Uses of Class
baobab.bio.permutation.SignedPermutationBPGraph

Packages that use SignedPermutationBPGraph
baobab.applogic   
baobab.applogic.strata   
baobab.applogic.trace   
baobab.applogic.trace.benchmark   
baobab.bio.permutation   
 

Uses of SignedPermutationBPGraph in baobab.applogic
 

Methods in baobab.applogic with parameters of type SignedPermutationBPGraph
 long AppLogicUtil.applyAllReversals(SignedPermutationBPGraph permutation, int reversalDistance, int performedReversals, long subResult)
           
 long AppLogicUtil.countAllSortingSequences(SignedPermutationBPGraph permutation, int reversalDistance)
           
 

Uses of SignedPermutationBPGraph in baobab.applogic.strata
 

Methods in baobab.applogic.strata with parameters of type SignedPermutationBPGraph
 StrataSortedSet StrataAppLogicUtil.enumerateStrata(SignedPermutationBPGraph permutation, int reversalDistance, int strataNum)
           
 

Uses of SignedPermutationBPGraph in baobab.applogic.trace
 

Methods in baobab.applogic.trace with parameters of type SignedPermutationBPGraph
 TraceSortedSet TraceAppLogicUtil.analyzeTraces(SignedPermutationBPGraph permutation, int reversalDistance, boolean removePrevious, int baseStep, int prevSize, boolean isFragmented, int x, int y, int z, PerfectReversalConstraint perfectConstraint, TerminusSymmetryReversalConstraint symmetryConstraint, StrataReversalConstraint strataConstraint)
           
 TraceSortedSet TraceAppLogicUtil.enumerateTraces(SignedPermutationBPGraph permutation, int reversalDistance, int x, int y, int z, int[] strata)
           
 void TraceAppLogicUtil.enumerateTracesByStrata(SignedPermutationBPGraph permutation, int reversalDistance, int lastBreakPoint, java.util.Vector<int[]> expectedReversals, int[] strataBoundaries, boolean strataOnly)
           
 TraceSortedSet TraceAppLogicUtil.readTraces(SignedPermutationBPGraph permutation, int numberOfElements, boolean isSubTrace, int x, int y, int z)
           
 

Uses of SignedPermutationBPGraph in baobab.applogic.trace.benchmark
 

Methods in baobab.applogic.trace.benchmark with parameters of type SignedPermutationBPGraph
 void BenchmarkTraceAppLogicUtil.analyzeTracesBenchmark0(SignedPermutationBPGraph permutation, int reversalDistance, boolean removePrevious, int baseStep, int prevSize, boolean isFragmented, int x, int y, int z, PerfectReversalConstraint perfectConstraint, TerminusSymmetryReversalConstraint symmetryConstraint, StrataReversalConstraint strataConstraint)
           
 void BenchmarkTraceAppLogicUtil.analyzeTracesBenchmark1(SignedPermutationBPGraph permutation, int reversalDistance, boolean removePrevious, int baseStep, int prevSize, boolean isFragmented, PerfectReversalConstraint perfectConstraint, TerminusSymmetryReversalConstraint symmetryConstraint, StrataReversalConstraint strataConstraint)
           
 void BenchmarkTraceAppLogicUtil.analyzeTracesBenchmark2(SignedPermutationBPGraph permutation, int reversalDistance, boolean removePrevious, int baseStep, int prevSize, boolean isFragmented, PerfectReversalConstraint perfectConstraint, TerminusSymmetryReversalConstraint symmetryConstraint, StrataReversalConstraint strataConstraint)
           
 

Uses of SignedPermutationBPGraph in baobab.bio.permutation
 

Subclasses of SignedPermutationBPGraph in baobab.bio.permutation
 class ComplexSignedPermutationBPGraph
          The ComplexSignedPermutationBPGraph class represents a signed permutation pair and its breakpoint graph (the ComplexSignedPermutationBPGraph class deals with hurdles)
 class WeightedSignedPermutationBPGraph
          The WeightedSignedPermutationBPGraph class represents a weighted signed permutation pair and its breakpoint graph (the WeightedSignedPermutationBPGraph class does not deal with hurdles)
 

Methods in baobab.bio.permutation that return SignedPermutationBPGraph
 SignedPermutationBPGraph SignedPermutationBPGraph.collapse(boolean monooriented)
          Collapses this permutation (eliminating adjacencies)
static SignedPermutationBPGraph RandomPermutationBPGraph.createRandomSignedPermutation(int permutationSize, int reversalDistance, boolean isLinear, java.util.Vector<int[]> performedReversals, java.lang.Long seed)
           
static SignedPermutationBPGraph RandomPermutationBPGraph.createRandomSignedPermutation(int permutationSize, int reversalDistance, java.util.Vector<int[]> performedReversals, java.lang.Long seed)
           
static SignedPermutationBPGraph RandomPermutationBPGraph.createRandomStratifiedSignedPermutation(int permutationSize, int reversalDistance, boolean isLinear, java.util.Vector<int[]> performedReversals, int[] strataBoundaries, boolean ascendingStratification, long seed)
           
static SignedPermutationBPGraph RandomPermutationBPGraph.createRandomStratifiedSignedPermutation(int permutationSize, int reversalDistance, boolean isLinear, java.util.Vector<int[]> performedReversals, java.util.Vector<java.lang.Integer> strataBoundaries, boolean ascendingStratification, long seed)
           
 SignedPermutationBPGraph SignedPermutationBPGraph.getNotCollapsed()
           
 SignedPermutationBPGraph SignedPermutationBPGraphReversalFilter.getPermutation()
           
 SignedPermutationBPGraph ComplexSignedPermutationBPGraph.revert(BPGraphPoint start, BPGraphPoint end)
          Reverts the permutation between the specified points
 SignedPermutationBPGraph SignedPermutationBPGraph.revert(BPGraphPoint start, BPGraphPoint end)
          Reverts the permutation between the specified points
 SignedPermutationBPGraph ComplexSignedPermutationBPGraph.revert(BPGraphReversalBlock block)
          Reverts the specified block of the permutation
 SignedPermutationBPGraph SignedPermutationBPGraph.revert(BPGraphReversalBlock block)
          Reverts the specified block of the permutation
 SignedPermutationBPGraph ComplexSignedPermutationBPGraph.revert(int start, int end)
          Reverts the permutation between the specified positions
 SignedPermutationBPGraph SignedPermutationBPGraph.revert(int start, int end)
          Reverts the permutation between the specified positions
 SignedPermutationBPGraph ComplexSignedPermutationBPGraph.revertToNewPermutation(BPGraphPoint start, BPGraphPoint end)
          Make a new permutation, by reverting the permutation between the specified positions
 SignedPermutationBPGraph SignedPermutationBPGraph.revertToNewPermutation(BPGraphPoint start, BPGraphPoint end)
          Make a new permutation, by reverting the permutation between the specified positions
 SignedPermutationBPGraph SignedPermutationBPGraph.revertToNewPermutation(int start, int end)
          Make a new permutation, by reverting the permutation between the specified positions
 

Methods in baobab.bio.permutation with parameters of type SignedPermutationBPGraph
 boolean SignedPermutationBPGraph.equals(SignedPermutationBPGraph perm)
           
 java.util.Vector<int[]> StrataReversalConstraint.getNextReversals(SignedPermutationBPGraph permutation)
           
 int TerminusSymmetryReversalConstraint.qualifyInterval(SignedPermutationBPGraph permutation, int start, int end)
           
 void PerfectReversalConstraint.update(SignedPermutationBPGraph permutation)
           
 

Constructors in baobab.bio.permutation with parameters of type SignedPermutationBPGraph
ComplexSignedPermutationBPGraph(SignedPermutationBPGraph other)
          Creates a complex signed permutation over a simple signed permutation
PerfectReversalConstraint(SignedPermutationBPGraph permutation, boolean progressiveDetection, int maxNonPerfectReversalScore)
           
ReversalConstraint(SignedPermutationBPGraph permutation, int priority)
           
SignedBPGraphReversalBlock(SignedPermutationBPGraph permutation, BPGraphPoint start, BPGraphPoint end)
          Creates a new block
SignedBPGraphReversalBlock(SignedPermutationBPGraph permutation, int start, int end)
          Creates a new block