From 3cdf68e08d438a0ced0f5f8d957a6aafd68cb43a Mon Sep 17 00:00:00 2001
From: Mike Buland <mike@xagasoft.com>
Date: Thu, 2 Aug 2012 15:20:58 -0600
Subject: New commit method

---
 default.bld             |  3 +++
 src/phenotypebinary.cpp | 56 +++++++++++++++++++++++++++++++++++++++++++++++++
 src/tests/binary.cpp    | 18 ++++++++++------
 3 files changed, 71 insertions(+), 6 deletions(-)

diff --git a/default.bld b/default.bld
index a6be035..65c8adb 100644
--- a/default.bld
+++ b/default.bld
@@ -1,3 +1,6 @@
+CXXFLAGS += "-pg";
+LDFLAGS += "-pg";
+
 target "libgenetic.a"
 {
 	rule "lib";
diff --git a/src/phenotypebinary.cpp b/src/phenotypebinary.cpp
index 0d32c9f..9d9e26c 100644
--- a/src/phenotypebinary.cpp
+++ b/src/phenotypebinary.cpp
@@ -18,6 +18,8 @@ Genetic::PhenotypeBinary::PhenotypeBinary( int iSize, bool bRandom ) :
 	aGenes = new uint_fast32_t[iWords];
 	if( bRandom )
 		randomize();
+	else
+		memset( aGenes, 0, sizeof(uint_fast32_t)*iWords );
 }
 
 Genetic::PhenotypeBinary::~PhenotypeBinary()
@@ -57,12 +59,16 @@ Genetic::Phenotype *Genetic::PhenotypeBinary::makeEmptyOffspring(
 Genetic::Phenotype &Genetic::PhenotypeBinary::copyFrom( const Phenotype &rSrc,
 		int iStart, int iCount, int iDest )
 {
+	if( iCount <= 0 )
+		return *this;
+
 	const PhenotypeBinary &rbSrc =
 		dynamic_cast<const Genetic::PhenotypeBinary &>(rSrc);
 	if( iDest < 0 )
 		iDest = iStart;
 
 	// Fist draft, very sloppy: bit by bit copy, this is stupid, but easy
+	/*
 	for( int j = 0; j < iCount; j++ )
 	{
 		int wd = wordWithBit(j+iDest);
@@ -76,6 +82,56 @@ Genetic::Phenotype &Genetic::PhenotypeBinary::copyFrom( const Phenotype &rSrc,
 			aGenes[wd] |= (1<<((j+iDest)%BPW));
 		}
 	}
+	*/
+
+	{
+		if( iDest == iStart )
+		{
+			if( wordWithBit(iStart) == wordWithBit(iStart+iCount-1) )
+			{
+				uint_fast32_t uMask = -1;
+				uMask = (uMask << (iStart%BPW)) &
+					(uMask >> (BPW-(((iStart+iCount))%BPW)));
+//				sio << Fmt().radix(2).width(32).fill('0') << uMask << sio.nl;
+				aGenes[wordWithBit( iDest )] =
+					(aGenes[wordWithBit( iDest )]&(~uMask)) |
+					(rbSrc.aGenes[wordWithBit( iStart )]&uMask);
+			}
+			else
+			{
+				int iStartWord = wordWithBit( iStart );
+				int iEndWord = wordWithBit( iStart+iCount );
+
+//				sio << wordWithBit( iStart+iCount ) << "/" << iWords << sio.nl;
+//				sio << iStart << " + " << iCount << " = "  << iStart+iCount << " / " << iSize << sio.nl;
+
+
+				uint_fast32_t uMask = -1;
+				uMask = uMask << (iStart%BPW);
+//				sio << Fmt().radix(2).width(32).fill('0') << uMask << sio.nl;
+				aGenes[wordWithBit( iDest )] =
+					(aGenes[wordWithBit( iDest )]&(~uMask)) |
+					(rbSrc.aGenes[wordWithBit( iStart )]&uMask);
+
+				for( int j = iStartWord+1; j < iEndWord; j++ )
+					aGenes[j] = rbSrc.aGenes[j];
+				
+				uMask = ((uint_fast32_t)-1) >> (BPW-(((iStart+iCount))%BPW));
+//				sio << Fmt().radix(2).width(32).fill('0') << uMask << sio.nl;
+				aGenes[wordWithBit( iDest+iCount-1 )] =
+					(aGenes[wordWithBit( iDest+iCount-1 )]&(~uMask)) |
+					(rbSrc.aGenes[wordWithBit( iStart+iCount-1 )]&uMask);
+			}
+		}
+		else if( iDest < iStart )
+		{
+			sio << "iDest < iStart not finished." << sio.nl;
+		}
+		else
+		{
+			sio << "iDest > iStart not finished." << sio.nl;
+		}
+	}	
 
 	/*
 	iStart%BPW
diff --git a/src/tests/binary.cpp b/src/tests/binary.cpp
index 717c171..727feec 100644
--- a/src/tests/binary.cpp
+++ b/src/tests/binary.cpp
@@ -13,24 +13,30 @@ int main( int argc, char *argv[] )
 	Bu::Random::setGenerator<Bu::RandomCmwc>();
 	Bu::Random::seed( time( NULL ) );
 
-	Genetic::OperatorBasic op( new Genetic::PhenotypeBinary( 45 ), 0.1 );
+	Genetic::OperatorBasic op( new Genetic::PhenotypeBinary( 422*1024 ), 0.0 );
 	Genetic::Phenotype *pPb1 = op.random();
 	Genetic::Phenotype *pPb2 = op.random();
 	Genetic::Phenotype *pPb3;
 
-	sio << pPb1->toString() << sio.nl;
-	sio << pPb2->toString() << sio.nl;
+//	sio << pPb1->toString() << sio.nl;
+//	sio << pPb2->toString() << sio.nl;
 
 	Genetic::PhenotypeList lParents;
 	lParents.append( pPb1 );
 	lParents.append( pPb2 );
-	pPb3 = op.mate( lParents );
 
-	sio << pPb3->toString() << sio.nl;
+	for( int j = 0; j < 1000; j++ )
+	{
+		delete op.mate( lParents );
+	}
+
+//	pPb3 = pPb1->makeEmptyOffspring();
+//	pPb3->copyFrom( *pPb1, 4, 88 );
+//	sio << pPb3->toString() << sio.nl;
 
 	delete pPb1;
 	delete pPb2;
-	delete pPb3;
+//	delete pPb3;
 
 	return 0;
 }
-- 
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