chromType(const size_t chrom) const
@@ -650,7 +666,7 @@
/** return the type of all chromosomes (\c CUSTOMIZED, \c AUTOSOME,
- * \c CHROMOSOME_X or \c CHROMOSOME_Y).
+ * \c CHROMOSOME_X, \c CHROMOSOME_Y, or \c MITOCHONDRIAL).
* <group>2-chromosome</group>
*/
vectoru chromTypes() const
Modified: trunk/src/individual.cpp
===================================================================
--- trunk/src/individual.cpp 2012-02-22 19:03:33 UTC (rev 4377)
+++ trunk/src/individual.cpp 2012-02-22 22:24:07 UTC (rev 4378)
@@ -125,7 +125,8 @@
size_t t = chromType(ch);
if ((s == FEMALE && t == CHROMOSOME_Y) || // female chromsome Y
(s == MALE && // second copy of chromosome X and first copy of chromosome Y
- ((p == 1 && t == CHROMOSOME_X) || (p == 0 && t == CHROMOSOME_Y))))
+ ((p == 1 && t == CHROMOSOME_X) || (p == 0 && t == CHROMOSOME_Y))) ||
+ (p > 0 && t == MITOCHONDRIAL)) // mitochondiral DNA only uses the first homologous copy
return false;
return true;
@@ -261,6 +262,8 @@
if (((chType == CHROMOSOME_X && p == 1) ||
(chType == CHROMOSOME_Y && p == 0)) && sex() == MALE)
continue;
+ if (chType == MITOCHONDRIAL && p > 0)
+ continue;
alleles.push_back(allele(idx, p, ch));
}
}
@@ -282,6 +285,8 @@
if (((chromTypes[idx] == CHROMOSOME_X && p == 1) ||
(chromTypes[idx] == CHROMOSOME_Y && p == 0)) && sex() == MALE)
continue;
+ if (chromTypes[idx] == MITOCHONDRIAL && p > 0)
+ continue;
alleles.push_back(allele(loci[idx], p));
}
}
Modified: trunk/src/individual.h
===================================================================
--- trunk/src/individual.h 2012-02-22 19:03:33 UTC (rev 4377)
+++ trunk/src/individual.h 2012-02-22 22:24:07 UTC (rev 4378)
@@ -1019,6 +1019,11 @@
break;
p = 1;
valid = it.valid();
+ } else if (m_chromType == MITOCHONDRIAL) {
+ // only the first homologous copy is valid
+ DBG_ASSERT(p == 0, SystemError, "Only the first homologous copy of mitochondrial DNA can be iterated.");
+ ++ it;
+ valid = it.valid();
}
}
Modified: trunk/src/outputer.cpp
===================================================================
--- trunk/src/outputer.cpp 2012-02-22 19:03:33 UTC (rev 4377)
+++ trunk/src/outputer.cpp 2012-02-22 22:24:07 UTC (rev 4378)
@@ -64,6 +64,9 @@
case CUSTOMIZED:
out << " (CUSTOMIZED, ";
break;
+ case MITOCHONDRIAL:
+ out << " (MITOCHONDRIAL, ";
+ break;
default:
throw ValueError("Wrong chromosome type");
}
Modified: trunk/src/penetrance.cpp
===================================================================
--- trunk/src/penetrance.cpp 2012-02-22 19:03:33 UTC (rev 4377)
+++ trunk/src/penetrance.cpp 2012-02-22 22:24:07 UTC (rev 4378)
@@ -153,6 +153,8 @@
if (((chromTypes[idx] == CHROMOSOME_X && p == 1) ||
(chromTypes[idx] == CHROMOSOME_Y && p == 0)) && ind->sex() == MALE)
continue;
+ if (chromTypes[idx] == MITOCHONDRIAL && p > 0)
+ continue;
alleles.push_back(ind->allele(loci[idx], p));
}
}
@@ -179,6 +181,8 @@
++end_idx;
} else if (chromTypes[i] == CHROMOSOME_X && ind->sex() == MALE)
++end_idx;
+ else if (chromTypes[i] == MITOCHONDRIAL)
+ ++end_idx;
else
end_idx += ply;
if (key.size() != end_idx - begin_idx) {
Modified: trunk/src/selector.cpp
===================================================================
--- trunk/src/selector.cpp 2012-02-22 19:03:33 UTC (rev 4377)
+++ trunk/src/selector.cpp 2012-02-22 22:24:07 UTC (rev 4378)
@@ -87,6 +87,8 @@
if (((chromTypes[idx] == CHROMOSOME_X && p == 1) ||
(chromTypes[idx] == CHROMOSOME_Y && p == 0)) && ind->sex() == MALE)
continue;
+ if (chromTypes[idx] == MITOCHONDRIAL && p > 0)
+ continue;
alleles.push_back(ind->allele(loci[idx], p));
}
}
@@ -113,6 +115,8 @@
++end_idx;
} else if (chromTypes[i] == CHROMOSOME_X && ind->sex() == MALE)
++end_idx;
+ else if (chromTypes[i] == MITOCHONDRIAL)
+ ++end_idx;
else
end_idx += ply;
if (key.size() != end_idx - begin_idx) {
Modified: trunk/src/simuPOP_cfg.h
===================================================================
--- trunk/src/simuPOP_cfg.h 2012-02-22 19:03:33 UTC (rev 4377)
+++ trunk/src/simuPOP_cfg.h 2012-02-22 22:24:07 UTC (rev 4378)
@@ -146,8 +146,8 @@
// according to MSVC manual, unsigned int is 32 bit, regardless of
// platform. Because uint32_t is not handled correctly by swig under
// windows, I am using unsigned int here.
-typedef unsigned int Allele;
-typedef unsigned int & AlleleRef;
+typedef unsigned long Allele;
+typedef unsigned long & AlleleRef;
//# else
// under a unix platform, uint32_t seems to work fine.
//typedef uint32_t Allele;
@@ -219,7 +219,8 @@
CUSTOMIZED = 11,
AUTOSOME = 12,
CHROMOSOME_X = 13,
- CHROMOSOME_Y = 14
+ CHROMOSOME_Y = 14,
+ MITOCHONDRIAL = 15,
};
// For numOffspring and gene conversion
Modified: trunk/src/simuPOP_doc.i
===================================================================
--- trunk/src/simuPOP_doc.i 2012-02-22 19:03:33 UTC (rev 4377)
+++ trunk/src/simuPOP_doc.i 2012-02-22 22:24:07 UTC (rev 4378)
@@ -1665,6 +1665,8 @@
%ignore simuPOP::GenoStruTrait::setGenoStruIdx(size_t idx);
+%ignore simuPOP::GenoStruTrait::swapGenoStru(GenoStruTrait &rhs);
+
%feature("docstring") simuPOP::GenoStruTrait::lociDist "
Usage:
@@ -3406,7 +3408,7 @@
Usage:
- iterator(c)
+ iterator(iter)
";
@@ -3450,6 +3452,14 @@
";
+%feature("docstring") simuPOP::mutantvector::iterator::getComIndex "
+
+Usage:
+
+ x.getComIndex()
+
+";
+
%feature("docstring") simuPOP::mutantvector::iterator::getContainer "
Usage:
@@ -9016,12 +9026,12 @@
Usage:
Stat(popSize=False, numOfMales=False, numOfAffected=False,
- numOfSegSites=[], alleleFreq=[], heteroFreq=[], homoFreq=[],
- genoFreq=[], haploFreq=[], haploHeteroFreq=[], haploHomoFreq=[],
- sumOfInfo=[], meanOfInfo=[], varOfInfo=[], maxOfInfo=[],
- minOfInfo=[], LD=[], association=[], neutrality=[],
- structure=[], HWE=[], vars=ALL_AVAIL, suffix=\"\", output=\"\",
- begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL,
+ numOfSegSites=[], numOfMutants=[], alleleFreq=[], heteroFreq=[],
+ homoFreq=[], genoFreq=[], haploFreq=[], haploHeteroFreq=[],
+ haploHomoFreq=[], sumOfInfo=[], meanOfInfo=[], varOfInfo=[],
+ maxOfInfo=[], minOfInfo=[], LD=[], association=[],
+ neutrality=[], structure=[], HWE=[], vars=ALL_AVAIL, suffix=\"\",
+ output=\"\", begin=0, end=-1, step=1, at=[], reps=ALL_AVAIL,
subPops=ALL_AVAIL, infoFields=[])
Details:
@@ -9737,6 +9747,32 @@
";
+%ignore simuPOP::statNumOfMutants;
+
+%feature("docstring") simuPOP::statNumOfMutants::statNumOfMutants "
+
+Usage:
+
+ statNumOfMutants(loci, subPops, vars, suffix)
+
+";
+
+%feature("docstring") simuPOP::statNumOfMutants::describe "
+
+Usage:
+
+ x.describe(format=True)
+
+";
+
+%feature("docstring") simuPOP::statNumOfMutants::apply "
+
+Usage:
+
+ x.apply(pop)
+
+";
+
%ignore simuPOP::statNumOfSegSites;
%feature("docstring") simuPOP::statNumOfSegSites::statNumOfSegSites "
Modified: trunk/src/stator.cpp
===================================================================
--- trunk/src/stator.cpp 2012-02-22 19:03:33 UTC (rev 4377)
+++ trunk/src/stator.cpp 2012-02-22 22:24:07 UTC (rev 4378)
@@ -1071,8 +1071,8 @@
#ifndef OPTIMIZED
size_t chromType = pop.chromType(pop.chromLocusPair(loc).first);
- DBG_FAILIF(chromType == CHROMOSOME_X || chromType == CHROMOSOME_Y,
- ValueError, "Heterozygosity count for sex chromosomes is not supported.");
+ DBG_FAILIF(chromType == CHROMOSOME_X || chromType == CHROMOSOME_Y || chromType == MITOCHONDRIAL,
+ ValueError, "Heterozygosity count for sex and mitochondrial chromosomes is not supported.");
#endif
size_t hetero = 0;
size_t homo = 0;
@@ -1229,6 +1229,8 @@
if (((chromTypes[idx] == CHROMOSOME_X && p == 1) ||
(chromTypes[idx] == CHROMOSOME_Y && p == 0)) && ind->sex() == MALE)
continue;
+ if (chromTypes[idx] == MITOCHONDRIAL && p > 0)
+ continue;
genotype.push_back(ind->allele(loc, p));
}
genotypes[genotype]++;
@@ -1382,6 +1384,8 @@
if (((chromType == CHROMOSOME_X && p == 1) ||
(chromType == CHROMOSOME_Y && p == 0)) && ind->sex() == MALE)
continue;
+ if (chromType == MITOCHONDRIAL && p > 0)
+ continue;
for (size_t idx = 0; idx < nLoci; ++idx)
haplotype[idx] = ind->allele(loci[idx], p);
haplotypes[haplotype]++;
@@ -2202,6 +2206,8 @@
if (ply == 2 && ((chromTypes[idx] == CHROMOSOME_X && p == 1) ||
(chromTypes[idx] == CHROMOSOME_Y && p == 0)) && ind->sex() == MALE)
continue;
+ if (chromTypes[idx] == MITOCHONDRIAL && p > 0)
+ continue;
alleleCnt[idx][*(geno + loci[idx])]++;
}
// haplotype frequency
@@ -2212,6 +2218,8 @@
if (((chromType == CHROMOSOME_X && p == 1) ||
(chromType == CHROMOSOME_Y && p == 0)) && ind->sex() == MALE)
continue;
+ if (chromType == MITOCHONDRIAL && p > 0)
+ continue;
haploCnt[idx][HAPLOCNT::key_type(*(geno + m_LD[idx][0]), *(geno + m_LD[idx][1]))]++;
}
}
@@ -2515,6 +2523,8 @@
if (ply == 2 && ((chromTypes[idx] == CHROMOSOME_X && p == 1) ||
(chromTypes[idx] == CHROMOSOME_Y && p == 0)) && ind->sex() == MALE)
continue;
+ if (chromTypes[idx] == MITOCHONDRIAL && p > 0)
+ continue;
if (ind->affected())
caseAlleleCnt[idx][*(geno + loci[idx])]++;
else
@@ -2527,7 +2537,7 @@
GenoIterator geno1 = ind->genoBegin(0);
GenoIterator geno2 = ind->genoBegin(1);
for (size_t idx = 0; idx < nLoci; ++idx) {
- if (chromTypes[idx] == CHROMOSOME_X || chromTypes[idx] == CHROMOSOME_Y)
+ if (chromTypes[idx] == CHROMOSOME_X || chromTypes[idx] == CHROMOSOME_Y || chromTypes[idx] == MITOCHONDRIAL)
continue;
Allele a1 = *(geno1 + loci[idx]);
Allele a2 = *(geno2 + loci[idx]);
@@ -2735,6 +2745,8 @@
if (((chromType == CHROMOSOME_X && p == 1) ||
(chromType == CHROMOSOME_Y && p == 0)) && ind->sex() == MALE)
continue;
+ if (chromType == MITOCHONDRIAL && p > 0)
+ continue;
for (size_t idx = 0; idx < nLoci; ++idx)
haplotype[idx] = ToAllele(ind->allele(loci[idx], p));
allHaplotypes.push_back(haplotype);
@@ -2926,7 +2938,7 @@
#ifndef OPTIMIZED
for (size_t idx = 0; idx < loci.size(); ++idx) {
size_t chromType = pop.chromType(pop.chromLocusPair(loci[idx]).first);
- DBG_FAILIF(chromType == CHROMOSOME_X || chromType == CHROMOSOME_Y, ValueError,
+ DBG_FAILIF(chromType == CHROMOSOME_X || chromType == CHROMOSOME_Y || chromType == MITOCHONDRIAL, ValueError,
"Fst can not be esimated from markers on sex chromosomes");
}
#endif
@@ -3079,8 +3091,8 @@
#ifndef OPTIMIZED
for (size_t i = 0; i < loci.size(); ++i) {
size_t chromType = pop.chromType(pop.chromLocusPair(loci[i]).first);
- DBG_FAILIF(chromType == CHROMOSOME_X || chromType == CHROMOSOME_Y, ValueError,
- "Can not run HWE test on loci on sex chromosomes.");
+ DBG_FAILIF(chromType == CHROMOSOME_X || chromType == CHROMOSOME_Y || chromType == MITOCHONDRIAL, ValueError,
+ "Can not run HWE test on loci on sex and mitochondrial chromosomes.");
}
#endif
// count for all specified subpopulations
Modified: trunk/src/transmitter.cpp
===================================================================
--- trunk/src/transmitter.cpp 2012-02-22 19:03:33 UTC (rev 4377)
+++ trunk/src/transmitter.cpp 2012-02-22 22:24:07 UTC (rev 4378)
@@ -387,8 +387,12 @@
GenoTransmitter::initialize(ind);
if (m_chroms.allAvail()) {
for (size_t ch = 0; ch < ind.numChrom(); ++ch)
- if (ind.chromType(ch) == CUSTOMIZED)
+ if (ind.chromType(ch) == MITOCHONDRIAL)
m_mitoChroms.push_back(ch);
+ if (m_mitoChroms.empty())
+ for (size_t ch = 0; ch < ind.numChrom(); ++ch)
+ if (ind.chromType(ch) == CUSTOMIZED)
+ m_mitoChroms.push_back(ch);
} else
m_mitoChroms = m_chroms.elems();
DBG_DO(DBG_TRANSMITTER, cerr << "Mitochondrial chromosomes " << m_mitoChroms << endl);
Modified: trunk/src/transmitter.h
===================================================================
--- trunk/src/transmitter.h 2012-02-22 19:03:33 UTC (rev 4377)
+++ trunk/src/transmitter.h 2012-02-22 22:24:07 UTC (rev 4378)
@@ -367,8 +367,10 @@
};
-/** This geno transmitter assumes that the first homologous copy of several (or
- * all) \c Customized chromosomes are copies of mitochondrial chromosomes. It
+/** This geno transmitter transmits the first homologous copy of \c Mitochondrial
+ * chromosomes. For backward-compatibility, it assumes that the first homologous
+ * copy of several (or all) \c Customized chromosomes are copies of mitochondrial
+ * chromosomes if no chromosome of type \c Mitochondrial is specified. This operator
* transmits these chromosomes randomly from the female parent to offspring.
* If this transmitter is applied to populations with more than one homologous
* copies of chromosomes, it transmits the first homologous copy of
@@ -377,8 +379,9 @@
class MitochondrialGenoTransmitter : public GenoTransmitter
{
public:
- /** Createa a mitochondrial genotype transmitter that treats all Customized
- * chromosomes, or a list of chromosomes specified by \e chroms, as human
+ /** Createa a mitochondrial genotype transmitter that treats all Mitochondiral
+ * chromosomes, Customized chromosomes if no Mitochondrial chromosomes are
+ * specified, or a list of chromosomes specified by \e chroms, as human
* mitochondrial chromosomes. These chromosomes should have the same
* length and the same number of loci. This operator transmits these
* chromosomes randomly from the female parent to offspring of both sexes.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <si...@us...> - 2012-02-23 03:27:05
|
Revision: 4381
http://simupop.svn.sourceforge.net/simupop/?rev=4381&view=rev
Author: simupop
Date: 2012-02-23 03:26:59 +0000 (Thu, 23 Feb 2012)
Log Message:
-----------
Force all mitochondrial DNAs to have the same length
Modified Paths:
--------------
trunk/src/__init__.py
trunk/src/genoStru.cpp
trunk/test/test_00_genoStru.py
Modified: trunk/src/__init__.py
===================================================================
--- trunk/src/__init__.py 2012-02-22 22:54:23 UTC (rev 4380)
+++ trunk/src/__init__.py 2012-02-23 03:26:59 UTC (rev 4381)
@@ -39,6 +39,7 @@
'AUTOSOME',
'CHROMOSOME_X',
'CHROMOSOME_Y',
+ 'MITOCHONDRIAL',
#
'CONSTANT',
'BINOMIAL_DISTRIBUTION',
Modified: trunk/src/genoStru.cpp
===================================================================
--- trunk/src/genoStru.cpp 2012-02-22 22:54:23 UTC (rev 4380)
+++ trunk/src/genoStru.cpp 2012-02-23 03:26:59 UTC (rev 4381)
@@ -257,12 +257,17 @@
"Chromosome X and Y should be both present for sexual transmission to work.");
//
m_mitochondrial.clear();
+ size_t mt_len = 0;
for (size_t i = 0; i < m_chromTypes.size(); ++i) {
if (m_chromTypes[i] == MITOCHONDRIAL) {
DBG_FAILIF(!m_mitochondrial.empty() && m_mitochondrial.back() != i - 1,
ValueError,
"There can be several mitochondrial chromosmes, but they need to be adjacent to each other.");
m_mitochondrial.push_back(static_cast<ULONG>(i));
+ if (mt_len == 0)
+ mt_len = m_numLoci[i];
+ else if (m_numLoci[i] != mt_len)
+ throw ValueError("All mitochondrial DNAs should have the same length");
}
}
//
Modified: trunk/test/test_00_genoStru.py
===================================================================
--- trunk/test/test_00_genoStru.py 2012-02-22 22:54:23 UTC (rev 4380)
+++ trunk/test/test_00_genoStru.py 2012-02-23 03:26:59 UTC (rev 4381)
@@ -183,14 +183,18 @@
def testChromType(self):
'Testing genoStruTrait::chromType(chron), chromTypes()'
- pop = Population(size=100, ploidy=2, loci=[2, 3, 2, 4],
- chromTypes=[AUTOSOME, CHROMOSOME_X, CHROMOSOME_Y, CUSTOMIZED])
+ pop = Population(size=100, ploidy=2, loci=[2, 3, 2, 4, 4],
+ chromTypes=[AUTOSOME, CHROMOSOME_X, CHROMOSOME_Y, MITOCHONDRIAL, CUSTOMIZED])
self.assertEqual(pop.chromType(0), AUTOSOME)
self.assertEqual(pop.chromType(1), CHROMOSOME_X)
self.assertEqual(pop.chromType(2), CHROMOSOME_Y)
- self.assertEqual(pop.chromType(3), CUSTOMIZED)
+ self.assertEqual(pop.chromType(3), MITOCHONDRIAL)
+ self.assertEqual(pop.chromType(4), CUSTOMIZED)
self.assertRaises(ValueError, Population, ploidy=4,
chromTypes=[AUTOSOME, CHROMOSOME_X, CHROMOSOME_Y, CUSTOMIZED])
+ #
+ self.assertRaises(ValueError, Population, loci=[3, 4],
+ chromTypes=[MITOCHONDRIAL]*2)
def testNumChrom(self):
'Testing genoStruTrait::numChrom()'
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <si...@us...> - 2012-02-23 05:01:32
|
Revision: 4382
http://simupop.svn.sourceforge.net/simupop/?rev=4382&view=rev
Author: simupop
Date: 2012-02-23 05:01:25 +0000 (Thu, 23 Feb 2012)
Log Message:
-----------
Add a test for selection over mitochondrial DNAs
Modified Paths:
--------------
trunk/src/selector.h
trunk/test/test_09_selection.py
Modified: trunk/src/selector.h
===================================================================
--- trunk/src/selector.h 2012-02-23 03:26:59 UTC (rev 4381)
+++ trunk/src/selector.h 2012-02-23 05:01:25 UTC (rev 4382)
@@ -182,7 +182,8 @@
* \c ALL_AVAIL. For each individual (parents if this operator is applied
* before mating, and offspring if this operator is applied during
* mating), genotypes at \e loci are collected one by one (e.g.
- * p0_loc0, p1_loc0, p0_loc1, p1_loc1... for a diploid individual) and
+ * p0_loc0, p1_loc0, p0_loc1, p1_loc1... for a diploid individual, with
+ * number of alleles varying for sex and mitochondrial DNAs) and
* are looked up in the dictionary. If a genotype cannot be found, it
* will be looked up again without phase information (e.g.
* <tt>(1,0)</tt> will match key <tt>(0,1)</tt>). If the genotype
Modified: trunk/test/test_09_selection.py
===================================================================
--- trunk/test/test_09_selection.py 2012-02-23 03:26:59 UTC (rev 4381)
+++ trunk/test/test_09_selection.py 2012-02-23 05:01:25 UTC (rev 4382)
@@ -115,6 +115,26 @@
self.assertEqual(ind.fitness, 0.9)
elif ind.allele(2,1) == 2 and ind.sex() == MALE:
self.assertEqual(ind.fitness, 0.8)
+ # mitochondrial DNA
+ pop = Population(size=1000, loci=[1, 2, 2], infoFields=['a', 'fitness', 'b'],
+ chromTypes=[AUTOSOME, MITOCHONDRIAL, MITOCHONDRIAL])
+ initSex(pop)
+ initGenotype(pop, freq=[.2, 0, .8])
+ MapSelector(loci=[2], fitness={(0,):0.9, (1,):0.8}).apply(pop)
+ for ind in pop.individuals():
+ if ind.allele(2,0) == 0:
+ self.assertEqual(ind.fitness, 0.9)
+ elif ind.allele(2,0) == 1:
+ self.assertEqual(ind.fitness, 0.8)
+ #
+ MapSelector(loci=[2], fitness={(0,):0.9, (1,):0.8, ():1}).apply(pop)
+ for ind in pop.individuals():
+ if ind.sex() == FEMALE:
+ self.assertEqual(ind.fitness, 1.0)
+ elif ind.allele(2,1) == 0 and ind.sex() == MALE:
+ self.assertEqual(ind.fitness, 0.9)
+ elif ind.allele(2,1) == 2 and ind.sex() == MALE:
+ self.assertEqual(ind.fitness, 0.8)
# multiple loci
pop = Population(size=1000, loci=[1, 2], infoFields=['a', 'fitness', 'b'],
chromTypes=[CHROMOSOME_X, CHROMOSOME_Y])
@@ -211,6 +231,19 @@
self.assertEqual(ind.fitness, 0.9)
elif ind.allele(2,1) == 2 and ind.sex() == MALE:
self.assertEqual(ind.fitness, 0.8)
+ # mitochondrial DNA
+ pop = Population(size=1000, loci=[1, 2, 2], infoFields=['a', 'fitness', 'b'],
+ chromTypes=[AUTOSOME, MITOCHONDRIAL, MITOCHONDRIAL])
+ initSex(pop)
+ initGenotype(pop, freq=[.2, 0, .8])
+ MapSelector(loci=[2], fitness={(0,):0.9, (1,):0.8, (2,):0.4}).apply(pop)
+ for ind in pop.individuals():
+ if ind.allele(2,0) == 0:
+ self.assertEqual(ind.fitness, 0.9)
+ elif ind.allele(2,0) == 1:
+ self.assertEqual(ind.fitness, 0.8)
+ elif ind.allele(2,0) == 2:
+ self.assertEqual(ind.fitness, 0.4)
# multiple loci
pop = Population(size=1000, loci=[1, 2], infoFields=['a', 'fitness', 'b'],
chromTypes=[CHROMOSOME_X, CHROMOSOME_Y])
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <si...@us...> - 2012-02-23 17:21:03
|
Revision: 4383
http://simupop.svn.sourceforge.net/simupop/?rev=4383&view=rev
Author: simupop
Date: 2012-02-23 17:20:52 +0000 (Thu, 23 Feb 2012)
Log Message:
-----------
Allow only one mitochondrial chromosome, add a section in the user's guide to discuss how to simulate one or multiple copies of mtDNAs
Modified Paths:
--------------
trunk/doc/userGuide.lyx
trunk/doc/userGuide.py
trunk/src/genoStru.cpp
trunk/src/genoStru.h
trunk/src/transmitter.cpp
trunk/src/transmitter.h
Modified: trunk/doc/userGuide.lyx
===================================================================
--- trunk/doc/userGuide.lyx 2012-02-23 05:01:25 UTC (rev 4382)
+++ trunk/doc/userGuide.lyx 2012-02-23 17:20:52 UTC (rev 4383)
@@ -3425,7 +3425,8 @@
\end_layout
\begin_layout Subsection
-Autosomes, sex chromosomes, and other types of chromosomes *
+Autosomes, sex chromosomes, mitochondrial, and other types of chromosomes
+ *
\end_layout
\begin_layout Standard
@@ -3434,13 +3435,13 @@
normal
\emph default
chromosomes in diploid, and in haploid populations.
- simuPOP supports three other types of chromosomes, namely
+ simuPOP supports four other types of chromosomes, namely
\emph on
chromosome X
\emph default
,
\emph on
-chromosome Y
+chromosome Y, mitochondrial,
\emph default
and
\emph on
@@ -3449,6 +3450,8 @@
chromosome types.
Sex chromosomes are only valid in haploid populations where chromosomes
X and Y are used to determine the sex of an offspring.
+ Mitochondrial DNAs can exists in haploid or diploid populations, and are
+ inherited maternally.
Customized chromosomes rely on user defined functions and operators to
be passed from parents to offspring.
\end_layout
@@ -3504,9 +3507,31 @@
\end_layout
\begin_layout Standard
-As an advanced feature of simuPOP, chromosomes that do not follow the inheritanc
-e patterns of autosomes or sex chromosomes can be handled separately (see
- section
+The evolution of mitochonrial DNAs follow the following rules
+\end_layout
+
+\begin_layout Itemize
+There can be only one copy of mitochondrial DNA, exists for both males and
+ females.
+\end_layout
+
+\begin_layout Itemize
+In a non-haploid population where all chromosomes have multiple homologous
+ copies, only the first copy is used for mitochondrial DNA.
+\end_layout
+
+\begin_layout Itemize
+mtDNAs are inherited maternally
+\end_layout
+
+\begin_layout Standard
+Customized chromosomes are used to model more complex types of chromosomes.
+ They rely on customized operators for inheritence.
+ For example, if you would like to model multiple copies of mitochondrial
+ DNAs (cytohets with multiple organellar chromosomes) in a cell, and the
+ process of genetic drift of somatic cytoplasmic segregation of mtDNAs,
+ you can use multiple customized chromosomes to model multiple cytohets
+ (see section
\begin_inset CommandInset ref
LatexCommand ref
reference "sub:Pre-defined-genotype-transmitters"
@@ -11444,9 +11469,9 @@
\family typewriter
MitochondrialGenoTransmitter
\family default
-: Treat all customized chromosomes or specified chromosomes as mitochondrial
- chromosomes and transmit maternal mitochondrial chromosomes randomly to
- an offspring.
+: Treat a single mitochondrial chromosome, or all customized chromosomes,
+ or specified chromosomes as mitochondrial chromosomes and transmit maternal
+ mitochondrial chromosomes randomly to an offspring.
This genotype transmitter can be applied to populations of
\series bold
any ploidy
@@ -25019,6 +25044,167 @@
\end_layout
\begin_layout Section
+Simulation of mitochondrial DNAs (mtDNAs)
+\end_layout
+
+\begin_layout Standard
+Mitochondrial DNAs resides in human mitochondrion.
+ A zygote inherits its organelles from the cytoplasm of the egg, and thus
+ organelle inheritance is generally maternal.
+ Whereas there is only one copy of a nuclear chromosome per gamete, there
+ are man copies of an organellar chromosome, forming a population of identical
+ organelle chromosomes that is transmitted to the offspring through the
+ egg.
+ Because these organellar chromosomes are identical, they are modelled in
+ simuPOP as a single chromosome with type
+\family typewriter
+MITOCHONDRIAL
+\family default
+.
+ In order to simulate mitochondrial DNAs, it is important to remember:
+\end_layout
+
+\begin_layout Itemize
+
+\family typewriter
+MendelianGenoTransmitter
+\family default
+ and
+\family typewriter
+Recombinator
+\family default
+ do not handle mitochondrial DNAs so you will have to explicitly use
+\family typewriter
+MitochondrialGenoTransmitter
+\family default
+ to transmit the mitochondrial DNAs from mother to offspring.
+ Note that
+\family typewriter
+CloneGenoTransmitter
+\family default
+ is a special transmitter that will copy everything including sex, information
+ fields to offspring.
+\end_layout
+
+\begin_layout Itemize
+The
+\family typewriter
+Stat
+\family default
+ operator recognizes this chromosome type and will report allele, haplotype,
+ and genotype counts, and other statistics correctly, although some diploid-spec
+ific statistics are not applicable.
+\end_layout
+
+\begin_layout Itemize
+Natural selections on mtDNAs is usually performed using operator
+\family typewriter
+MapSelector
+\family default
+ where single alleles are assigned a fitness value.
+ Operator
+\family typewriter
+MaSelector
+\family default
+ assumes two alleles and is not applicable.
+\end_layout
+
+\begin_layout Standard
+Example
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "mitochondrial"
+
+\end_inset
+
+ demonstrates the use of a
+\family typewriter
+Recombinator
+\family default
+ to recombine an autosome and two sex chromosomes, and a
+\family typewriter
+MitochondrialGenoTransmitter
+\family default
+ to transmit mitochondrial chromosomes.
+ Natural selection is applied to allele 3 at the 3rd locus on the mitochondrial
+ DNA, whose frequency in the population decreases as a result.
+\end_layout
+
+\begin_layout Standard
+\begin_inset CommandInset include
+LatexCommand lstinputlisting
+filename "log/mitochondrial.log"
+lstparams "caption={Transmission of mitochondrial chromosomes},label={mitochondrial}"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+You might wonder how a mutation can change the allele of all organelles
+ in the mitochondrion.
+ This is generally believed to be done through natural drift during cytoplasmic
+ segreagation, which is not a mitotic process because it takes place in
+ dividing asexual cells.
+ Because only one mitochondrial chromosome is allowed in simuPOP, you will
+ have to use customized chromosome types if you would like to simulate this
+ process.
+ Fortunately, operator
+\family typewriter
+MitochondrialGenoTransmitter
+\family default
+ can select random organelles from multiple customized chromosomes, if no
+ chromosome of type
+\family typewriter
+MITOCHONDRIAL
+\family default
+ is present.
+
+\end_layout
+
+\begin_layout Standard
+Example
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "mtDNA_evolve"
+
+\end_inset
+
+ demonstrates the fixation of mutant in cells with multiple organelles.
+ Althogh mutations are introduced to only one of the organelles, after a
+ number of cell divisions, the majority of the cells now have only one type
+ of allele.
+ This example uses a
+\family typewriter
+RandomSelection
+\family default
+ mating scheme to select cells randomly from the parental population.
+ Because no sexual reproduction is involved,
+\family typewriter
+MitochondrialGenoTransmitter
+\family default
+ passes the parental genotype to offspring regardless of sex of parent.
+ This example also demonstrates a disadvantage of using customized chromosomes
+ in that you will have to calculate statistics by yourself because only
+ you know the meaning of these chromosomes.
+ In this example, a function is written to count the number of mutants in
+ each cell (individual), and summarize the number of cells with 0, 1, 2,
+ 3, 4, and 5 copies of the mutant.
+\end_layout
+
+\begin_layout Standard
+\begin_inset CommandInset include
+LatexCommand lstinputlisting
+filename "log/mtDNA_evolve.log"
+lstparams "caption={Evolution of multiple organelles in mitochondrion},label={mtDNA_evolve}"
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section
Import and export dataset in other formats
\end_layout
@@ -25633,7 +25819,7 @@
\end_layout
\begin_layout Subsection
-Pre-defined genotype transmitters *
+Genotype transmitters *
\begin_inset CommandInset label
LatexCommand label
name "sub:Pre-defined-genotype-transmitters"
@@ -25661,80 +25847,6 @@
\end_layout
\begin_layout Standard
-All genotype transmitters only handle known chromosome types such as
-\family typewriter
-AUTOSOME
-\family default
-,
-\family typewriter
-CHROMOSOME_X
-\family default
- and
-\family typewriter
-CHROMOSOME_Y
-\family default
-.
- Customized chromosomes are left untouched because simuPOP does not know
- how they should be transmitted from parents to offspring.
- In case that Customized chromosomes are treated as mitochondrial chromosomes,
- a
-\family typewriter
-MitochondrialGenoTransmitter
-\family default
- can be used to transmit customized chromosomes randomly from mother to
- offspring.
- Example
-\begin_inset CommandInset ref
-LatexCommand ref
-reference "mitochondrial.log"
-
-\end_inset
-
- demonstrates the use of a
-\family typewriter
-Recombinator
-\family default
- to recombine an autosome and two sex chromosomes, and a
-\family typewriter
-MitochondrialGenoTransmitter
-\family default
- to transmit mitochondrial chromosomes.
- Note that the default
-\family typewriter
-MendelianGenoTransmitter
-\family default
- is replaced by these two operators.
- It will be (wastefully) applied if the new during-mating operators are
- used in the
-\family typewriter
-Simulator.evolve
-\family default
- function.
-\end_layout
-
-\begin_layout Standard
-\begin_inset CommandInset include
-LatexCommand lstinputlisting
-filename "log/mitochondrial.log"
-lstparams "caption={Transmission of mitochondrial chromosomes},label={mitochondrial.log}"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Subsection
-Customized genotype transmitter **
-\begin_inset CommandInset label
-LatexCommand label
-name "sub:Customized-genotype-transmitter"
-
-\end_inset
-
-
-\end_layout
-
-\begin_layout Standard
Although simuPOP provides a number of genotype transmitters, they may still
be cases where customized genotype transmitter is needed.
For example, a Recombinator can be used to recombine parental chromosomes
Modified: trunk/doc/userGuide.py
===================================================================
--- trunk/doc/userGuide.py 2012-02-23 05:01:25 UTC (rev 4382)
+++ trunk/doc/userGuide.py 2012-02-23 17:20:52 UTC (rev 4383)
@@ -219,8 +219,9 @@
#begin_ignore
sim.setRNG(seed=12345)
#end_ignore
-pop = sim.Population(size=6, ploidy=2, loci=[3, 3, 6, 4, 4, 4],
- chromTypes=[sim.AUTOSOME]*2 + [sim.CHROMOSOME_X, sim.CHROMOSOME_Y] + [sim.CUSTOMIZED]*2)
+pop = sim.Population(size=6, ploidy=2, loci=[3, 3, 3, 2, 2, 4, 4],
+ chromTypes=[sim.AUTOSOME]*2 + [sim.CHROMOSOME_X, sim.CHROMOSOME_Y, sim.MITOCHONDRIAL]
+ + [sim.CUSTOMIZED]*2)
sim.initGenotype(pop, freq=[0.3, 0.7])
sim.dump(pop, structure=False) # does not display genotypic structure information
#end_file
@@ -3488,7 +3489,7 @@
sim.setRNG(seed=12345)
#end_ignore
pop = sim.Population(1000, loci=[5]*4,
- chromTypes=[sim.AUTOSOME, sim.CHROMOSOME_X, sim.CHROMOSOME_Y, sim.CUSTOMIZED])
+ chromTypes=[sim.AUTOSOME, sim.CHROMOSOME_X, sim.CHROMOSOME_Y, sim.MITOCHONDRIAL])
pop.setVirtualSplitter(sim.SexSplitter())
pop.evolve(
initOps=[
@@ -3504,7 +3505,7 @@
sim.Stat(neutrality=range(5)),
sim.Stat(neutrality=range(5, 10), suffix='_X'),
sim.Stat(neutrality=range(10, 15), suffix='_Y'),
- sim.Stat(neutrality=range(15, 20), subPops=[(0, 'Female')], suffix='_mt'),
+ sim.Stat(neutrality=range(15, 20), suffix='_mt'),
sim.PyEval(r'"%.3f %.3f %.3f %.3f\n" % (Pi, Pi_X, Pi_Y, Pi_mt)'),
],
gen = 2
@@ -5394,7 +5395,73 @@
#end_file
+#begin_file log/mitochondrial.py
+#begin_ignore
+import simuOpt
+simuOpt.setOptions(quiet=True)
+#end_ignore
+import simuPOP as sim
+#begin_ignore
+sim.setRNG(seed=12345)
+#end_ignore
+pop = sim.Population(1000, loci=[5]*4,
+ # one autosome, two sex chromosomes, and one mitochondrial chromosomes
+ chromTypes=[sim.AUTOSOME, sim.CHROMOSOME_X, sim.CHROMOSOME_Y, sim.MITOCHONDRIAL],
+ infoFields=['fitness'])
+pop.evolve(
+ initOps=[
+ sim.InitSex(),
+ sim.InitGenotype(freq=[0.25]*4)
+ ],
+ preOps=[
+ sim.MapSelector(loci=17, fitness={(0,): 1, (1,): 1, (2,): 1, (3,): 0.4})
+ ],
+ matingScheme=sim.RandomMating(ops= [
+ sim.Recombinator(rates=0.1),
+ sim.MitochondrialGenoTransmitter(),
+ ]),
+ postOps=[
+ sim.Stat(alleleFreq=17, step=10),
+ sim.PyEval(r'"%.2f %.2f %.2f %.2f\n" % (alleleNum[17][0],'
+ 'alleleNum[17][1], alleleNum[17][2], alleleNum[17][3])', step=10),
+ ],
+ gen = 100
+)
+#end_file
+#begin_file log/mtDNA_evolve.py
+#begin_ignore
+import simuOpt
+simuOpt.setOptions(quiet=True)
+#end_ignore
+import simuPOP as sim
+#begin_ignore
+sim.setRNG(seed=12345)
+#end_ignore
+
+def alleleCount(pop):
+ summary = [0]* 6
+ for ind in pop.individuals():
+ geno = ind.genotype(ploidy=0)
+ summary[geno[0] + geno[2] + geno[4] + geno[6] + geno[8]] += 1
+ print('%d %s' % (pop.dvars().gen, summary))
+ return True
+
+pop = sim.Population(1000, loci=[2]*5, chromTypes=[sim.CUSTOMIZED]*5)
+pop.evolve(
+ # every one has miDNAs 10, 00, 00, 00, 00
+ initOps=[
+ sim.InitGenotype(haplotypes=[[1]+[0]*9]),
+ ],
+ # random select cells for cytoplasmic segregation
+ matingScheme=sim.RandomSelection(ops= [
+ sim.MitochondrialGenoTransmitter(),
+ ]),
+ postOps=sim.PyOperator(func=alleleCount, step=10),
+ gen = 51
+)
+#end_file
+
#begin_file log/importData.py
#begin_ignore
import simuOpt
@@ -5577,34 +5644,6 @@
)
#end_file
-#begin_file log/mitochondrial.py
-#begin_ignore
-import simuOpt
-simuOpt.setOptions(quiet=True)
-#end_ignore
-import simuPOP as sim
-#begin_ignore
-sim.setRNG(seed=12345)
-#end_ignore
-pop = sim.Population(10, loci=[5]*5,
- # one autosome, two sex chromosomes, and two mitochondrial chromosomes
- chromTypes=[sim.AUTOSOME, sim.CHROMOSOME_X, sim.CHROMOSOME_Y] + [sim.CUSTOMIZED]*2,
- infoFields=['father_idx', 'mother_idx'])
-pop.evolve(
- initOps=[
- sim.InitSex(),
- sim.InitGenotype(freq=[0.4] + [0.2]*3)
- ],
- matingScheme=sim.RandomMating(ops= [
- sim.Recombinator(rates=0.1),
- sim.MitochondrialGenoTransmitter(),
- sim.ParentsTagger()
- ]),
- postOps=sim.Dumper(structure=False),
- gen = 2
-)
-#end_file
-
#begin_file log/sexSpecificRec.py
#begin_ignore
import simuOpt
Modified: trunk/src/genoStru.cpp
===================================================================
--- trunk/src/genoStru.cpp 2012-02-23 05:01:25 UTC (rev 4382)
+++ trunk/src/genoStru.cpp 2012-02-23 17:20:52 UTC (rev 4383)
@@ -256,14 +256,13 @@
DBG_WARNIF(m_chromX * m_chromY < 0,
"Chromosome X and Y should be both present for sexual transmission to work.");
//
- m_mitochondrial.clear();
+ m_mitochondrial = -1;
size_t mt_len = 0;
for (size_t i = 0; i < m_chromTypes.size(); ++i) {
if (m_chromTypes[i] == MITOCHONDRIAL) {
- DBG_FAILIF(!m_mitochondrial.empty() && m_mitochondrial.back() != i - 1,
- ValueError,
- "There can be several mitochondrial chromosmes, but they need to be adjacent to each other.");
- m_mitochondrial.push_back(static_cast<ULONG>(i));
+ DBG_ASSERT(m_mitochondrial == -1, ValueError,
+ "Only one mitochondrial chromosome can be specified");
+ m_mitochondrial = i;
if (mt_len == 0)
mt_len = m_numLoci[i];
else if (m_numLoci[i] != mt_len)
Modified: trunk/src/genoStru.h
===================================================================
--- trunk/src/genoStru.h 2012-02-23 05:01:25 UTC (rev 4382)
+++ trunk/src/genoStru.h 2012-02-23 17:20:52 UTC (rev 4383)
@@ -73,7 +73,7 @@
public:
/// CPPONLY serialization library requires a default constructor
GenoStructure() : m_ploidy(2), m_totNumLoci(0),
- m_numLoci(0), m_chromTypes(), m_chromX(-1), m_chromY(-1), m_mitochondrial(), m_customized(),
+ m_numLoci(0), m_chromTypes(), m_chromX(-1), m_chromY(-1), m_mitochondrial(-1), m_customized(),
m_haplodiploid(false), m_lociPos(0), m_chromIndex(0),
m_chromNames(), m_alleleNames(), m_lociNames(), m_lociNameMap(), m_infoFields(0),
m_refCount(0)
@@ -208,7 +208,7 @@
int m_chromY;
/// indexes of mitochondrial chromosomes
- vectoru m_mitochondrial;
+ int m_mitochondrial;
/// indexes of customized chromosomes
vectoru m_customized;
@@ -482,7 +482,7 @@
* Return the indexes of mitochondrial chromosomes.
* <group>2-chromosome</group>
*/
- vectoru mitochondrialChroms() const
+ int mitochondrial() const
{
DBG_FAILIF(m_genoStruIdx == MaxTraitIndex, SystemError,
"totNumLoci: You have not set genoStructure. Please use setGenoStrucutre to set such info.");
Modified: trunk/src/transmitter.cpp
===================================================================
--- trunk/src/transmitter.cpp 2012-02-23 05:01:25 UTC (rev 4382)
+++ trunk/src/transmitter.cpp 2012-02-23 17:20:52 UTC (rev 4383)
@@ -411,16 +411,23 @@
bool MitochondrialGenoTransmitter::applyDuringMating(Population & pop, Population & offPop, RawIndIterator offspring,
- Individual * /* dad */, Individual * mom) const
+ Individual * dad, Individual * mom) const
{
// if offspring does not belong to subPops, do nothing, but does not fail.
if (!applicableToAllOffspring() && !applicableToOffspring(offPop, offspring))
return true;
initializeIfNeeded(*offspring);
- (void)mom; // avoid a warning message of unused varible in optimized modules
- DBG_FAILIF(mom == NULL, ValueError,
- "MitochondrialGenoTransmitter requires valid female parent.");
+ Individual * parent = NULL;
+ if (dad != NULL && mom == NULL)
+ // the case of single parent inheritance. Does not care about sex.
+ parent = dad;
+ else if (dad != NULL && mom != NULL)
+ parent = mom;
+ else {
+ DBG_FAILIF(true, ValueError,
+ "MitochondrialGenoTransmitter requires single parent, or valid female parent.");
+ }
if (m_numLoci == 0)
return true;
@@ -431,12 +438,12 @@
vectoru::iterator it_end = m_mitoChroms.end();
for (; it != it_end; ++it) {
size_t src = getRNG().randInt(static_cast<ULONG>(m_mitoChroms.size()));
- GenoIterator par = mom->genoBegin(0, m_mitoChroms[src]);
+ GenoIterator par = parent->genoBegin(0, m_mitoChroms[src]);
GenoIterator off = offspring->genoBegin(0, *it);
#ifdef BINARYALLELE
copyGenotype(par, off, m_numLoci);
#else
- GenoIterator par_end = mom->genoEnd(0, m_mitoChroms[src]);
+ GenoIterator par_end = parent->genoEnd(0, m_mitoChroms[src]);
# ifdef MUTANTALLELE
simuPOP::copy(par, par_end, off);
# else
Modified: trunk/src/transmitter.h
===================================================================
--- trunk/src/transmitter.h 2012-02-23 05:01:25 UTC (rev 4382)
+++ trunk/src/transmitter.h 2012-02-23 17:20:52 UTC (rev 4383)
@@ -367,20 +367,22 @@
};
-/** This geno transmitter transmits the first homologous copy of \c Mitochondrial
- * chromosomes. For backward-compatibility, it assumes that the first homologous
- * copy of several (or all) \c Customized chromosomes are copies of mitochondrial
- * chromosomes if no chromosome of type \c Mitochondrial is specified. This operator
- * transmits these chromosomes randomly from the female parent to offspring.
- * If this transmitter is applied to populations with more than one homologous
- * copies of chromosomes, it transmits the first homologous copy of
- * chromosomes and clears alleles (set to zero) on other homologous copies.
+/** This geno transmitter transmits the first homologous copy of a \c Mitochondrial
+ * chromosome. If no mitochondrial chromosome is present, it assumes that the first
+ * homologous copy of several (or all) \c Customized chromosomes are copies of
+ * mitochondrial chromosomes. This operator transmits the mitochondrial chromosome
+ * from the female parent to offspring for sexsual reproduction, and any parent to
+ * offspring for asexual reproduction. If there are multiple chromosomes, the
+ * organelles are selected randomly. If this transmitter is applied to populations
+ * with more than one homologous copies of chromosomes, it transmits the first
+ * homologous copy of chromosomes and clears alleles (set to zero) on other
+ * homologous copies.
*/
class MitochondrialGenoTransmitter : public GenoTransmitter
{
public:
- /** Createa a mitochondrial genotype transmitter that treats all Mitochondiral
- * chromosomes, Customized chromosomes if no Mitochondrial chromosomes are
+ /** Createa a mitochondrial genotype transmitter that treats the Mitochondiral
+ * chromosome, or Customized chromosomes if no Mitochondrial chromosome is
* specified, or a list of chromosomes specified by \e chroms, as human
* mitochondrial chromosomes. These chromosomes should have the same
* length and the same number of loci. This operator transmits these
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <si...@us...> - 2012-02-23 21:43:04
|
Revision: 4386
http://simupop.svn.sourceforge.net/simupop/?rev=4386&view=rev
Author: simupop
Date: 2012-02-23 21:42:57 +0000 (Thu, 23 Feb 2012)
Log Message:
-----------
Extend the calculation of Fst/Gst to non-diploid population, sex chromosomes, and mitochondrial chromosomes
Modified Paths:
--------------
trunk/ChangeLog
trunk/doc/userGuide.lyx
trunk/src/stator.cpp
trunk/src/stator.h
Modified: trunk/ChangeLog
===================================================================
--- trunk/ChangeLog 2012-02-23 20:51:46 UTC (rev 4385)
+++ trunk/ChangeLog 2012-02-23 21:42:57 UTC (rev 4386)
@@ -11,6 +11,7 @@
sites.
- Add MITOCHONDRIAL as a natural chromosome type so that operators such as
Stat can handle them correctly.
+ - Extend Stat(structure) to handle haploid population and non-autosomal chromosomes.
BUG:
- Fix a bug that prevents the correct handling of population structure when evolving
Modified: trunk/doc/userGuide.lyx
===================================================================
--- trunk/doc/userGuide.lyx 2012-02-23 20:51:46 UTC (rev 4385)
+++ trunk/doc/userGuide.lyx 2012-02-23 21:42:57 UTC (rev 4386)
@@ -18516,6 +18516,9 @@
F_it
\family default
) .
+ When hetergozygote count is unavailable (non-diploid population, loci on
+ sex chromosomes and mitochondrial chromosomes), simuPOP uses expected heterozyg
+osity to estimate this quantity.
\end_layout
\begin_layout Standard
Modified: trunk/src/stator.cpp
===================================================================
--- trunk/src/stator.cpp 2012-02-23 20:51:46 UTC (rev 4385)
+++ trunk/src/stator.cpp 2012-02-23 21:42:57 UTC (rev 4386)
@@ -2932,16 +2932,14 @@
const vectoru & loci = m_loci.elems(&pop);
- DBG_ASSERT(pop.ploidy() == 2, ValueError,
- "Fst statistics is available only for diploid populations.");
-
-#ifndef OPTIMIZED
+ bool use_observed_het;
for (size_t idx = 0; idx < loci.size(); ++idx) {
size_t chromType = pop.chromType(pop.chromLocusPair(loci[idx]).first);
- DBG_FAILIF(chromType == CHROMOSOME_X || chromType == CHROMOSOME_Y || chromType == MITOCHONDRIAL, ValueError,
- "Fst can not be esimated from markers on sex chromosomes");
+ if (idx == 0)
+ use_observed_het = pop.ploidy() == 2 and (chromType == AUTOSOME || chromType == CUSTOMIZED);
+ else if ((pop.ploidy() == 2 and (chromType == AUTOSOME || chromType == CUSTOMIZED)) != use_observed_het)
+ throw ValueError("Structure statistics can only be estimated from loci on chromosomes of the same type, because other wise the observed number of alleles will be different.");
}
-#endif
// selected (virtual) subpopulatons.
subPopList subPops = m_subPops.expandFrom(pop);
@@ -2968,32 +2966,54 @@
ALLELES & alleles = allAlleles[idx];
size_t cnt = 0;
- // go through all alleles
- IndAlleleIterator a = pop.alleleIterator(loc, it->subPop());
- for (; a.valid(); ++cnt) {
- Allele a1 = *a++;
- Allele a2 = *a++;
- ++af[a1];
- ++af[a2];
- hf[a1] += a1 != a2;
- hf[a2] += a1 != a2;
- alleles[a1] = true;
- alleles[a2] = true;
- }
- // heterozygote frequency
- map<size_t, float>::iterator it = af.begin();
- map<size_t, float>::iterator itEnd = af.end();
- for (; it != itEnd; ++it)
- it->second /= 2 * cnt;
- // heterozygote frequency
- it = hf.begin();
- itEnd = hf.end();
- for (; it != itEnd; ++it)
- it->second /= cnt;
- //
- DBG_FAILIF(spSize != 0 && spSize != cnt, SystemError,
- "Subpopulation size counts are inconsistent. (locus not on autosome?)");
- spSize = cnt;
+ if (use_observed_het) {
+ // go through all alleles
+ IndAlleleIterator a = pop.alleleIterator(loc, it->subPop());
+ for (; a.valid(); ++cnt) {
+ Allele a1 = *a++;
+ Allele a2 = *a++;
+ ++af[a1];
+ ++af[a2];
+ hf[a1] += a1 != a2;
+ hf[a2] += a1 != a2;
+ alleles[a1] = true;
+ alleles[a2] = true;
+ }
+ // allele frequency
+ map<size_t, float>::iterator it = af.begin();
+ map<size_t, float>::iterator itEnd = af.end();
+ for (; it != itEnd; ++it)
+ it->second /= 2 * cnt;
+ // heterozygote frequency
+ it = hf.begin();
+ itEnd = hf.end();
+ for (; it != itEnd; ++it)
+ it->second /= cnt;
+ //
+ spSize = cnt;
+ } else {
+ // go through all alleles
+ IndAlleleIterator a = pop.alleleIterator(loc, it->subPop());
+ for (; a.valid(); ++cnt) {
+ Allele c = *a++;
+ ++af[c];
+ ++hf[c];
+ alleles[c] = true;
+ }
+ // allele frequency
+ map<size_t, float>::iterator it = af.begin();
+ map<size_t, float>::iterator itEnd = af.end();
+ for (; it != itEnd; ++it)
+ // h_a = 2 * f_a * (1 - f_a)
+ it->second /= cnt;
+ // heterozygote frequency calculate from allele frequency
+ it = hf.begin();
+ itEnd = hf.end();
+ for (; it != itEnd; ++it)
+ it->second = 2 * (it->second / cnt) * (1 - it->second / cnt);
+ //
+ spSize = cnt;
+ }
}
// (virtual) subpopulation size
n_i.push_back(spSize);
Modified: trunk/src/stator.h
===================================================================
--- trunk/src/stator.h 2012-02-23 20:51:46 UTC (rev 4385)
+++ trunk/src/stator.h 2012-02-23 21:42:57 UTC (rev 4386)
@@ -1239,6 +1239,14 @@
* than two alleles) and multi-loci cases. This statistics should
* be used if you would like to obtain a \e true Fst value of a large
* Population.
+ * Nei's Gst uses only allele frequency information so it is available
+ * for all population type (haploid, diploid etc). Weir and Cockerham's
+ * Fst uses heterozygosity frequency so it is best for autosome of
+ * diploid populations. For non-diploid population, sex, and mitochondrial
+ * DNAs, simuPOP uses expected heterozygosity (1 - sum p_i^2) when
+ * heterozygosity is needed. These statistics output the following
+ * variables:
+ *
* \li \c F_st (default) The WC84 \e Fst statistic estimated for all
* specified loci.
* \li \c F_is The WC84 \e Fis statistic estimated for all specified loci.
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <si...@us...> - 2012-02-24 04:19:40
|
Revision: 4388
http://simupop.svn.sourceforge.net/simupop/?rev=4388&view=rev
Author: simupop
Date: 2012-02-24 04:19:33 +0000 (Fri, 24 Feb 2012)
Log Message:
-----------
Fix tests
Modified Paths:
--------------
trunk/ChangeLog
trunk/src/selector.h
trunk/test/test_08_stat.py
trunk/test/test_09_selection.py
Modified: trunk/ChangeLog
===================================================================
--- trunk/ChangeLog 2012-02-24 01:54:04 UTC (rev 4387)
+++ trunk/ChangeLog 2012-02-24 04:19:33 UTC (rev 4388)
@@ -16,6 +16,7 @@
BUG:
- Fix a bug that prevents the correct handling of population structure when evolving
populations with changing population structure.
+ - Ensure 2^64 maximum allele states for the long module under 64 bit system
version 1.0.6 - Rev 4260 (July 11, 2011)
Major new feature:
Modified: trunk/src/selector.h
===================================================================
--- trunk/src/selector.h 2012-02-24 01:54:04 UTC (rev 4387)
+++ trunk/src/selector.h 2012-02-24 04:19:33 UTC (rev 4388)
@@ -268,8 +268,8 @@
* \li and in general 2**n for diploid and 3**n for haploid cases if there
* are \c n loci.
*
- * This operator does not support haplodiploid populations and sex
- * chromosomes.
+ * This operator does not support haplodiploid populations, sex and
+ * mitochondrial chromosomes.
*/
MaSelector(const lociList & loci, const vectorf & fitness, const uintList & wildtype = vectoru(1, 0),
int begin = 0, int end = -1, int step = 1,
Modified: trunk/test/test_08_stat.py
===================================================================
--- trunk/test/test_08_stat.py 2012-02-24 01:54:04 UTC (rev 4387)
+++ trunk/test/test_08_stat.py 2012-02-24 04:19:33 UTC (rev 4388)
@@ -426,7 +426,7 @@
for hap in [(0,1,4), (2,5)]:
homo = sum([[ind.allele(x, 0) for x in hap] == [ind.allele(x, 1) for x in hap] for ind in pop.individuals()])
self.assertEqual(pop.dvars().haploHeteroNum[hap], 6000 - homo)
- self.assertEqual(pop.dvars().haploHeteroFreq[hap], 1 - homo / 6000.)
+ self.assertAlmostEqual(pop.dvars().haploHeteroFreq[hap], 1 - homo / 6000., 6)
pop.setVirtualSplitter(SexSplitter())
stat(pop, haploHomoFreq=[(0,1,4), (2,5)], subPops=[(0,0)])
for hap in [(0,1,4), (2,5)]:
Modified: trunk/test/test_09_selection.py
===================================================================
--- trunk/test/test_09_selection.py 2012-02-24 01:54:04 UTC (rev 4387)
+++ trunk/test/test_09_selection.py 2012-02-24 04:19:33 UTC (rev 4388)
@@ -116,8 +116,8 @@
elif ind.allele(2,1) == 2 and ind.sex() == MALE:
self.assertEqual(ind.fitness, 0.8)
# mitochondrial DNA
- pop = Population(size=1000, loci=[1, 2, 2], infoFields=['a', 'fitness', 'b'],
- chromTypes=[AUTOSOME, MITOCHONDRIAL, MITOCHONDRIAL])
+ pop = Population(size=1000, loci=[1, 2], infoFields=['a', 'fitness', 'b'],
+ chromTypes=[AUTOSOME, MITOCHONDRIAL])
initSex(pop)
initGenotype(pop, freq=[.2, 0, .8])
MapSelector(loci=[2], fitness={(0,):0.9, (1,):0.8}).apply(pop)
@@ -232,8 +232,8 @@
elif ind.allele(2,1) == 2 and ind.sex() == MALE:
self.assertEqual(ind.fitness, 0.8)
# mitochondrial DNA
- pop = Population(size=1000, loci=[1, 2, 2], infoFields=['a', 'fitness', 'b'],
- chromTypes=[AUTOSOME, MITOCHONDRIAL, MITOCHONDRIAL])
+ pop = Population(size=1000, loci=[1, 2], infoFields=['a', 'fitness', 'b'],
+ chromTypes=[AUTOSOME, MITOCHONDRIAL])
initSex(pop)
initGenotype(pop, freq=[.2, 0, .8])
MapSelector(loci=[2], fitness={(0,):0.9, (1,):0.8, (2,):0.4}).apply(pop)
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|
|
From: <si...@us...> - 2012-02-24 14:24:41
|
Revision: 4390
http://simupop.svn.sourceforge.net/simupop/?rev=4390&view=rev
Author: simupop
Date: 2012-02-24 14:24:30 +0000 (Fri, 24 Feb 2012)
Log Message:
-----------
Fix a bug that prevents MlPenetrance from being used in the evolve function.
Modified Paths:
--------------
trunk/ChangeLog
trunk/src/penetrance.h
trunk/test/test_15_penetrance.py
Modified: trunk/ChangeLog
===================================================================
--- trunk/ChangeLog 2012-02-24 05:39:58 UTC (rev 4389)
+++ trunk/ChangeLog 2012-02-24 14:24:30 UTC (rev 4390)
@@ -16,6 +16,7 @@
BUG:
- Fix a bug that prevents the correct handling of population structure when evolving
populations with changing population structure.
+ - Fix a bug that prevents MlPenetrance from being used in the evolve function.
- Ensure 2^64 maximum allele states for the long module under 64 bit system
version 1.0.6 - Rev 4260 (July 11, 2011)
Modified: trunk/src/penetrance.h
===================================================================
--- trunk/src/penetrance.h 2012-02-24 05:39:58 UTC (rev 4389)
+++ trunk/src/penetrance.h 2012-02-24 14:24:30 UTC (rev 4390)
@@ -330,7 +330,7 @@
/// HIDDEN Deep copy of a multi-loci penetrance operator
virtual BaseOperator * clone() const
{
- throw ValueError("Multi-loci penetrance operator can not be nested.");
+ return new MlPenetrance(*this);
}
Modified: trunk/test/test_15_penetrance.py
===================================================================
--- trunk/test/test_15_penetrance.py 2012-02-24 05:39:58 UTC (rev 4389)
+++ trunk/test/test_15_penetrance.py 2012-02-24 14:24:30 UTC (rev 4390)
@@ -116,7 +116,6 @@
maPenetrance(pop, loci=[3,5], wildtype=0,
penetrance=[0, .3, .5, 0.3, 0.6, 0.8, 0.1, 1, 0.8])
-
def testMlPenetrance(self):
'Testing multi-locus penetrance'
pop = Population(1000, loci=[3,5], infoFields=['penetrance'])
@@ -140,6 +139,42 @@
mode=MULTIPLICATIVE
)
+ def testEvolveMaPenetrance(self):
+ 'Testing using MaPenetrance in evolve function'
+ pop = Population(1000, loci=[3,5])
+ pop.evolve(
+ initOps=[
+ InitSex(),
+ InitGenotype(freq=[.3, .7]),
+ ],
+ #
+ preOps= MaPenetrance(loci = 0, wildtype=0,
+ penetrance=[0, .3, .5]),
+ matingScheme=RandomMating(),
+ gen=4
+ )
+
+ def testEvolveMlPenetrance(self):
+ 'Testing using MlPenetrance in evolve function'
+ pop = Population(1000, loci=[3,5])
+ pop.evolve(
+ initOps=[
+ InitSex(),
+ InitGenotype(freq=[.3, .7]),
+ ],
+ #
+ preOps=MlPenetrance(ops=[
+ MaPenetrance(loci = 0, wildtype=0,
+ penetrance=[0, .3, .5]),
+ MapPenetrance(loci = 1,
+ penetrance={(0,0):0, (0,1):1, (1,1):1})
+ ],
+ mode=ADDITIVE
+ ),
+ matingScheme=RandomMating(),
+ gen=4
+ )
+
def testPyPenetrance(self):
'Testing python penetrance operator'
def pen(geno):
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|
|
From: <si...@us...> - 2012-02-27 22:45:27
|
Revision: 4397
http://simupop.svn.sourceforge.net/simupop/?rev=4397&view=rev
Author: simupop
Date: 2012-02-27 22:45:20 +0000 (Mon, 27 Feb 2012)
Log Message:
-----------
Re-enable openMP for macOSX with llvm-gcc 4.2 after adjusting the code to avoid a compiler failure
Modified Paths:
--------------
trunk/setup.py
trunk/src/operator.cpp
Modified: trunk/setup.py
===================================================================
--- trunk/setup.py 2012-02-27 04:52:06 UTC (rev 4396)
+++ trunk/setup.py 2012-02-27 22:45:20 UTC (rev 4397)
@@ -73,9 +73,6 @@
if int(version[0]) < 4 or int(version[1]) < 2:
print('Support for openMP is turned off because version %s.%s.%s of gcc does not support this feature' % version)
USE_OPENMP = False
- if int(version[0]) == 4 and int(version[1]) == 2 and int(version[2]) == 1 and 'LLVM' in output:
- print('Support for openMP is turned off because of a bug in LLVM-gcc version 4.2.1.')
- USE_OPENMP = False
except:
print('Can not obtain version of gcc, and openMP is disable')
USE_OPENMP = False
Modified: trunk/src/operator.cpp
===================================================================
--- trunk/src/operator.cpp 2012-02-27 04:52:06 UTC (rev 4396)
+++ trunk/src/operator.cpp 2012-02-27 22:45:20 UTC (rev 4397)
@@ -1058,12 +1058,14 @@
BaseOperator * opPtr = op.clone();
opPtr->initializeIfNeeded(*pop->rawIndBegin());
+ // NOTE: putting d and m in the applyDuringMating function will cause
+ // compiling error gor gcc/llvm under mac.
+ Individual * d = dad < 0 ? NULL : &pop->individual(static_cast<size_t>(dad));
+ Individual * m = mom < 0 ? NULL : &pop->individual(static_cast<size_t>(mom));
#pragma omp parallel for
// i needs to be int since some openMP implementation does not handle unsigned index
for (int i = static_cast<int>(off.first); i < static_cast<int>(off.second); ++i)
- opPtr->applyDuringMating(*pop, *offPop, pop->rawIndBegin() + i,
- dad < 0 ? NULL : &pop->individual(static_cast<size_t>(dad)),
- mom < 0 ? NULL : &pop->individual(static_cast<size_t>(mom)));
+ opPtr->applyDuringMating(*pop, *offPop, pop->rawIndBegin() + i, d, m);
}
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|
|
From: <ti...@us...> - 2012-03-01 17:15:39
|
Revision: 4403
http://simupop.svn.sourceforge.net/simupop/?rev=4403&view=rev
Author: tiwcpe8
Date: 2012-03-01 17:15:33 +0000 (Thu, 01 Mar 2012)
Log Message:
-----------
Add more test case in testMutants and fixed bug in mutants function
Modified Paths:
--------------
trunk/src/individual.cpp
trunk/test/test_01_individual.py
Modified: trunk/src/individual.cpp
===================================================================
--- trunk/src/individual.cpp 2012-02-28 23:17:30 UTC (rev 4402)
+++ trunk/src/individual.cpp 2012-03-01 17:15:33 UTC (rev 4403)
@@ -289,17 +289,21 @@
// has to be all chromosomes
DBG_FAILIF(beginCh != 0 || endCh != numChrom(), ValueError,
"If multiple ploidy are chosen, all chromosomes has to be chosen.");
- compressed_vector<Allele>::index_array_type::iterator idx_beginP = (m_genoPtr + beginP * totNumLoci()).getIndexIterator();
- compressed_vector<Allele>::index_array_type::iterator idx_endP = (m_genoPtr + endP * totNumLoci()).getIndexIterator();
- compressed_vector<Allele>::value_array_type::iterator value_beginP = (m_genoPtr + beginP * totNumLoci()).getValueIterator();
+ size_t begin = beginP * totNumLoci();
+ size_t end = endP * totNumLoci();
+ compressed_vector<Allele>::index_array_type::iterator idx_beginP = (m_genoPtr + begin).getIndexIterator();
+ compressed_vector<Allele>::index_array_type::iterator idx_endP = (m_genoPtr + end).getIndexIterator();
+ compressed_vector<Allele>::value_array_type::iterator value_beginP = (m_genoPtr + begin).getValueIterator();
mutantAllele.reserve(idx_endP - idx_beginP);
for(;idx_beginP != idx_endP; ++idx_beginP, ++value_beginP)
mutantAllele.push_back(std::pair<size_t, size_t>(*idx_beginP, *value_beginP));
return mutantAllele;
} else {
- compressed_vector<Allele>::index_array_type::iterator idx_beginP = (m_genoPtr + beginP * totNumLoci() + chromBegin(beginCh)).getIndexIterator();
- compressed_vector<Allele>::index_array_type::iterator idx_endP = (m_genoPtr + endP * totNumLoci() + chromEnd(endCh -1)).getIndexIterator();
- compressed_vector<Allele>::value_array_type::iterator value_beginP = (m_genoPtr + beginP * totNumLoci() + chromBegin(beginCh)).getValueIterator();
+ size_t begin = beginP * totNumLoci() + chromBegin(beginCh);
+ size_t end = beginP * totNumLoci() + chromEnd(endCh -1);
+ compressed_vector<Allele>::index_array_type::iterator idx_beginP = (m_genoPtr + begin).getIndexIterator();
+ compressed_vector<Allele>::index_array_type::iterator idx_endP = (m_genoPtr + end).getIndexIterator();
+ compressed_vector<Allele>::value_array_type::iterator value_beginP = (m_genoPtr + begin).getValueIterator();
mutantAllele.reserve(idx_endP - idx_beginP);
for(;idx_beginP != idx_endP; ++idx_beginP, ++value_beginP)
mutantAllele.push_back(std::pair<size_t, size_t>(*idx_beginP, *value_beginP));
@@ -435,8 +439,20 @@
for (size_t j = 0; j < chroms.size(); ++j) {
size_t chrom = chroms[j];
GenoIterator ptr = m_genoPtr + p * totNumLoci() + chromBegin(chrom);
+#ifdef MUTANTALLELE
+ mutant_vectora ctmp;
+ ctmp.resize(numLoci(chrom));
+ for (size_t i = 0; i < numLoci(chrom); i++, ++idx) {
+ Allele atmp = ToAllele(geno[idx % sz]);
+ if (atmp != 0)
+ ctmp.push_back(i, atmp);
+ }
+ simuPOP::copy(ctmp.begin(), ctmp.end(), ptr);
+#else
for (size_t i = 0; i < numLoci(chrom); i++, ++idx)
*(ptr + i) = ToAllele(geno[idx % sz]);
+#endif
+
}
}
}
Modified: trunk/test/test_01_individual.py
===================================================================
--- trunk/test/test_01_individual.py 2012-02-28 23:17:30 UTC (rev 4402)
+++ trunk/test/test_01_individual.py 2012-03-01 17:15:33 UTC (rev 4403)
@@ -14,9 +14,11 @@
from simuOpt import setOptions
setOptions(quiet=True)
new_argv = []
+alleleType = 'short'
for arg in sys.argv:
if arg in ['short', 'long', 'binary', 'mutant']:
setOptions(alleleType = arg)
+ alleleType = arg
elif arg.startswith('-j'):
setOptions(numThreads = int(arg[2:]))
else:
@@ -153,27 +155,37 @@
def testMutants(self):
'Testing individual::genotype(), genotype(p), genotype(p, chrom)'
- pop = self.getPop()
- ind = pop.individual(0)
- ind.setGenotype([2, 3, 4])
- gt = ind.mutants()
- self.assertEqual(gt, ((0,2),(1,3),(2,4),(3,2),(4,3),(5,4),(6,2),(7,3),(8,4),(9,2),(10,3),(11,4),(12,2),(13,3),(14,4),(15,2),(16,3),(17,4),(18,2),(19,3),(20,4),(21,2),(22,3),(23,4)))
- # ploidy 1
- gt = ind.mutants(1)
- self.assertEqual(gt, ((12,2),(13,3),(14,4),(15,2),(16,3),(17,4),(18,2),(19,3),(20,4),(21,2),(22,3),(23,4)))
- # ploidy 1, ch 1
- gt = ind.mutants(1, 1)
- self.assertEqual(gt, ((17,4),(18,2),(19,3),(20,4),(21,2),(22,3),(23,4)))
- #
- self.assertRaises(IndexError, ind.mutants, 2)
- self.assertRaises(IndexError, ind.mutants, 0, 2)
- # accept single form
- pop.setGenotype(1)
- self.assertEqual(pop.individual(0).allele(0), 1)
- pop.individual(0).setGenotype(0)
- self.assertEqual(pop.individual(0).allele(0), 0)
+ if alleleType == 'mutant':
+ pop = self.getPop()
+ ind = pop.individual(0)
+ ind.setGenotype([2, 3, 4])
+ gt = ind.mutants()
+ self.assertEqual(gt, ((0,2),(1,3),(2,4),(3,2),(4,3),(5,4),(6,2),(7,3),(8,4),(9,2),(10,3),(11,4),(12,2),(13,3),(14,4),(15,2),(16,3),(17,4),(18,2),(19,3),(20,4),(21,2),(22,3),(23,4)))
+ # ploidy 1
+ gt = ind.mutants(1)
+ self.assertEqual(gt, ((12,2),(13,3),(14,4),(15,2),(16,3),(17,4),(18,2),(19,3),(20,4),(21,2),(22,3),(23,4)))
+ # ploidy 1, ch 1
+ gt = ind.mutants(1, 1)
+ self.assertEqual(gt, ((17,4),(18,2),(19,3),(20,4),(21,2),(22,3),(23,4)))
+ #
+ self.assertRaises(IndexError, ind.mutants, 2)
+ self.assertRaises(IndexError, ind.mutants, 0, 2)
+ # accept single form
+ pop.setGenotype(1)
+ self.assertEqual(pop.individual(0).allele(0), 1)
+ pop.individual(0).setGenotype(0)
+ self.assertEqual(pop.individual(0).allele(0), 0)
+ # case: Genotype has zero value
+ ind.setGenotype([2, 0, 4, 0, 6])
+ gt = ind.mutants()
+ self.assertEqual(gt,((0, 2), (2, 4), (4, 6), (5, 2), (7, 4), (9, 6), (10, 2), (12, 4), (14, 6), (15, 2), (17, 4), (19, 6), (20, 2), (22, 4)))
+ gt = ind.mutants(1)
+ self.assertEqual(gt,((12, 4), (14, 6), (15, 2), (17, 4), (19, 6), (20, 2), (22, 4)))
+ gt = ind.mutants(1, 1)
+ self.assertEqual(gt,((17, 4), (19, 6), (20, 2), (22, 4)))
+
def testSetGenotype(self):
'Testing individual::setGenotype(geno), setgenotype(geno, p), '
'setGenotype(geno, p, chrom)'
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|
|
From: <si...@us...> - 2012-03-02 05:53:01
|
Revision: 4405
http://simupop.svn.sourceforge.net/simupop/?rev=4405&view=rev
Author: simupop
Date: 2012-03-02 05:52:54 +0000 (Fri, 02 Mar 2012)
Log Message:
-----------
Move RevertFixedSites from sandbox to the core
Modified Paths:
--------------
trunk/src/__init__.py
trunk/src/mutator.cpp
trunk/src/mutator.h
trunk/src/sandbox.cpp
trunk/src/sandbox.h
trunk/src/sandbox.py
trunk/test/test_03_operator.py
Modified: trunk/src/__init__.py
===================================================================
--- trunk/src/__init__.py 2012-03-01 21:17:49 UTC (rev 4404)
+++ trunk/src/__init__.py 2012-03-02 05:52:54 UTC (rev 4405)
@@ -174,6 +174,7 @@
'AminoAcidMutator',
'ContextMutator',
'KAlleleMutator',
+ 'RevertFixedSites',
#
'MapSelector',
'MaSelector',
@@ -237,6 +238,7 @@
'stepwiseMutate',
'snpMutate',
'acgtMutate',
+ 'revertFixedSites',
#
'stat',
#
@@ -1106,6 +1108,10 @@
'Function form of operator ``PointMutator``'
PointMutator(*args, **kwargs).apply(pop)
+def revertFixedSites(pop, *args, **kwargs):
+ 'Function form of operator ``RevertFixedSites``'
+ RevertFixedSites(*args, **kwargs).apply(pop)
+
def stat(pop, *args, **kwargs):
'''Apply operator ``Stat`` with specified parameters to population *pop*.
Resulting statistics could be accessed from the local namespace of ``pop``
Modified: trunk/src/mutator.cpp
===================================================================
--- trunk/src/mutator.cpp 2012-03-01 21:17:49 UTC (rev 4404)
+++ trunk/src/mutator.cpp 2012-03-02 05:52:54 UTC (rev 4405)
@@ -459,4 +459,44 @@
}
+bool RevertFixedSites::apply(Population & pop) const
+{
+ if (pop.popSize() == 0 || pop.totNumLoci() == 0)
+ return true;
+
+ const vectoru & loci = m_loci.elems(&pop);
+
+ const subPopList subPops = applicableSubPops(pop);
+ subPopList::const_iterator sp = subPops.begin();
+ subPopList::const_iterator spEnd = subPops.end();
+
+ for (; sp != spEnd; ++sp) {
+ if (sp->isVirtual())
+ pop.activateVirtualSubPop(*sp);
+
+ for (size_t idx = 0; idx < loci.size(); ++idx) {
+ size_t loc = loci[idx];
+ bool fixed = true;
+ IndAlleleIterator a = pop.alleleIterator(loc, sp->subPop());
+ for (; a.valid(); ++a) {
+ if (! (*a)) {
+ fixed = false;
+ break;
+ }
+ }
+ // revert fixed allele
+ if (fixed) {
+ IndAlleleIterator a = pop.alleleIterator(loc, sp->subPop());
+ for (; a.valid(); ++a)
+ *a = 0;
+ }
+ }
+
+ if (sp->isVirtual())
+ pop.deactivateVirtualSubPop(sp->subPop());
+ }
+ return true;
}
+
+
+}
Modified: trunk/src/mutator.h
===================================================================
--- trunk/src/mutator.h 2012-03-01 21:17:49 UTC (rev 4404)
+++ trunk/src/mutator.h 2012-03-02 05:52:54 UTC (rev 4405)
@@ -644,5 +644,59 @@
vectoru m_inds;
};
+
+/** This operator checks all loci of a population and revert a mutant to
+ * wildtype allele if it is fixed in the population. If a list of (virtual)
+ * subpopulations are specified, alleles are reverted in each subpopulation,
+ * regardless if the allele is fixed in other subpopulations.
+ */
+class RevertFixedSites : public BaseOperator
+{
+public:
+ /** Create an operator to revert alleles at fixed loci from value non-zero to zero.
+ * If parameter \e subPops are specified, only individuals in these subpopulations
+ * are considered.
+ */
+ RevertFixedSites(const lociList & loci = lociList(),
+ const stringFunc & output = "", int begin = 0, int end = -1, int step = 1,
+ const intList & at = vectori(),
+ const intList & reps = intList(), const subPopList & subPops = subPopList(),
+ const stringList & infoFields = vectorstr())
+ : BaseOperator("", begin, end, step, at, reps, subPops, infoFields),
+ m_loci(loci)
+ {
+ }
+
+
+ /// destructor
+ virtual ~RevertFixedSites()
+ {
+ }
+
+
+ /// HIDDEN Deep copy of a Migrator
+ virtual BaseOperator * clone() const
+ {
+ return new RevertFixedSites(*this);
+ }
+
+
+ /// HIDDEN apply the Migrator to populaiton \e pop.
+ virtual bool apply(Population & pop) const;
+
+ /// HIDDEN
+ string describe(bool format = true) const
+ {
+ (void)format; // avoid warning about unused parameter
+ return "Revert fixed alleles to wildtype allele if it is fixed in the population.";
+ }
+
+private:
+ lociList m_loci;
+
+};
+
+
+
}
#endif
Modified: trunk/src/sandbox.cpp
===================================================================
--- trunk/src/sandbox.cpp 2012-03-01 21:17:49 UTC (rev 4404)
+++ trunk/src/sandbox.cpp 2012-03-02 05:52:54 UTC (rev 4405)
@@ -30,7 +30,7 @@
#ifdef MUTANTALLELE
-bool RevertFixedSites::apply(Population & pop) const
+bool SB_RevertFixedSites::apply(Population & pop) const
{
if (pop.popSize() == 0 || pop.totNumLoci() == 0)
return true;
@@ -712,7 +712,7 @@
// ########################### THE OLD VERSION FOR LONG ALLELE TYPE ####
#else
-bool RevertFixedSites::apply(Population & pop) const
+bool SB_RevertFixedSites::apply(Population & pop) const
{
if (pop.popSize() == 0 || pop.totNumLoci() == 0)
return true;
Modified: trunk/src/sandbox.h
===================================================================
--- trunk/src/sandbox.h 2012-03-01 21:17:49 UTC (rev 4404)
+++ trunk/src/sandbox.h 2012-03-02 05:52:54 UTC (rev 4405)
@@ -51,13 +51,13 @@
* to wildtype allele if it is fixed in the population. If a valid output is
* specifieid, fixed alleles will be outputed with a leading generation number.
*/
-class RevertFixedSites : public BaseOperator
+class SB_RevertFixedSites : public BaseOperator
{
public:
/** Create an operator to revert alleles at fixed loci from value 1 to 0.
* Parameter \e subPops is ignored.
*/
- RevertFixedSites(const stringFunc & output = "", int begin = 0, int end = -1, int step = 1,
+ SB_RevertFixedSites(const stringFunc & output = "", int begin = 0, int end = -1, int step = 1,
const intList & at = vectori(),
const intList & reps = intList(), const subPopList & subPops = subPopList(),
const stringList & infoFields = vectorstr())
@@ -67,7 +67,7 @@
/// destructor
- virtual ~RevertFixedSites()
+ virtual ~SB_RevertFixedSites()
{
}
@@ -75,7 +75,7 @@
/// HIDDEN Deep copy of a Migrator
virtual BaseOperator * clone() const
{
- return new RevertFixedSites(*this);
+ return new SB_RevertFixedSites(*this);
}
@@ -394,13 +394,13 @@
* to wildtype allele if it is fixed in the population. If a valid output is
* specifieid, fixed alleles will be outputed with a leading generation number.
*/
-class RevertFixedSites : public BaseOperator
+class SB_RevertFixedSites : public BaseOperator
{
public:
/** Create an operator to revert alleles at fixed loci from value 1 to 0.
* Parameter \e subPops is ignored.
*/
- RevertFixedSites(const stringFunc & output = "", int begin = 0, int end = -1, int step = 1,
+ SB_RevertFixedSites(const stringFunc & output = "", int begin = 0, int end = -1, int step = 1,
const intList & at = vectori(),
const intList & reps = intList(), const subPopList & subPops = subPopList(),
const stringList & infoFields = vectorstr())
@@ -410,7 +410,7 @@
/// destructor
- virtual ~RevertFixedSites()
+ virtual ~SB_RevertFixedSites()
{
}
@@ -418,7 +418,7 @@
/// HIDDEN Deep copy of a Migrator
virtual BaseOperator * clone() const
{
- return new RevertFixedSites(*this);
+ return new SB_RevertFixedSites(*this);
}
Modified: trunk/src/sandbox.py
===================================================================
--- trunk/src/sandbox.py 2012-03-01 21:17:49 UTC (rev 4404)
+++ trunk/src/sandbox.py 2012-03-02 05:52:54 UTC (rev 4405)
@@ -35,8 +35,8 @@
"""
__all__ = [
- 'revertFixedSites',
- 'RevertFixedSites',
+ 'sb_revertFixedSites',
+ 'SB_RevertFixedSites',
'MutSpaceMutator',
'MutSpaceSelector',
'MutSpaceRecombinator',
@@ -73,6 +73,6 @@
else:
from simuPOP_std import *
-def revertFixedSites(pop):
+def sb_revertFixedSites(pop):
'''Apply operator ``RevertFixedSites`` to ``pop``'''
- RevertFixedSites().apply(pop)
+ SB_RevertFixedSites().apply(pop)
Modified: trunk/test/test_03_operator.py
===================================================================
--- trunk/test/test_03_operator.py 2012-03-01 21:17:49 UTC (rev 4404)
+++ trunk/test/test_03_operator.py 2012-03-02 05:52:54 UTC (rev 4405)
@@ -533,6 +533,163 @@
else:
self.assertEqual(ind.a, 2.0)
+ def testRevertFixedSites(self):
+ 'Testing operator TestRevertFixedSites'
+ #
+ # for diploid
+ pop = Population([1000]*2, loci=10)
+ initGenotype(pop, freq=[0.4, 0.6])
+ initGenotype(pop, loci=[2, 4], freq=[0, 0.5, 0.5])
+ revertFixedSites(pop)
+ stat(pop, alleleFreq=ALL_AVAIL)
+ for loc in range(10):
+ if loc in [2, 4]:
+ self.assertEqual(pop.dvars().alleleFreq[loc][0], 1)
+ else:
+ self.assertNotEqual(pop.dvars().alleleFreq[loc][0], 0)
+ # for one subpopulation
+ pop = Population([1000]*2, loci=10)
+ initGenotype(pop, freq=[0.4, 0.6])
+ initGenotype(pop, loci=[2, 4], freq=[0, 0.5, 0.5])
+ revertFixedSites(pop, subPops=[1])
+ stat(pop, alleleFreq=ALL_AVAIL)
+ for loc in range(10):
+ if loc in [2, 4]:
+ self.assertEqual(pop.dvars().alleleFreq[loc][0], 0.5)
+ else:
+ self.assertNotEqual(pop.dvars().alleleFreq[loc][0], 1)
+ # parameter loci
+ pop = Population([1000]*2, loci=10)
+ initGenotype(pop, freq=[0.4, 0.6])
+ initGenotype(pop, loci=[2, 4], freq=[0, 0.5, 0.5])
+ revertFixedSites(pop, loci=range(4))
+ stat(pop, alleleFreq=ALL_AVAIL)
+ for loc in range(10):
+ if loc == 2:
+ self.assertEqual(pop.dvars().alleleFreq[loc][0], 1)
+ else:
+ self.assertNotEqual(pop.dvars().alleleFreq[loc][0], 1)
+ # for one virtual subpopulation
+ #
+ pop = Population([1000]*2, loci=10)
+ initSex(pop, sex=[MALE, FEMALE])
+ pop.setVirtualSplitter(SexSplitter())
+ initGenotype(pop, freq=[0.4, 0.6])
+ initGenotype(pop, loci=[2, 4], freq=[0, 0.5, 0.5])
+ revertFixedSites(pop, subPops=[(0,0), (1,1)])
+ stat(pop, alleleFreq=ALL_AVAIL, vars='alleleFreq_sp')
+ for loc in range(10):
+ if loc == 2:
+ self.assertEqual(pop.dvars(0).alleleFreq[loc][0], 0.5)
+ self.assertEqual(pop.dvars(1).alleleFreq[loc][0], 0.5)
+ else:
+ self.assertNotEqual(pop.dvars(0).alleleFreq[loc][0], 0)
+ self.assertNotEqual(pop.dvars(1).alleleFreq[loc][0], 0)
+ #
+ # haploid, sex chromosome etc
+ #
+ pop = Population([1000]*2, ploidy=1, loci=10)
+ initGenotype(pop, freq=[0.4, 0.6])
+ initGenotype(pop, loci=[2, 4], freq=[0, 0.5, 0.5])
+ revertFixedSites(pop)
+ stat(pop, alleleFreq=ALL_AVAIL)
+ for loc in range(10):
+ if loc in [2, 4]:
+ self.assertEqual(pop.dvars().alleleFreq[loc][0], 1)
+ else:
+ self.assertNotEqual(pop.dvars().alleleFreq[loc][0], 0)
+ # for one subpopulation
+ pop = Population([1000]*2,ploidy=1, loci=10)
+ initGenotype(pop, freq=[0.4, 0.6])
+ initGenotype(pop, loci=[2, 4], freq=[0, 0.5, 0.5])
+ revertFixedSites(pop, subPops=[1])
+ stat(pop, alleleFreq=ALL_AVAIL)
+ for loc in range(10):
+ if loc in [2, 4]:
+ self.assertEqual(pop.dvars().alleleFreq[loc][0], 0.5)
+ else:
+ self.assertNotEqual(pop.dvars().alleleFreq[loc][0], 1)
+ # parameter loci
+ pop = Population([1000]*2, ploidy=1, loci=10)
+ initGenotype(pop, freq=[0.4, 0.6])
+ initGenotype(pop, loci=[2, 4], freq=[0, 0.5, 0.5])
+ revertFixedSites(pop, loci=range(4))
+ stat(pop, alleleFreq=ALL_AVAIL)
+ for loc in range(10):
+ if loc == 2:
+ self.assertEqual(pop.dvars().alleleFreq[loc][0], 1)
+ else:
+ self.assertNotEqual(pop.dvars().alleleFreq[loc][0], 1)
+ # for one virtual subpopulation
+ #
+ pop = Population([1000]*2, ploidy=1, loci=10)
+ initSex(pop, sex=[MALE, FEMALE])
+ pop.setVirtualSplitter(SexSplitter())
+ initGenotype(pop, freq=[0.4, 0.6])
+ initGenotype(pop, loci=[2, 4], freq=[0, 0.5, 0.5])
+ revertFixedSites(pop, subPops=[(0,0), (1,1)])
+ stat(pop, alleleFreq=ALL_AVAIL, vars='alleleFreq_sp')
+ for loc in range(10):
+ if loc == 2:
+ self.assertEqual(pop.dvars(0).alleleFreq[loc][0], 0.5)
+ self.assertEqual(pop.dvars(1).alleleFreq[loc][0], 0.5)
+ else:
+ self.assertNotEqual(pop.dvars(0).alleleFreq[loc][0], 0)
+ self.assertNotEqual(pop.dvars(1).alleleFreq[loc][0], 0)
+ #
+ # sex chromosome
+ #
+ pop = Population([1000]*2, loci=[3, 7], chromTypes=[CHROMOSOME_X, CHROMOSOME_Y])
+ initGenotype(pop, freq=[0.4, 0.6])
+ initGenotype(pop, loci=[2, 4], freq=[0, 0.5, 0.5])
+ revertFixedSites(pop)
+ stat(pop, alleleFreq=ALL_AVAIL)
+ for loc in range(10):
+ if loc in [2, 4]:
+ self.assertEqual(pop.dvars().alleleFreq[loc][0], 1)
+ else:
+ self.assertNotEqual(pop.dvars().alleleFreq[loc][0], 0)
+ # for one subpopulation
+ pop = Population([1000]*2, loci=[3, 7], chromTypes=[CHROMOSOME_X, CHROMOSOME_Y])
+ initGenotype(pop, freq=[0.4, 0.6])
+ initGenotype(pop, loci=[2, 4], freq=[0, 0.5, 0.5])
+ revertFixedSites(pop, subPops=[1])
+ stat(pop, alleleFreq=ALL_AVAIL)
+ for loc in range(10):
+ if loc in [2, 4]:
+ self.assertEqual(pop.dvars().alleleFreq[loc][0], 0.5)
+ else:
+ self.assertNotEqual(pop.dvars().alleleFreq[loc][0], 1)
+ # parameter loci
+ pop = Population([1000]*2, loci=[3, 7], chromTypes=[CHROMOSOME_X, CHROMOSOME_Y])
+ initGenotype(pop, freq=[0.4, 0.6])
+ initGenotype(pop, loci=[2, 4], freq=[0, 0.5, 0.5])
+ revertFixedSites(pop, loci=range(4))
+ stat(pop, alleleFreq=ALL_AVAIL)
+ for loc in range(10):
+ if loc == 2:
+ self.assertEqual(pop.dvars().alleleFreq[loc][0], 1)
+ else:
+ self.assertNotEqual(pop.dvars().alleleFreq[loc][0], 1)
+ # for one virtual subpopulation
+ #
+ pop = Population([1000]*2, loci=[3, 7], chromTypes=[CHROMOSOME_X, CHROMOSOME_Y])
+ initSex(pop, sex=[MALE, FEMALE])
+ pop.setVirtualSplitter(SexSplitter())
+ initGenotype(pop, freq=[0.4, 0.6])
+ initGenotype(pop, loci=[2, 4], freq=[0, 0.5, 0.5])
+ revertFixedSites(pop, subPops=[(0,0), (1,0)])
+ stat(pop, alleleFreq=ALL_AVAIL, subPops=[(0,0), (1,0)], vars='alleleFreq_sp')
+ for loc in range(10):
+ if loc in [2, 4]:
+ self.assertEqual(pop.dvars((0,0)).alleleFreq[loc][0], 1)
+ self.assertEqual(pop.dvars((1,0)).alleleFreq[loc][0], 1)
+ else:
+ self.assertNotEqual(pop.dvars((0,0)).alleleFreq[loc][0], 0)
+ self.assertNotEqual(pop.dvars((1,0)).alleleFreq[loc][0], 0)
+
+
+
if __name__ == '__main__':
unittest.main()
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|
|
From: <si...@us...> - 2012-03-02 18:28:42
|
Revision: 4416
http://simupop.svn.sourceforge.net/simupop/?rev=4416&view=rev
Author: simupop
Date: 2012-03-02 18:28:36 +0000 (Fri, 02 Mar 2012)
Log Message:
-----------
Add test and change interface again
Modified Paths:
--------------
trunk/src/stator.h
trunk/test/test_08_stat.py
Modified: trunk/src/stator.h
===================================================================
--- trunk/src/stator.h 2012-03-02 18:13:27 UTC (rev 4415)
+++ trunk/src/stator.h 2012-03-02 18:28:36 UTC (rev 4416)
@@ -986,18 +986,17 @@
*
* <b>numOfSegSites</b>: Parameter \e numOfSegSites accepts a list of loci
* (loci indexes, names, or \c ALL_AVAIL) and count the number of loci with
- * at least two different alleles (segregating sites) or loci with at least
- * one non-zero allele (non-zero sites, which includes all segregating sites,
- * and sites with fixed non-zero alleles) for individuals in all or
- * specified (virtual) subpopulations. This parameter sets variables
+ * at least two different alleles (segregating sites) or loci with only one
+ * non-zero allele (no zero allele, not segragating) for individuals in all
+ * or specified (virtual) subpopulations. This parameter sets variables
* \li \c numOfSegSites (default): Number of segregating sites in all or
* specified (virtual) subpopulations.
* \li \c numOfSegSites_sp: Number of segregating sites in each (virtual)
* subpopulation.
- * \li \c numOfNonZeroSites: Number of sites with at least one non-zero
- * allele, in all or specified (virtual) subpopulations.
- * \li \c numOfNonZeroSites_sp: Number of sites with at least one non-zero
- * allele in each (virtual) subpopulations.
+ * \li \c numOfFixedSites: Number of sites with one non-zero allele in all
+ * or specified (virtual) subpopulations.
+ * \li \c numOfFixedSites_sp: Number of sites with one non-zero allele in
+ * in each (virtual) subpopulations.
*
* <b>alleleFreq</b>: This parameter accepts a list of loci (loci indexes,
* names, or \c ALL_AVAIL), at which allele frequencies will be calculated.
Modified: trunk/test/test_08_stat.py
===================================================================
--- trunk/test/test_08_stat.py 2012-03-02 18:13:27 UTC (rev 4415)
+++ trunk/test/test_08_stat.py 2012-03-02 18:28:36 UTC (rev 4416)
@@ -153,10 +153,26 @@
# selected loci
stat(pop, numOfSegSites=range(100, 1000))
self.assertEqual(pop.dvars().numOfSegSites, 0)
+ #
+ # number of non-zero sites
+ pop = Population(size=1000, loci=[10]*10)
+ # 20 segreagating sites with 0
+ initGenotype(pop, loci= range(20), freq=[0.5, 0.5])
+ # 10 segragating sites without 0, fixed for binary module
+ initGenotype(pop, loci= range(30, 40), freq=[0, 0.5, 0.5])
+ # 10 fixed sites
+ initGenotype(pop, loci= range(50, 60), freq=[0, 1])
+ stat(pop, numOfSegSites=ALL_AVAIL, vars=['numOfSegSites', 'numOfFixedSites'])
+ if moduleInfo()['alleleType'] == 'binary':
+ self.assertEqual(pop.dvars().numOfSegSites, 20)
+ self.assertEqual(pop.dvars().numOfFixedSites, 20)
+ else:
+ self.assertEqual(pop.dvars().numOfSegSites, 30)
+ self.assertEqual(pop.dvars().numOfFixedSites, 10)
def testNumOfMutants(self):
- 'Testing the number of segregating sites'
+ 'Testing the number of mutants'
pop = Population(size=1000, loci=[100]*100)
# 100 mutations
for i in range(100):
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|
|
From: <si...@us...> - 2012-03-03 22:48:29
|
Revision: 4420
http://simupop.svn.sourceforge.net/simupop/?rev=4420&view=rev
Author: simupop
Date: 2012-03-03 22:48:21 +0000 (Sat, 03 Mar 2012)
Log Message:
-----------
Lineage patch 2: structural changes to add modules lin and linop
Modified Paths:
--------------
trunk/MANIFEST.in
trunk/SConstruct
trunk/setup.py
trunk/simuOpt.py
trunk/src/__init__.py
Added Paths:
-----------
trunk/src/simuPOP_lin.i
trunk/src/simuPOP_linop.i
Modified: trunk/MANIFEST.in
===================================================================
--- trunk/MANIFEST.in 2012-03-03 22:45:52 UTC (rev 4419)
+++ trunk/MANIFEST.in 2012-03-03 22:48:21 UTC (rev 4420)
@@ -42,6 +42,8 @@
# source files
include src/customizedTypes.c
+include src/customizedLineageTypes.c
+include src/customizedTemplates.cpp
include src/utility.cpp
include src/genoStru.cpp
include src/individual.cpp
@@ -78,6 +80,8 @@
include src/simuPOP_laop.py
include src/simuPOP_ba.py
include src/simuPOP_baop.py
+include src/simuPOP_lin.py
+include src/simuPOP_linop.py
include src/gsl_wrap.c
# source wrap files
@@ -89,6 +93,8 @@
include src/simuPOP_laop.i
include src/simuPOP_ba.i
include src/simuPOP_baop.i
+include src/simuPOP_lin.i
+include src/simuPOP_linop.i
include src/gsl.i
# source python files (modules)
Modified: trunk/SConstruct
===================================================================
--- trunk/SConstruct 2012-03-03 22:45:52 UTC (rev 4419)
+++ trunk/SConstruct 2012-03-03 22:48:21 UTC (rev 4420)
@@ -212,7 +212,7 @@
#
targets = []
exe_targets = []
-all_modu = ['std', 'op', 'la', 'laop', 'ba', 'baop', 'mu', 'muop']
+all_modu = ['std', 'op', 'la', 'laop', 'ba', 'baop', 'mu', 'muop', 'lin', 'linop']
all_exe = [x + '_exe' for x in all_modu]
for key in all_modu:
if key in BUILD_TARGETS:
Modified: trunk/setup.py
===================================================================
--- trunk/setup.py 2012-03-03 22:45:52 UTC (rev 4419)
+++ trunk/setup.py 2012-03-03 22:48:21 UTC (rev 4420)
@@ -424,6 +424,10 @@
('_SECURE_SCL', 1), ('_HAS_ITERATOR_DEBUGGING', 0)],
'muop': [('SIMUPOP_MODULE', 'simuPOP_muop'), ('MUTANTALLELE', None), ('OPTIMIZED', None),
('_SECURE_SCL', 0), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ 'lin': [('SIMUPOP_MODULE', 'simuPOP_lin'), ('LINEAGE', None),
+ ('_SECURE_SCL', 1), ('_HAS_ITERATOR_DEBUGGING', 0)],
+ 'linop': [('SIMUPOP_MODULE', 'simuPOP_linop'), ('LINEAGE', None), ('OPTIMIZED', None),
+ ('_SECURE_SCL', 0), ('_HAS_ITERATOR_DEBUGGING', 0)],
}
@@ -436,6 +440,8 @@
'baop': ['src/simuPOP_baop_wrap.cpp', 'src/simuPOP_baop.i', '-DBINARYALLELE -DOPTIMIZED'],
'mu': ['src/simuPOP_mu_wrap.cpp', 'src/simuPOP_mu.i', '-DMUTANTALLELE'],
'muop': ['src/simuPOP_muop_wrap.cpp', 'src/simuPOP_muop.i', '-DMUTANTALLELE -DOPTIMIZED'],
+ 'lin': ['src/simuPOP_lin_wrap.cpp', 'src/simuPOP_lin.i', '-DLINEAGE'],
+ 'linop': ['src/simuPOP_linop_wrap.cpp', 'src/simuPOP_linop.i', '-DLINEAGE -DOPTIMIZED'],
}
if os.name == 'nt':
@@ -553,7 +559,7 @@
if __name__ == '__main__':
SIMUPOP_VER, SIMUPOP_REV = simuPOP_version()
# create source file for each module
- MODULES = ['std', 'op', 'la', 'laop', 'ba', 'baop', 'mu', 'muop']
+ MODULES = ['std', 'op', 'la', 'laop', 'ba', 'baop', 'mu', 'muop', 'lin', 'linop']
#
# Generate Wrapping files
#
Modified: trunk/simuOpt.py
===================================================================
--- trunk/simuOpt.py 2012-03-03 22:45:52 UTC (rev 4419)
+++ trunk/simuOpt.py 2012-03-03 22:48:21 UTC (rev 4420)
@@ -119,10 +119,10 @@
simuOptions['Optimized'] = True
# AlleleType: from environmental variable SIMUALLELETYPE
-if os.getenv('SIMUALLELETYPE') in ['short', 'long', 'binary','mutant']:
+if os.getenv('SIMUALLELETYPE') in ['short', 'long', 'binary', 'mutant', 'lineage']:
simuOptions['AlleleType'] = os.getenv('SIMUALLELETYPE')
elif os.getenv('SIMUALLELETYPE') is not None:
- print 'Environmental variable SIMUALLELETYPE can only be short, long, binary, or mutant'
+ print 'Environmental variable SIMUALLELETYPE can only be short, long, binary, mutant, or lineage.'
# Debug: from environmental variable SIMUDEBUG
if os.getenv('SIMUDEBUG') is not None:
@@ -162,11 +162,12 @@
load, and how the module should be loaded.
alleleType
- Use the standard, binary,long or mutant allele version of the simuPOP module
- if ``alleleType`` is set to 'short', 'binary', 'long', or 'mutant respectively.
- If this parameter is not set, this function will try to get its value
- from environmental variable ``SIMUALLELETYPE``. The standard (short)
- module will be used if the environmental variable is not defined.
+ Use the standard, binary,long or mutant allele version of the simuPOP
+ module if ``alleleType`` is set to 'short', 'binary', 'long', 'mutant',
+ or 'lineage' respectively. If this parameter is not set, this function
+ will try to get its value from environmental variable ``SIMUALLELETYPE``.
+ The standard (short) module will be used if the environmental variable
+ is not defined.
optimized
Load the optimized version of a module if this parameter is set to
@@ -226,10 +227,10 @@
elif optimized is not None:
raise TypeError('Parameter optimized can be either True or False.')
# Allele type
- if alleleType in ['long', 'binary', 'short', 'mutant']:
+ if alleleType in ['long', 'binary', 'short', 'mutant', 'lineage']:
simuOptions['AlleleType'] = alleleType
elif alleleType is not None:
- raise TypeError('Parameter alleleType can be either short, long, binary, or mutant.')
+ raise TypeError('Parameter alleleType can be either short, long, binary, mutant or lineage.')
# Graphical toolkit
if gui in [True, False, 'wxPython', 'Tkinter', 'batch']:
simuOptions['GUI'] = gui
Modified: trunk/src/__init__.py
===================================================================
--- trunk/src/__init__.py 2012-03-03 22:45:52 UTC (rev 4419)
+++ trunk/src/__init__.py 2012-03-03 22:48:21 UTC (rev 4420)
@@ -294,6 +294,8 @@
from simuPOP.simuPOP_baop import *
elif simuOptions['AlleleType'] == 'mutant':
from simuPOP.simuPOP_muop import *
+ elif simuOptions['AlleleType'] == 'lineage':
+ from simuPOP.simuPOP_linop import *
else:
from simuPOP.simuPOP_op import *
else:
@@ -305,6 +307,8 @@
from simuPOP.simuPOP_ba import *
elif simuOptions['AlleleType'] == 'mutant':
from simuPOP.simuPOP_mu import *
+ elif simuOptions['AlleleType'] == 'lineage':
+ from simuPOP.simuPOP_lin import *
else:
from simuPOP.simuPOP_std import *
Added: trunk/src/simuPOP_lin.i
===================================================================
--- trunk/src/simuPOP_lin.i (rev 0)
+++ trunk/src/simuPOP_lin.i 2012-03-03 22:48:21 UTC (rev 4420)
@@ -0,0 +1,30 @@
+//
+// $File: simuPOP_lin.i $
+// $LastChangedDate$
+// $Rev$
+//
+// This file is part of simuPOP, a forward-time population genetics
+// simulation environment. Please visit http://simupop.sourceforge.net
+// for details.
+//
+// Copyright (C) 2004 - 2009 Bo Peng (bp...@md...)
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program. If not, see <http://www.gnu.org/licenses/>.
+//
+
+%module simuPOP_lin
+
+#define LINEAGE
+%include "simuPOP_common.i"
+
Added: trunk/src/simuPOP_linop.i
===================================================================
--- trunk/src/simuPOP_linop.i (rev 0)
+++ trunk/src/simuPOP_linop.i 2012-03-03 22:48:21 UTC (rev 4420)
@@ -0,0 +1,30 @@
+//
+// $File: simuPOP_linop.i $
+// $LastChangedDate$
+// $Rev$
+//
+// This file is part of simuPOP, a forward-time population genetics
+// simulation environment. Please visit http://simupop.sourceforge.net
+// for details.
+//
+// Copyright (C) 2004 - 2009 Bo Peng (bp...@md...)
+//
+// This program is free software: you can redistribute it and/or modify
+// it under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program. If not, see <http://www.gnu.org/licenses/>.
+//
+
+%module simuPOP_linop
+
+#define OPTIMIZED
+#define LINEAGE
+%include "simuPOP_common.i"
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