[simuPOP-devel] SF.net SVN: simupop:[4535] trunk/src

[<si...@us...>]

Revision: 4535
          http://simupop.svn.sourceforge.net/simupop/?rev=4535&view=rev
Author:   simupop
Date:     2012-03-30 03:20:13 +0000 (Fri, 30 Mar 2012)
Log Message:
-----------
Greatly simplify fillGenotype

Modified Paths:
--------------
    trunk/src/mutant_vector.h
    trunk/src/transmitter.cpp
    trunk/src/utility.cpp
    trunk/src/utility.h

Modified: trunk/src/mutant_vector.h
===================================================================
--- trunk/src/mutant_vector.h	2012-03-30 02:59:08 UTC (rev 4534)
+++ trunk/src/mutant_vector.h	2012-03-30 03:20:13 UTC (rev 4535)
@@ -414,6 +414,17 @@
 		storage_invariants();
 	}
 
+	// clear some ... added by Bo
+	inline void clear(size_t beg, size_t end)
+	{
+		if (beg == end)
+			return;
+		BOOST_UBLAS_CHECK(beg < end && end <= size_, external_logic());
+		size_t b = _lower_bound(index_data_.begin(), index_data_.begin() + filled_, beg, std::less<size_type> ()) - index_data_.begin();
+		size_t e = _lower_bound(index_data_.begin(), index_data_.begin() + filled_, end, std::less<size_type> ()) - index_data_.begin();
+		for (size_t i = b; i < e; ++i)
+			value_data_[i] = 0;
+	}
 
 	class const_val_iterator;
 
@@ -794,6 +805,16 @@
 		}
 
 
+		size_t index() const
+		{
+			return m_index;
+		}
+
+		val_iterator getValIterator() const
+		{
+			return (*this)().val_begin(m_index);
+		}
+
 		const_reference value() const
 		{
 			static const Allele zero = 0;
@@ -1226,6 +1247,16 @@
 		}
 
 
+		size_t index() const
+		{
+			return m_index;
+		}
+
+		const_val_iterator getValIterator() const
+		{
+			return (*this)().val_begin(m_index);
+		}
+
 		const_reference value() const
 		{
 			static const Allele zero = 0;

Modified: trunk/src/transmitter.cpp
===================================================================
--- trunk/src/transmitter.cpp	2012-03-30 02:59:08 UTC (rev 4534)
+++ trunk/src/transmitter.cpp	2012-03-30 03:20:13 UTC (rev 4535)
@@ -64,8 +64,8 @@
 #else
 	DBG_FAILIF(m_chromIdx.empty(), ValueError, "GenoTransmitter is not initialized properly");
 #  ifdef MUTANTALLELE
-	fillGenotype(ind.genoBegin(ploidy) + m_chromIdx[chrom],
-		ind.genoBegin(ploidy) + m_chromIdx[chrom + 1], 0);
+	clearGenotype(ind.genoBegin(ploidy) + m_chromIdx[chrom],
+		ind.genoBegin(ploidy) + m_chromIdx[chrom + 1]);
 #  else
 	fill(ind.genoBegin(ploidy) + m_chromIdx[chrom],
 		ind.genoBegin(ploidy) + m_chromIdx[chrom + 1], 0);

Modified: trunk/src/utility.cpp
===================================================================
--- trunk/src/utility.cpp	2012-03-30 02:59:08 UTC (rev 4534)
+++ trunk/src/utility.cpp	2012-03-30 03:20:13 UTC (rev 4535)
@@ -4559,38 +4559,9 @@
 }
 
 
-void fillGenotype(GenoIterator begin, GenoIterator end, Allele value)
+void clearGenotype(GenoIterator begin, GenoIterator end)
 {
-	vectorm::index_array_type::iterator index_begin = begin.getIndexIterator();
-	vectorm::index_array_type::iterator index_end = end.getIndexIterator();
-	vectorm::value_array_type::iterator value_begin = begin.getValueIterator();
-	size_t diff_size = index_end - index_begin;
-	size_t filled_size = begin.getContainer()->filled();
-
-	if (value == 0) {
-		std::copy(index_begin + diff_size, begin.getContainer()->index_data().begin() + filled_size, index_begin);
-		std::copy(value_begin + diff_size, begin.getContainer()->value_data().begin() + filled_size, value_begin);
-		begin.getContainer()->set_filled(filled_size - diff_size);
-		//  If the fill function is extensively use, reserve() can be remove in order to improve performance .
-		begin.getContainer()->reserve(filled_size - diff_size);
-	} else {
-		size_t value_size = end - begin;
-		size_t insert_size = value_size - diff_size;
-		if (filled_size + insert_size >= begin.getContainer()->nnz_capacity()) {
-			begin.getContainer()->reserve(filled_size + insert_size, true);
-			// After using reserve(), index_begin and value_begin no longer valid, get a new one
-			index_begin = begin.getIndexIterator();
-			value_begin = begin.getValueIterator();
-		}
-		std::copy_backward(index_begin, begin.getContainer()->index_data().begin() + filled_size, begin.getContainer()->index_data().begin() + filled_size + insert_size);
-		for (size_t i = 0; i < value_size; i++) {
-			*(index_begin + i) = *index_begin + i;
-		}
-		std::copy_backward(value_begin, begin.getContainer()->value_data().begin() + filled_size, begin.getContainer()->value_data().begin() + filled_size + insert_size);
-		std::fill(value_begin, value_begin + value_size, value);
-		begin.getContainer()->set_filled(filled_size + insert_size);
-
-	}
+	begin.getContainer()->clear(begin.index(), end.index());
 }
 
 

Modified: trunk/src/utility.h
===================================================================
--- trunk/src/utility.h	2012-03-30 02:59:08 UTC (rev 4534)
+++ trunk/src/utility.h	2012-03-30 03:20:13 UTC (rev 4535)
@@ -2147,7 +2147,7 @@
 void copyGenotype(ConstGenoIterator begin, ConstGenoIterator end, GenoIterator it);
 
 /// CPPONLY
-void fillGenotype(GenoIterator begin, GenoIterator end, Allele value);
+void clearGenotype(GenoIterator begin, GenoIterator end);
 #endif
 
 

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