From 2406848173c445a94a1710106116ad796a8bacb9 Mon Sep 17 00:00:00 2001
From: Mike Buland <mike@xagasoft.com>
Date: Sat, 4 Aug 2012 18:34:57 -0600
Subject: Made some changes to make serializing workable.

There's no official format yet, but that's coming, most likely.
---
 src/explicitsimulation.h |  3 +++
 src/phenotype.h          |  4 ++++
 src/phenotypebinary.cpp  | 42 ++++++++++++++++++++++++++++++++----------
 src/phenotypebinary.h    |  8 +++-----
 4 files changed, 42 insertions(+), 15 deletions(-)

diff --git a/src/explicitsimulation.h b/src/explicitsimulation.h
index 7713c71..e71b489 100644
--- a/src/explicitsimulation.h
+++ b/src/explicitsimulation.h
@@ -22,11 +22,14 @@ namespace Genetic
 		virtual ~ExplicitSimulation();
 
 		void timestep();
+		const Population &getPopulation() const { return xPop; }
 
 		Genetic::PhenotypeId selectWeighted();
 
 		double getMinFitness() const { return dMinFitness; }
 		double getMaxFitness() const { return dMaxFitness; }
+		double getFitness( Genetic::PhenotypeId id ) const
+			{ return hFitness.get( id ); }
 
 	protected:
 		void updateFitness();
diff --git a/src/phenotype.h b/src/phenotype.h
index 0eafb78..27173e2 100644
--- a/src/phenotype.h
+++ b/src/phenotype.h
@@ -1,6 +1,7 @@
 #ifndef GENETIC_PHENOTYPE_H
 #define GENETIC_PHENOTYPE_H
 
+#include <bu/stream.h>
 #include <bu/string.h>
 #include <bu/hash.h>
 #include <bu/variant.h>
@@ -33,6 +34,9 @@ namespace Genetic
 
 		virtual Bu::String toString()=0;
 
+		virtual void write( Bu::Stream &rStream ) {};
+		virtual void read( Bu::Stream &rStream ) {};
+
 		bool hasProperty( const Bu::String &sKey ) const;
 		Bu::Variant getProperty( const Bu::String &sKey ) const;
 		void setProperty( const Bu::String &sKey, Bu::Variant vValue );
diff --git a/src/phenotypebinary.cpp b/src/phenotypebinary.cpp
index 9d9e26c..8ecd394 100644
--- a/src/phenotypebinary.cpp
+++ b/src/phenotypebinary.cpp
@@ -155,6 +155,38 @@ Bu::String Genetic::PhenotypeBinary::toString()
 	return sRet;
 }
 
+void Genetic::PhenotypeBinary::write( Bu::Stream &rStream )
+{
+	uint32_t uSize = htobe32( iSize );
+	rStream.write( &uSize, 4 );
+	uSize = (iSize/8) + ((iSize%8)?1:0);
+	for( int j = 0; j < uSize; j++ )
+	{
+		rStream.write(
+			&((char *)&aGenes[j/sizeof(uint_fast32_t)])[j%sizeof(uint_fast32_t)],
+			1
+			);
+	}
+}
+
+void Genetic::PhenotypeBinary::read( Bu::Stream &rStream )
+{
+	uint32_t uSize;
+	rStream.read( &uSize, 4 );
+	iSize = be32toh( uSize );
+	iWords = wordsForBits(iSize);
+	delete[] aGenes;
+	aGenes = new uint_fast32_t[iWords];
+	uSize = (iSize/8) + ((iSize%8)?1:0);
+	for( int j = 0; j < uSize; j++ )
+	{
+		rStream.read(
+			&((char *)&aGenes[j/sizeof(uint_fast32_t)])[j%sizeof(uint_fast32_t)],
+			1
+			);
+	}
+}
+
 void Genetic::PhenotypeBinary::extractBits( uint32_t &rTarget, int iStart,
 		int iBits )
 {
@@ -189,13 +221,3 @@ void Genetic::PhenotypeBinary::extractBits( uint64_t &rTarget, int iStart,
 	}
 }
 
-void Genetic::PhenotypeBinary::write( Bu::Stream &rStream )
-{
-	rStream.write( aGenes, sizeof(uint_fast32_t)*iWords );
-}
-
-void Genetic::PhenotypeBinary::read( Bu::Stream &rStream )
-{
-	rStream.read( aGenes, sizeof(uint_fast32_t)*iWords );
-}
-
diff --git a/src/phenotypebinary.h b/src/phenotypebinary.h
index f312187..92146d2 100644
--- a/src/phenotypebinary.h
+++ b/src/phenotypebinary.h
@@ -3,8 +3,6 @@
 
 #include "genetic/phenotype.h"
 
-#include <bu/stream.h>
-
 namespace Genetic
 {
 	class PhenotypeBinary : public Phenotype
@@ -21,12 +19,12 @@ namespace Genetic
 				int iCount, int iDest=-1 );
 		virtual Bu::String toString();
 
+		virtual void write( Bu::Stream &rStream );
+		virtual void read( Bu::Stream &rStream );
+
 		void extractBits( uint32_t &rTarget, int iStart, int iBits );
 		void extractBits( uint64_t &rTarget, int iStart, int iBits );
 
-		void write( Bu::Stream &rStream );
-		void read( Bu::Stream &rStream );
-
 	private:
 		int iSize;
 		int iWords;
-- 
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