📄 smoother.java
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/*** This code was written by Kent Paul Dolan, from scratch. So far as I** know, it is an original (though obvious) algorithm. See accompanying** file TravellerDoc.html for status for your use.*/package com.well.www.user.xanthian.java.genetic.reproducers.asexual;import com.coyotegulch.tools.*;import com.coyotegulch.genetic.*;import com.well.www.user.xanthian.java.genetic.*;import com.well.www.user.xanthian.java.tools.*;import com.well.www.user.xanthian.java.ui.*;public class Smoother implements AsexualReproducer{/*** Because we do (perhaps may times) N*( M! ) permutations, we cannot** afford the computational burden of the global permute limit; support** a local one as well. Unlike Optimize Near A Point, we are not helped** particularly by favorable geometry as we approach the solution,** either, and for large genomes, our worst case is our usual case.** ** FIXME Tune this limit; the algorithm grows immensely more powerful** with increased limit, but it also grows sloooooow!*/ private static final int LOCAL_PERMUTE_LIMIT = 6; private static boolean DB = false; private static boolean VDB = false; private static VisualDebugger m_vdb = null; public Chromosome reproduce(Chromosome parent) { try {/*** Debugging hook abbreviation. During development, turn on debugging** just for this class by setting this variable to true, here. When the** code is stable, set it to false here, and control debugging from the** checkbox controls panel, instead. This variable is global to this** class, so it controls debugging thoughout the class when set here at** the top of the entry method for the class.*/ DB = false; if (CheckBoxControls.getState(CheckBoxControls.CBC_DEBUG_PRINTOUTS)) { DB = true; System.out.println ( "Entered Smoother.reproduce( Chromosome parent)" ); }/*** Pass the input as a less burdensome type.*/ TravellerChromosome child = algorithm( (TravellerChromosome) parent ); child.setOriginator( "Smoother" ); child.checkValidity(); return (Chromosome) child; } catch (Exception e) { System.err.println ( "Smoother.reproduce() threw!" ); }/*** This code should never be reached, it is just here to pacify javac.*/ return parent; } private TravellerChromosome algorithm( TravellerChromosome parent ) { VDB = false; if (CheckBoxControls.getState(CheckBoxControls.CBC_DEBUG_VISUAL_WINDOWS)) { VDB = true; } if (VDB) { if ( m_vdb == null ) { m_vdb = new VisualDebugger( "Smoother" ); } } else { if ( m_vdb != null ) { m_vdb.closeWindow(); m_vdb = null; } } if (VDB) { m_vdb.toFront(); } MersenneTwister mt = MersenneTwister.getTwister(); TravellerChromosome offspring = new TravellerChromosome( parent ); offspring.canonicalize(); double startingFitness = offspring.testFitness(); if (VDB) { m_vdb.setup( offspring ); } TravellerWorld world = parent.getWorld(); int genomeLength = ValuatorControls.getNumberOfCities();/*** To cut off N points, we need N + 1 cleavage indices; the rest of the** genome acts as the N+1st permutee.*/ int permuteSize = 1 + ( new PermutationController() ) .getAPermuteSize ( Math.min ( genomeLength - 1, LOCAL_PERMUTE_LIMIT ) ); int cleavageIndices[] = new int[permuteSize]; pickCleavageIndices( cleavageIndices, genomeLength, mt ); int failureCount = 0; while( failureCount < genomeLength ) { if ( bladeful( cleavageIndices, offspring, world, mt ) ) { failureCount = 0; } else { failureCount++; } advanceBlade( cleavageIndices, genomeLength ); if (VDB) { m_vdb.step( offspring ); } }/*** Who knows what order the result has? Better fix it.*/ offspring.canonicalize(); double finalFitness = offspring.testFitness();/*** We only change for the better, so if we haven't changed, we haven't** improved. Report back so that adaptive permutation high limit can** eventually be updated.*/ if ( Math.abs( finalFitness - startingFitness ) < TravellerStatus.LITTLE_FUZZ ) { PermutationController.reportFailure(); } else { PermutationController.reportSuccess(); } if (VDB) { m_vdb.done( parent, offspring ); } return offspring; } private boolean inList( int c, int list[] ) { for (int i = 0; i < list.length; i++) { if (c == list[i]) { return true; } } return false; } private int listIndex( int c, int list[] ) { for (int i = 0; i < list.length; i++) { if (c == list[i]) { return i; } } return -1; } private boolean bladeful ( int cleavageIndices[], TravellerChromosome mutant, TravellerWorld world, MersenneTwister mt ) { double fitnessAtStart = mutant.testFitness(); if (DB) { System.out.println( fitnessAtStart + " fitness at start of bladeful" ); }/*** Create a local _copy_ of the input parameter; remind self not to** scribble on it!*/ TravellerChromosome readOnlyVersion = new TravellerChromosome( mutant ); int permuteSize = cleavageIndices.length; int genomeLength = ValuatorControls.getNumberOfCities(); PermutationGenerator pg = new PermutationGenerator( permuteSize, false );/*** Create cleavage point auxiliary arrays.*/ int sublistBeginCities[] = new int[permuteSize]; int sublistEndCities[] = new int[permuteSize]; for (int i = 0; i < permuteSize; i++) { sublistBeginCities[i] = -1; sublistEndCities[i] = -1; }/*** Fill in auxiliary array information. For computing relative fitness,** we don't need the whole sublists, the interior lengths don't change.** We just need the end points to connect to each other.*/ for (int i = 0; i < permuteSize; i++) { sublistBeginCities[i] = mutant.getCity(cleavageIndices[i]); sublistEndCities[i] = mutant.getCity ( ( cleavageIndices[(i + 1) % permuteSize] - 1 + genomeLength ) % genomeLength ); } int bestPermutation[] = new int[permuteSize];/*** Choose the original configuration as the best found, for a start.*/ for (int i = 0; i < permuteSize; i++) { bestPermutation[i] = i; } double bestFitness = Double.MAX_VALUE; Integer [] nextPermutation = null; while ( pg.morePermutations() ) { try { nextPermutation = pg.getNext(); } catch (Exception e) { System.out.println ( "caught pg.getNext() throw in Smoother" ); } double currentFitness = 0.0D; for (int i = 0; i < permuteSize; i++) { int nextIndex = ( i + 1 ) % permuteSize; currentFitness += world.getDistance ( ( sublistEndCities[nextPermutation[i].intValue()] ), ( sublistBeginCities[nextPermutation[nextIndex].intValue()] ) ); } if (currentFitness < bestFitness) { bestFitness = currentFitness; // Notice that this time we are actually capturing the // permutation rather than what it indexes; we have a // bunch of work to do to construct the final product // mutant at the end of all this foolishness. for (int i = 0; i < permuteSize; i++) { bestPermutation[i] = nextPermutation[i].intValue(); } } } // We are going to scribble on mutant, so use the local name of // the input parameter as an unclobbered data source for city names. // Starting at the beginning of the output chromosome, mutant, // write the sublists in their permuted order, flipped as needed. int writeToIndex = 0; for (int i = 0; i < permuteSize; i++) { int currentCleavageIndicesIndex = bestPermutation[i]; int nextCleavageIndicesIndex = ( currentCleavageIndicesIndex + 1 ) % permuteSize; int currentChromosomeIndex = cleavageIndices[currentCleavageIndicesIndex]; int nextChromosomeIndex = ( cleavageIndices[nextCleavageIndicesIndex] - 1 + genomeLength ) % genomeLength; int j = currentChromosomeIndex; while ( true ) { mutant.setCity( writeToIndex, readOnlyVersion.getCity(j)); writeToIndex++; if ( j == nextChromosomeIndex ) { break; } j = ( j + 1 ) % genomeLength; } }/*** This is dubious; we are modifying mutant during the cycle. Luckily,** this only changes mutant at the beginning and end of the genome** array, and we also walk the array from end to end. Still, the first** two steps and the last two steps may rearrange the genome under us,** so this algorithm isn't perfect. The alternative, used in Dewrinkler** where it is unavoidable, is to new() a temp copy of the genome and** canonicalize so that we can test its fitness.*/ mutant.canonicalize(); // System.out.println( mutant.toString() ); double fitnessAtEnd = mutant.testFitness(); // System.out.println( fitnessAtEnd + " fitness at end of bladeful " ); return ( ( fitnessAtStart - fitnessAtEnd ) > TravellerStatus.LITTLE_FUZZ ); } private void pickCleavageIndices ( int cleavageIndices[], int genomeLength, MersenneTwister mt ) { int permuteSize = cleavageIndices.length; for (int i = 0; i < permuteSize; i++) { cleavageIndices[i] = i; } } private void advanceBlade ( int cleavageIndices[], int genomeLength ) { for ( int i = 0; i < cleavageIndices.length; i++ ) { cleavageIndices[i] = ( (cleavageIndices[i] + 1 ) % genomeLength) ; } // System.out.println( Debugging.dump( cleavageIndices ) ); }}
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