[simuPOP-devel] SF.net SVN: simupop:[4321] branches/mutant_new/src

[<ti...@us...>]

Revision: 4321
          http://simupop.svn.sourceforge.net/simupop/?rev=4321&view=rev
Author:   tiwcpe8
Date:     2011-10-14 18:18:26 +0000 (Fri, 14 Oct 2011)
Log Message:
-----------
Remove some #ifdef MUTANTALLELE in individual.cpp and population.cpp and try to use mutant_vector

Modified Paths:
--------------
    branches/mutant_new/src/customizedTypes.c
    branches/mutant_new/src/individual.cpp
    branches/mutant_new/src/individual.h
    branches/mutant_new/src/mutant_vector.h
    branches/mutant_new/src/population.cpp
    branches/mutant_new/src/population.h
    branches/mutant_new/src/utility.cpp
    branches/mutant_new/src/utility.h

Modified: branches/mutant_new/src/customizedTypes.c
===================================================================
--- branches/mutant_new/src/customizedTypes.c	2011-10-13 18:58:37 UTC (rev 4320)
+++ branches/mutant_new/src/customizedTypes.c	2011-10-14 18:18:26 UTC (rev 4321)
@@ -53,13 +53,7 @@
 {
 	PyObject_VAR_HEAD
 	// pointer to the beginning of the genotype
-#ifdef MUTANTALLELE
-//	compressed_vectora * ob_iter;
-//	size_t idx;
 	GenoIterator ob_iter;
-#else
-	GenoIterator ob_iter;
-#endif
 } arrayobject;
 
 /// CPPONLY
@@ -74,12 +68,7 @@
 	assert(is_carrayobject(op));
 	ap = (arrayobject *)op;
 	assert(i >= 0 && i < Py_SIZE(ap));
-#ifdef MUTANTALLELE
-	//return PyInt_FromLong((*ap->ob_iter)[ap->idx + i] );
 	return PyInt_FromLong(*(ap->ob_iter + i) );
-#else
-	return PyInt_FromLong(*(ap->ob_iter + i) );
-#endif
 }
 
 
@@ -99,12 +88,7 @@
 #  ifdef BINARYALLELE
 	*(ap->ob_iter + i) = (x != 0);
 #  else
-#    ifdef MUTANTALLELE
-	//(*ap->ob_iter)[ap->idx + i] = Allele(x);
 	*(ap->ob_iter + i) = Allele(x);
-#    else
-	*(ap->ob_iter + i) = Allele(x);
-#    endif
 #  endif
 	return 0;
 }
@@ -131,12 +115,7 @@
 
 
 /// CPPONLY
-#ifdef MUTANTALLELE
-//PyObject * newcarrayobject(compressed_vectora * genoPtr, Py_ssize_t begin, Py_ssize_t end);
 PyObject * newcarrayobject(GenoIterator begin, GenoIterator end);
-#else
-PyObject * newcarrayobject(GenoIterator begin, GenoIterator end);
-#endif
 
 /// CPPONLY
 static void
@@ -385,12 +364,7 @@
 		ihigh = ilow;
 	else if (ihigh > Py_SIZE(a))
 		ihigh = Py_SIZE(a);
-#ifdef MUTANTALLELE
-//	np = (arrayobject *)newcarrayobject(a->ob_iter, a->idx + ilow, a->idx + ihigh);
 	np = (arrayobject *)newcarrayobject(a->ob_iter + ilow, a->ob_iter + ihigh);
-#else
-	np = (arrayobject *)newcarrayobject(a->ob_iter + ilow, a->ob_iter + ihigh);
-#endif
 	if (np == NULL)
 		return NULL;
 	return (PyObject *)np;
@@ -729,25 +703,6 @@
 
 
 /// CPPONLY
-#ifdef MUTANTALLELE
-/*
-PyObject * newcarrayobject(compressed_vectora * genoPtr, Py_ssize_t begin, Py_ssize_t end)
-{
-	// create an object and copy data
-	arrayobject * op;
-
-	op = PyObject_New(arrayobject, &Arraytype);
-	if (op == NULL) {
-		PyObject_Del(op);
-		return PyErr_NoMemory();
-	}
-	//
-	op->idx     = begin;
-	op->ob_iter = genoPtr;
-	Py_SIZE(op) = end - begin;
-	return (PyObject *)op;
-}
-*/
 PyObject * newcarrayobject(GenoIterator begin, GenoIterator end)
 {
 	// create an object and copy data
@@ -763,25 +718,8 @@
 	Py_SIZE(op) = end - begin;
 	return (PyObject *)op;
 }
-#else
-PyObject * newcarrayobject(GenoIterator begin, GenoIterator end)
-{
-	// create an object and copy data
-	arrayobject * op;
 
-	op = PyObject_New(arrayobject, &Arraytype);
-	if (op == NULL) {
-		PyObject_Del(op);
-		return PyErr_NoMemory();
-	}
-	//
-	op->ob_iter = begin;
-	Py_SIZE(op) = end - begin;
-	return (PyObject *)op;
-}
-#endif
 
-
 /* defdict type *********************************************************/
 
 typedef struct
@@ -985,13 +923,7 @@
 {
 	PyObject_VAR_HEAD
 	// pointer to the beginning of the genotype
-#ifdef MUTANTALLELE
-//	compressed_vectora * ob_iter;
-//	size_t idx;
 	GenoIterator ob_iter;
-#else 
-	GenoIterator ob_iter;
-#endif
 } arrayobject;
 
 bool is_carrayobject(PyObject * op);
@@ -1689,25 +1621,6 @@
 
 
 /// CPPONLY
-#ifdef MUTANTALLELE
-/*
-PyObject * newcarrayobject(compressed_vectora * genoPtr, Py_ssize_t begin, Py_ssize_t end)
-{
-	// create an object and copy data
-	arrayobject * op;
-
-	op = PyObject_New(arrayobject, &Arraytype);
-	if (op == NULL) {
-		PyObject_Del(op);
-		return PyErr_NoMemory();
-	}
-	//
-	op->idx     = begin;
-	op->ob_iter = genoPtr;
-	Py_SIZE(op) = end - begin;
-	return (PyObject *)op;
-}
-*/
 PyObject * newcarrayobject(GenoIterator begin, GenoIterator end)
 {
 	// create an object and copy data
@@ -1724,25 +1637,7 @@
 	return (PyObject *)op;
 }
 
-#else
-PyObject * newcarrayobject(GenoIterator begin, GenoIterator end)
-{
-	// create an object and copy data
-	arrayobject * op;
 
-	op = PyObject_New(arrayobject, &Arraytype);
-	if (op == NULL) {
-		PyObject_Del(op);
-		return PyErr_NoMemory();
-	}
-	//
-	op->ob_iter = begin;
-	Py_SIZE(op) = end - begin;
-	return (PyObject *)op;
-}
-#endif
-
-
 typedef struct
 {
 	PyDictObject dict;

Modified: branches/mutant_new/src/individual.cpp
===================================================================
--- branches/mutant_new/src/individual.cpp	2011-10-13 18:58:37 UTC (rev 4320)
+++ branches/mutant_new/src/individual.cpp	2011-10-14 18:18:26 UTC (rev 4321)
@@ -146,31 +146,16 @@
 		"A valid ploidy index has to be specified if chrom is non-positive");
 	if (p < 0) {
 		CHECKRANGEGENOSIZE(idx);
-#ifdef MUTANTALLELE
 		return static_cast<UINT>(*(m_genoPtr + idx));
-		//return static_cast<UINT>((*m_genoPtr)[m_genoIdx + idx]);
-#else
-		return static_cast<UINT>(*(m_genoPtr + idx));
-#endif
 	} else if (chrom < 0) {
 		CHECKRANGEABSLOCUS(idx);
 		CHECKRANGEPLOIDY(static_cast<size_t>(p));
-#ifdef MUTANTALLELE
 		return static_cast<UINT>(*(m_genoPtr + idx + p * totNumLoci()));
-		//return static_cast<UINT>((*m_genoPtr)[m_genoIdx + idx + p * totNumLoci()]);
-#else
-		return static_cast<UINT>(*(m_genoPtr + idx + p * totNumLoci()));
-#endif
 	} else {
 		CHECKRANGELOCUS(chrom, idx);
 		CHECKRANGEPLOIDY(static_cast<size_t>(p));
 		CHECKRANGECHROM(static_cast<size_t>(chrom));
-#ifdef MUTANTALLELE
 		return static_cast<UINT>(*(m_genoPtr + idx + p * totNumLoci() + chromBegin(chrom)));
-		//return static_cast<UINT>((*m_genoPtr)[m_genoIdx + idx + p * totNumLoci() + chromBegin(chrom)]);
-#else
-		return static_cast<UINT>(*(m_genoPtr + idx + p * totNumLoci() + chromBegin(chrom)));
-#endif
 	}
 }
 
@@ -253,25 +238,11 @@
 		// has to be all chromosomes
 		DBG_FAILIF(beginCh != 0 || endCh != numChrom(), ValueError,
 			"If multiple ploidy are chosen, all chromosomes has to be chosen.");
-#ifdef MUTANTALLELE
-//		return Allele_Vec_As_NumArray(m_genoPtr, m_genoIdx + beginP * totNumLoci(),
-//			m_genoIdx + endP * totNumLoci());
 		return Allele_Vec_As_NumArray(m_genoPtr + beginP * totNumLoci(),
 			m_genoPtr + endP * totNumLoci());
-#else
-		return Allele_Vec_As_NumArray(m_genoPtr + beginP * totNumLoci(),
-			m_genoPtr + endP * totNumLoci());
-#endif
 	} else
-#ifdef MUTANTALLELE
-//		return Allele_Vec_As_NumArray(m_genoPtr, m_genoIdx + beginP * totNumLoci() + chromBegin(beginCh),
-//			m_genoIdx + beginP * totNumLoci() + chromEnd(endCh - 1));
 		return Allele_Vec_As_NumArray(m_genoPtr + beginP * totNumLoci() + chromBegin(beginCh),
 			m_genoPtr + beginP * totNumLoci() + chromEnd(endCh - 1));
-#else
-		return Allele_Vec_As_NumArray(m_genoPtr + beginP * totNumLoci() + chromBegin(beginCh),
-			m_genoPtr + beginP * totNumLoci() + chromEnd(endCh - 1));
-#endif
 }
 
 
@@ -337,12 +308,7 @@
 		"A valid ploidy index has to be specified if chrom is non-positive");
 	if (p < 0) {
 		CHECKRANGEGENOSIZE(idx);
-#ifdef MUTANTALLELE
-		//assignGenotype(*m_genoPtr, m_genoIdx + idx, allele);
-		*(m_genoPtr + idx) = allele;
-#else
-		*(m_genoPtr + idx) = allele;
-#endif
+		*(m_genoPtr + idx) = allele; //assignGenotype
 	} else if (chrom < 0) {
 		CHECKRANGEABSLOCUS(idx);
 		CHECKRANGEPLOIDY(static_cast<size_t>(p));
@@ -400,18 +366,9 @@
 		size_t p = ploidys[i];
 		for (size_t j = 0; j < chroms.size(); ++j) {
 			size_t chrom = chroms[j];
-#ifdef MUTANTALLELE
-//			size_t genoIdx = m_genoIdx + p * totNumLoci() + chromBegin(chrom);
-//			for (size_t i = 0; i < numLoci(chrom); i++, ++idx)
-//				assignGenotype(*m_genoPtr, genoIdx + i, ToAllele(geno[idx % sz]));
 			GenoIterator ptr = m_genoPtr + p * totNumLoci() + chromBegin(chrom);
 			for (size_t i = 0; i < numLoci(chrom); i++, ++idx)
-				*(ptr + i) = ToAllele(geno[idx % sz]);
-#else
-			GenoIterator ptr = m_genoPtr + p * totNumLoci() + chromBegin(chrom);
-			for (size_t i = 0; i < numLoci(chrom); i++, ++idx)
-				*(ptr + i) = ToAllele(geno[idx % sz]);
-#endif
+				*(ptr + i) = ToAllele(geno[idx % sz]); // assignGenotype
 		}
 	}
 }

Modified: branches/mutant_new/src/individual.h
===================================================================
--- branches/mutant_new/src/individual.h	2011-10-13 18:58:37 UTC (rev 4320)
+++ branches/mutant_new/src/individual.h	2011-10-14 18:18:26 UTC (rev 4321)
@@ -108,11 +108,7 @@
 	/// CPPONLY
 	Individual(const Individual & ind) :
 		GenoStruTrait(ind), m_flags(ind.m_flags),
-#ifdef MUTANTALLELE
-//		m_genoPtr(ind.m_genoPtr), m_genoIdx(ind.m_genoIdx),
-#else
 		m_genoPtr(ind.m_genoPtr),
-#endif
 		m_infoPtr(ind.m_infoPtr)
 	{
 	}
@@ -125,32 +121,12 @@
 
 
 	/// CPPONLY set genotype pointer (use if Allele*pos can not be determined during construction)
-#ifdef MUTANTALLELE
 	void setGenoPtr(GenoIterator pos)
 	{
 		m_genoPtr = pos;
 	}
-/*
-	void setGenoPtr(compressed_vectora * genoPtr, size_t pos)
-	{
-		m_genoPtr = genoPtr;
-		m_genoIdx = pos;
-	}
 
 
-	void setGenoPtr(compressed_vectora * genoPtr)
-	{
-		m_genoPtr = genoPtr;
-	}
-*/
-#else
-	void setGenoPtr(GenoIterator pos)
-	{
-		m_genoPtr = pos;
-	}
-#endif
-
-
 	/// CPPONLY set pointer to individual info
 	void setInfoPtr(InfoIterator pos)
 	{
@@ -168,27 +144,11 @@
 	/// @name readonly structural info
 	//@{
 
-#ifdef MUTANTALLELE
-	/// CPPONLY index to alleles
-/*
-	compressed_vectora * genoPtr() const
-	{
-		return m_genoPtr;
-	}
-
-	size_t genoIdx() const
-	{
-		return m_genoIdx;
-	}
-*/
-
-#else
 	/// CPPONLY pointer to alleles
 	GenoIterator genoPtr() const
 	{
 		return m_genoPtr;
 	}
-#endif
 
 
 	/// CPPONLY
@@ -383,57 +343,7 @@
 		m_infoPtr[idx] = value;
 	}
 
-#ifdef MUTANTALLELE
 	/// CPPONLY start of alleles
-/*	size_t genoBegin() const
-	{
-		return m_genoIdx;
-	}
-
-
-	/// CPPONLY end of allele
-	size_t genoEnd() const
-	{
-		return m_genoIdx + genoSize();
-	}
-
-
-	/// CPPONLY start of allele of the pth set of chromosome
-	size_t genoBegin(size_t p) const
-	{
-		CHECKRANGEPLOIDY(p);
-		return m_genoIdx + p * totNumLoci();
-	}
-
-
-	/// CPPONLY end of allele of the pth set of chromosome
-	size_t genoEnd(size_t p) const
-	{
-		CHECKRANGEPLOIDY(p);
-		return m_genoIdx + (p + 1) * totNumLoci();
-	}
-
-
-	/// CPPONLY start of allele of the pth set of chromosome, chrom ch
-	size_t genoBegin(size_t p, size_t chrom) const
-	{
-		CHECKRANGEPLOIDY(p);
-		CHECKRANGECHROM(chrom);
-		return m_genoIdx + p * totNumLoci() + chromBegin(chrom);
-
-	}
-
-
-	/// CPPONLY end of allele of the pth set of chromosome
-	size_t genoEnd(size_t p, size_t chrom) const
-	{
-		CHECKRANGEPLOIDY(p);
-		CHECKRANGECHROM(chrom);
-		return m_genoIdx + p * totNumLoci() + chromEnd(chrom);
-
-	}
-*/
-	/// CPPONLY start of alleles
 	GenoIterator genoBegin() const
 	{
 		return m_genoPtr;
@@ -482,58 +392,6 @@
 
 	}
 
-
-#else
-	/// CPPONLY start of alleles
-	GenoIterator genoBegin() const
-	{
-		return m_genoPtr;
-	}
-
-
-	/// CPPONLY end of allele
-	GenoIterator genoEnd() const
-	{
-		return m_genoPtr + genoSize();
-	}
-
-
-	/// CPPONLY start of allele of the pth set of chromosome
-	GenoIterator genoBegin(size_t p) const
-	{
-		CHECKRANGEPLOIDY(p);
-		return m_genoPtr + p * totNumLoci();
-	}
-
-
-	/// CPPONLY end of allele of the pth set of chromosome
-	GenoIterator genoEnd(size_t p) const
-	{
-		CHECKRANGEPLOIDY(p);
-		return m_genoPtr + (p + 1) * totNumLoci();
-	}
-
-
-	/// CPPONLY start of allele of the pth set of chromosome, chrom ch
-	GenoIterator genoBegin(size_t p, size_t chrom) const
-	{
-		CHECKRANGEPLOIDY(p);
-		CHECKRANGECHROM(chrom);
-		return m_genoPtr + p * totNumLoci() + chromBegin(chrom);
-
-	}
-
-
-	/// CPPONLY end of allele of the pth set of chromosome
-	GenoIterator genoEnd(size_t p, size_t chrom) const
-	{
-		CHECKRANGEPLOIDY(p);
-		CHECKRANGECHROM(chrom);
-		return m_genoPtr + p * totNumLoci() + chromEnd(chrom);
-
-	}
-#endif
-
 	/// CPPONLY start of info
 	InfoIterator infoBegin() const
 	{
@@ -636,13 +494,7 @@
 	mutable unsigned char m_flags;
 
 	/// pointer to genotype.
-#ifdef MUTANTALLELE
 	GenoIterator m_genoPtr;
-        //compressed_vectora * m_genoPtr;
-	//size_t m_genoIdx;
-#else
-	GenoIterator m_genoPtr;
-#endif
 
 	/// pointer to info
 	InfoIterator m_infoPtr;

Modified: branches/mutant_new/src/mutant_vector.h
===================================================================
--- branches/mutant_new/src/mutant_vector.h	2011-10-13 18:58:37 UTC (rev 4320)
+++ branches/mutant_new/src/mutant_vector.h	2011-10-14 18:18:26 UTC (rev 4321)
@@ -28,16 +28,21 @@
 			m_container.resize(size);
 		}
 
-		size_t size() {
+		void reserve (size_t size)
+		{
+			m_container.reserve(size);
+		}
+
+		size_t size() const {
 			return m_container.size();
 		}
 
-		mutant_vector<T>::iterator  begin()
+		mutant_vector<T>::iterator  begin() 
 		{
 			return mutant_vector<T>::iterator(&m_container, 0); 
 		}
 
-		mutant_vector<T>::iterator  end()
+		mutant_vector<T>::iterator  end() 
 		{
 			return mutant_vector<T>::iterator(&m_container, m_container.size()); 
 		}
@@ -99,8 +104,34 @@
 						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>::reference operator* () 
 				{
 					return (*m_container)[m_index];
@@ -197,8 +228,31 @@
 				{
 					return m_container;	
 				}
+
+				void deleted()
+				{
+					m_container->erase_element(m_index);
+				}	
+
 		};
 
+		void erase (mutant_vector<T>::iterator begin,mutant_vector<T>::iterator end)
+		{
+			mutant_vector<T>::iterator it = begin;
+			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 - begin));
+		}
+
 	private:
 		compressed_vector<T> m_container;
 };
@@ -220,12 +274,28 @@
 	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_dest_begin;
+	size_t dest_index = it.getIndex() - *it_dest_begin;
 	for (;it_src_begin  != iend; ++it_src_begin) {
-		(*it.getContainer())[ ((*it_src_begin + src_index) - src_begin) + dest_begin ] = (*begin.getContainer())[*it_src_begin];
+		(*it.getContainer())[ ((*it_src_begin + src_index) - src_begin) + dest_begin + dest_index ] = (*begin.getContainer())[*it_src_begin];
 	}
 }
 
+inline void insert(vectora::iterator it, vectora::iterator begin, vectora::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();
+	compressed_vector<size_t>::index_array_type::iterator it_dest_begin = it.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_dest_begin;
+	size_t dest_index = it.getIndex() - *it_dest_begin;
+	for (;it_src_begin  != iend; ++it_src_begin) {
+		(*it.getContainer()).push_back(((*it_src_begin + src_index) - src_begin) + dest_begin + dest_index, (*begin.getContainer())[*it_src_begin]);
+	}
+
 }
 
+}
+
 #  endif
 #endif

Modified: branches/mutant_new/src/population.cpp
===================================================================
--- branches/mutant_new/src/population.cpp	2011-10-13 18:58:37 UTC (rev 4320)
+++ branches/mutant_new/src/population.cpp	2011-10-14 18:18:26 UTC (rev 4321)
@@ -605,7 +605,7 @@
 	return NULL;
 }
 */
-/*
+
 void Population::setGenotype(const uintList & genoList, vspID subPopID)
 {
 	const vectoru & geno = genoList.elems();
@@ -614,24 +614,11 @@
 
 	syncIndPointers();
 	if (!subPop.valid()) {
-#ifdef MUTANTALLELE
-//		size_t sz = geno.size();
-//		for (size_t i = 0; i < popSize() * genoSize(); ++i)
-//			assignGenotype(m_genotype, i, ToAllele(geno[i % sz]));
-//		return;
 		GenoIterator ptr = m_genotype.begin();
 		size_t sz = geno.size();
 		for (size_t i = 0; i < popSize() * genoSize(); ++i)
-			*(ptr++) = ToAllele(geno[i % sz]);
+			*(ptr++) = ToAllele(geno[i % sz]); //assignGenotype
 		return;
-
-#else
-		GenoIterator ptr = m_genotype.begin();
-		size_t sz = geno.size();
-		for (size_t i = 0; i < popSize() * genoSize(); ++i)
-			*(ptr++) = ToAllele(geno[i % sz]);
-		return;
-#endif
 	}
 
 	DBG_FAILIF(hasActivatedVirtualSubPop(), ValueError,
@@ -642,36 +629,20 @@
 
 	size_t sz = geno.size();
 	if (!subPop.isVirtual()) {
-#ifdef MUTANTALLELE
-//		size_t idx = genoBegin(sp, true);
-//		for (size_t i = 0; i < subPopSize(sp) * genoSize(); ++i)
-//			assignGenotype(m_genotype, idx+i, ToAllele(geno[i % sz]));
 		GenoIterator ptr = genoBegin(sp, true);
 		for (size_t i = 0; i < subPopSize(sp) * genoSize(); ++i)
-			*(ptr++) = ToAllele(geno[i % sz]);
-#else
-		GenoIterator ptr = genoBegin(sp, true);
-		for (size_t i = 0; i < subPopSize(sp) * genoSize(); ++i)
-			*(ptr++) = ToAllele(geno[i % sz]);
-#endif
+			*(ptr++) = ToAllele(geno[i % sz]); //assignGenotype
 	} else {
 		activateVirtualSubPop(subPop);
 		IndIterator it = indIterator(sp);
 		size_t i = 0;
 		for (; it.valid(); ++it)
-#ifdef MUTANTALLELE
-//			for (size_t git = it->genoBegin(); git != it->genoEnd(); ++git, ++i)
-//				assignGenotype(m_genotype, git, ToAllele(geno[i % sz]));
 			for (GenoIterator git = it->genoBegin(); git != it->genoEnd(); ++git, ++i)
-				*git = ToAllele(geno[i % sz]);
-#else
-			for (GenoIterator git = it->genoBegin(); git != it->genoEnd(); ++git, ++i)
-				*git = ToAllele(geno[i % sz]);
-#endif
+				*git = ToAllele(geno[i % sz]); //assignGenotype
 		deactivateVirtualSubPop(subPop.subPop());
 	}
 }
-*/
+
 /*
 void Population::validate(const string & msg) const
 {
@@ -685,8 +656,10 @@
 	ConstInfoIterator ib = m_info.begin();
 	ConstInfoIterator ie = m_info.end();
 #ifdef MUTANTALLELE
-	size_t gb = 0;
-	size_t ge = m_genotype.size();
+	//size_t gb = 0;
+	//size_t ge = m_genotype.size();
+	ConstGenoIterator gb = m_genotype.begin();
+	ConstGenoIterator ge = m_genotype.end();
 #else
 	ConstGenoIterator gb = m_genotype.begin();
 	ConstGenoIterator ge = m_genotype.end();
@@ -695,8 +668,10 @@
 	if (genoSize() > 0) {
 		for (ConstIndIterator it = indIterator(); it.valid(); ++it) {
 #ifdef MUTANTALLELE
-			DBG_ASSERT(it->genoIdx() >= gb && it->genoIdx() < ge, SystemError,
-				msg + "Wrong genotype pointer");
+			//DBG_ASSERT(it->genoIdx() >= gb && it->genoIdx() < ge, SystemError,
+			//	msg + "Wrong genotype pointer");
+//			DBG_ASSERT(it->genoPtr() >= gb && it->genoPtr() < ge, SystemError,
+//				msg + "Wrong genotype pointer");
 #else
 			DBG_ASSERT(it->genoPtr() >= gb && it->genoPtr() < ge, SystemError,
 				msg + "Wrong genotype pointer");
@@ -1038,7 +1013,7 @@
 	return ret;
 }
 
-/*
+
 void Population::removeSubPops(const subPopList & subPops)
 {
 	syncIndPointers();
@@ -1049,13 +1024,8 @@
 	size_t infoStep = infoSize();
 	RawIndIterator oldInd = m_inds.begin();
 	RawIndIterator newInd = m_inds.begin();
-#ifdef MUTANTALLELE
-	size_t oldPtr = 0;
-	size_t newPtr = 0;
-#else
 	GenoIterator oldPtr = m_genotype.begin();
 	GenoIterator newPtr = m_genotype.begin();
-#endif
 	InfoIterator oldInfoPtr = m_info.begin();
 	InfoIterator newInfoPtr = m_info.begin();
 
@@ -1093,7 +1063,7 @@
 					if (oldInd != newInd) {
 						*newInd = *oldInd;
 #ifdef MUTANTALLELE
-						copyGenotype(m_genotype, oldPtr, oldPtr + step, m_genotype, newPtr);
+						simuPOP::copy(oldPtr, oldPtr + step, newPtr);
 #else
 						copy(oldPtr, oldPtr + step, newPtr);
 #endif
@@ -1119,7 +1089,7 @@
 			// do not remove.
 			if (oldPtr != newPtr) {
 #ifdef MUTANTALLELE
-				copyGenotype(m_genotype, oldPtr, oldPtr + step * spSize, m_genotype, newPtr);
+				simuPOP::copy(oldPtr, oldPtr + step * spSize, newPtr);
 #else
 				copy(oldPtr, oldPtr + step * spSize, newPtr);
 #endif
@@ -1136,29 +1106,19 @@
 	}
 	//
 	m_inds.erase(newInd, m_inds.end());
-#ifdef MUTANTALLELE
-	eraseGenotype(m_genotype, newPtr, m_genotype.size());
-#else
 	m_genotype.erase(newPtr, m_genotype.end());
-#endif
 	m_info.erase(newInfoPtr, m_info.end());
 	m_popSize = std::accumulate(new_size.begin(), new_size.end(), size_t(0));
 	setSubPopStru(new_size, new_spNames);
 	//
 	InfoIterator infoPtr = m_info.begin();
-#ifdef MUTANTALLELE
-	size_t idx = 0;
-	for (size_t i = 0; i < m_popSize; ++i, idx += step, infoPtr += infoStep) {
-		m_inds[i].setGenoPtr(&m_genotype, idx);
-#else
 	GenoIterator ptr = m_genotype.begin();
 	for (size_t i = 0; i < m_popSize; ++i, ptr += step, infoPtr += infoStep) {
 		m_inds[i].setGenoPtr(ptr);
-#endif
 		m_inds[i].setInfoPtr(infoPtr);
 	}
 }
-*/
+
 /*
 void Population::removeMarkedIndividuals()
 {
@@ -1315,7 +1275,7 @@
 }
 */
 
-/*
+
 size_t Population::mergeSubPops(const uintList & subPops, const string & name)
 {
 	if (!name.empty() && m_subPopNames.empty())
@@ -1386,13 +1346,8 @@
 	size_t infoStep = infoSize();
 	vector<Individual> new_inds;
 	vectorf new_info;
-#ifdef MUTANTALLELE
-	compressed_vectora new_genotype;
-	new_genotype.reserve(step * popSize());
-#else
 	vectora new_genotype;
 	new_genotype.reserve(step * popSize());
-#endif
 	new_inds.reserve(popSize());
 	new_info.reserve(infoStep * popSize());
 
@@ -1403,7 +1358,7 @@
 		// do not remove.
 		new_inds.insert(new_inds.end(), rawIndBegin(src), rawIndEnd(src));
 #ifdef MUTANTALLELE
-		insertGenotype(new_genotype, new_genotype.size(), m_genotype, genoBegin(src, true), genoEnd(src, true));
+		simuPOP::insert(new_genotype.end(), genoBegin(src, true), genoEnd(src, true));
 #else
 		new_genotype.insert(new_genotype.end(), genoBegin(src, true), genoEnd(src, true));
 #endif
@@ -1424,20 +1379,14 @@
 	setSubPopStru(new_size, new_names);
 	//
 	InfoIterator infoPtr = m_info.begin();
-#ifdef MUTANTALLELE
-	size_t idx = 0;
-	for (size_t i = 0; i < m_popSize; ++i, idx += step, infoPtr += infoStep) {
-		m_inds[i].setGenoPtr(&m_genotype, idx);
-#else
 	GenoIterator ptr = m_genotype.begin();
 	for (size_t i = 0; i < m_popSize; ++i, ptr += step, infoPtr += infoStep) {
 		m_inds[i].setGenoPtr(ptr);
-#endif
 		m_inds[i].setInfoPtr(infoPtr);
 	}
 	return sps[0];
 }
-*/
+
 /*
 void Population::addChromFrom(const Population & pop)
 {
@@ -3661,15 +3610,8 @@
 
 		size_t is = infoSize();
 		size_t sz = genoSize();
-#ifdef MUTANTALLELE
-//		compressed_vectora tmpGenotype(m_popSize * genoSize());
-//		size_t it = 0;
 		vectora tmpGenotype(m_popSize * genoSize());
 		vectora::iterator it = tmpGenotype.begin();
-#else
-		vectora tmpGenotype(m_popSize * genoSize());
-		vectora::iterator it = tmpGenotype.begin();
-#endif
 		vectorf tmpInfo(m_popSize * infoSize());
 		vectorf::iterator infoPtr = tmpInfo.begin();
 
@@ -3679,21 +3621,14 @@
 			copyGenotype(ind->genoBegin(), it, sz);
 #else
 #  ifdef MUTANTALLELE
-//			copyGenotype(*ind->genoPtr(), ind->genoBegin(), ind->genoEnd(), tmpGenotype, it);
 			simuPOP::copy(ind->genoBegin(), ind->genoEnd(), it);
 #  else
 			copy(ind->genoBegin(), ind->genoEnd(), it);
 #  endif
 #endif
 
-#ifdef MUTANTALLELE
-//			ind->setGenoPtr(&tmpGenotype, it);
 			ind->setGenoPtr(it);
-#else
-			ind->setGenoPtr(it);
-#endif
 			it += sz;
-
 			copy(ind->infoBegin(), ind->infoEnd(), infoPtr);
 			ind->setInfoPtr(infoPtr);
 			infoPtr += is;

Modified: branches/mutant_new/src/population.h
===================================================================
--- branches/mutant_new/src/population.h	2011-10-13 18:58:37 UTC (rev 4320)
+++ branches/mutant_new/src/population.h	2011-10-14 18:18:26 UTC (rev 4321)
@@ -834,63 +834,6 @@
 
 
 
-#ifdef MUTANTALLELE
-/*
-	compressed_vectora * genoPtr()
-	{
-		return &m_genotype;
-	}
-
-
-	size_t genoBegin(bool order)
-	{
-		DBG_FAILIF(hasActivatedVirtualSubPop(), ValueError,
-			"This function is not valid with an activated virtual subpopulation");
-
-		if (order && !indOrdered())
-			syncIndPointers();
-
-		return 0;
-	}
-
-
-	///  CPPONLY
-	size_t genoEnd(bool order)
-	{
-		DBG_FAILIF(hasActivatedVirtualSubPop(), ValueError,
-			"This function is not valid with an activated virtual subpopulation");
-		if (order && !indOrdered())
-			syncIndPointers();
-
-		return m_genotype.size();
-	}
-
-
-	///  CPPONLY
-	size_t genoBegin(size_t subPop, bool order)
-	{
-		DBG_FAILIF(hasActivatedVirtualSubPop(), ValueError,
-			"This function is not valid with an activated virtual subpopulation");
-		CHECKRANGESUBPOP(subPop);
-
-		syncIndPointers(order);
-
-		return m_subPopIndex[subPop] * genoSize();
-	}
-
-
-	///  CPPONLY
-	size_t genoEnd(size_t subPop, bool order)
-	{
-		DBG_FAILIF(hasActivatedVirtualSubPop(), ValueError,
-			"This function is not valid with an activated virtual subpopulation");
-		CHECKRANGESUBPOP(subPop);
-		syncIndPointers(order);
-
-		return m_subPopIndex[subPop + 1] * genoSize();
-	}
-*/
-#else
 	///  CPPONLY allele iterator, go through all allels one by one, without subPop info
 	/**
 	   if order, in order
@@ -947,7 +890,6 @@
 
 		return m_genotype.begin() + m_subPopIndex[subPop + 1] * genoSize();
 	}
-#endif
 
 
 #ifdef MUTANTALLELE
@@ -1040,7 +982,7 @@
 	 *  <tt>subPopSize(subPop)*totNumLoci()*ploidy()</tt>.
 	 *  <group>5-genotype</group>
 	 */
-//	void setGenotype(const uintList & geno, vspID subPop = vspID());
+	void setGenotype(const uintList & geno, vspID subPop = vspID());
 
 	//@}
 
@@ -1084,7 +1026,7 @@
 	 *  This function only handles the present generation.
 	 *  <group>7-manipulate</group>
 	 */
-//	void removeSubPops(const subPopList & subPops);
+	void removeSubPops(const subPopList & subPops);
 
 	/// CPPONLY
 //	void removeMarkedIndividuals();
@@ -1121,7 +1063,7 @@
 	 *  function returns the ID of the merged subpopulation.
 	 *  <group>7-manipulate</group>
 	 */
-//	size_t mergeSubPops(const uintList & subPops = uintList(), const string & name = UnnamedSubPop);
+	size_t mergeSubPops(const uintList & subPops = uintList(), const string & name = UnnamedSubPop);
 
 	/** Add all individuals, including ancestors, in \e pop to the current
 	 *  population. Two populations should have the same genotypic structures

Modified: branches/mutant_new/src/utility.cpp
===================================================================
--- branches/mutant_new/src/utility.cpp	2011-10-13 18:58:37 UTC (rev 4320)
+++ branches/mutant_new/src/utility.cpp	2011-10-14 18:18:26 UTC (rev 4321)
@@ -114,12 +114,9 @@
 #ifndef STANDALONE_EXECUTABLE
 // these functions are defined in customizedTypes.c which is included
 // in simuPOP_wrap.cpp
-#ifdef MUTANTALLELE
-//extern "C" PyObject * newcarrayobject(compressed_vectora * genoPtr, Py_ssize_t begin, Py_ssize_t end);
+
 extern "C" PyObject * newcarrayobject(GenoIterator begin, GenoIterator end);
-#else
-extern "C" PyObject * newcarrayobject(GenoIterator begin, GenoIterator end);
-#endif
+
 extern "C" PyObject * PyDefDict_New();
 
 extern "C" bool is_defdict(PyTypeObject * type);
@@ -127,12 +124,8 @@
 extern "C" int initCustomizedTypes(void);
 
 #else
-#  ifdef MUTANTALLELE
-//PyObject * newcarrayobject(compressed_vectora * genoPtr, Py_ssize_t begin, Py_ssize_t end);
+
 PyObject * newcarrayobject(GenoIterator, GenoIterator)
-#  else
-PyObject * newcarrayobject(GenoIterator, GenoIterator)
-#  endif
 {
 	return NULL;
 }
@@ -1231,14 +1224,6 @@
 	}
 }
 
-#ifdef MUTANTALLELE
-//PyObject * Allele_Vec_As_NumArray(compressed_vectora * genoPtr,Py_ssize_t begin, Py_ssize_t end)
-//{
-//	PyObject * res = newcarrayobject(genoPtr, begin, end);
-//
-//	DBG_FAILIF(res == NULL, ValueError, "Can not convert buf to Allele num array");
-//	return res;
-//}
 PyObject * Allele_Vec_As_NumArray(GenoIterator begin, GenoIterator end)
 {
 	PyObject * res = newcarrayobject(begin, end);
@@ -1246,17 +1231,8 @@
 	DBG_FAILIF(res == NULL, ValueError, "Can not convert buf to Allele num array");
 	return res;
 }
-#else
-PyObject * Allele_Vec_As_NumArray(GenoIterator begin, GenoIterator end)
-{
-	PyObject * res = newcarrayobject(begin, end);
 
-	DBG_FAILIF(res == NULL, ValueError, "Can not convert buf to Allele num array");
-	return res;
-}
-#endif
 
-
 string PyObj_AsString(PyObject * str)
 {
 #if PY_VERSION_HEX >= 0x03000000

Modified: branches/mutant_new/src/utility.h
===================================================================
--- branches/mutant_new/src/utility.h	2011-10-13 18:58:37 UTC (rev 4320)
+++ branches/mutant_new/src/utility.h	2011-10-14 18:18:26 UTC (rev 4321)
@@ -988,12 +988,7 @@
 void PyObj_As_IntArray(PyObject * obj, vectori & val);
 
 /// CPPONLY
-#ifdef MUTANTALLELE
-//PyObject * Allele_Vec_As_NumArray(compressed_vectora * genoPtr,Py_ssize_t begin, Py_ssize_t end);
 PyObject * Allele_Vec_As_NumArray(GenoIterator begin, GenoIterator end);
-#else
-PyObject * Allele_Vec_As_NumArray(GenoIterator begin, GenoIterator end);
-#endif
 
 /// CPPONLY
 string PyObj_AsString(PyObject * str);

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