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Packages that use SignedPermutationBPGraph | |
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baobab.applogic | |
baobab.applogic.strata | |
baobab.applogic.trace | |
baobab.applogic.trace.benchmark | |
baobab.bio.permutation |
Uses of SignedPermutationBPGraph in baobab.applogic |
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Methods in baobab.applogic with parameters of type SignedPermutationBPGraph | |
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long |
AppLogicUtil.applyAllReversals(SignedPermutationBPGraph permutation,
int reversalDistance,
int performedReversals,
long subResult)
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long |
AppLogicUtil.countAllSortingSequences(SignedPermutationBPGraph permutation,
int reversalDistance)
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Uses of SignedPermutationBPGraph in baobab.applogic.strata |
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Methods in baobab.applogic.strata with parameters of type SignedPermutationBPGraph | |
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StrataSortedSet |
StrataAppLogicUtil.enumerateStrata(SignedPermutationBPGraph permutation,
int reversalDistance,
int strataNum)
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Uses of SignedPermutationBPGraph in baobab.applogic.trace |
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Methods in baobab.applogic.trace with parameters of type SignedPermutationBPGraph | |
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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)
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TraceSortedSet |
TraceAppLogicUtil.enumerateTraces(SignedPermutationBPGraph permutation,
int reversalDistance,
int x,
int y,
int z,
int[] strata)
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void |
TraceAppLogicUtil.enumerateTracesByStrata(SignedPermutationBPGraph permutation,
int reversalDistance,
int lastBreakPoint,
java.util.Vector<int[]> expectedReversals,
int[] strataBoundaries,
boolean strataOnly)
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TraceSortedSet |
TraceAppLogicUtil.readTraces(SignedPermutationBPGraph permutation,
int numberOfElements,
boolean isSubTrace,
int x,
int y,
int z)
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Uses of SignedPermutationBPGraph in baobab.applogic.trace.benchmark |
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Methods in baobab.applogic.trace.benchmark with parameters of type SignedPermutationBPGraph | |
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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)
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void |
BenchmarkTraceAppLogicUtil.analyzeTracesBenchmark1(SignedPermutationBPGraph permutation,
int reversalDistance,
boolean removePrevious,
int baseStep,
int prevSize,
boolean isFragmented,
PerfectReversalConstraint perfectConstraint,
TerminusSymmetryReversalConstraint symmetryConstraint,
StrataReversalConstraint strataConstraint)
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void |
BenchmarkTraceAppLogicUtil.analyzeTracesBenchmark2(SignedPermutationBPGraph permutation,
int reversalDistance,
boolean removePrevious,
int baseStep,
int prevSize,
boolean isFragmented,
PerfectReversalConstraint perfectConstraint,
TerminusSymmetryReversalConstraint symmetryConstraint,
StrataReversalConstraint strataConstraint)
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Uses of SignedPermutationBPGraph in baobab.bio.permutation |
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Subclasses of SignedPermutationBPGraph in baobab.bio.permutation | |
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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 | |
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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)
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static SignedPermutationBPGraph |
RandomPermutationBPGraph.createRandomSignedPermutation(int permutationSize,
int reversalDistance,
java.util.Vector<int[]> performedReversals,
java.lang.Long seed)
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static SignedPermutationBPGraph |
RandomPermutationBPGraph.createRandomStratifiedSignedPermutation(int permutationSize,
int reversalDistance,
boolean isLinear,
java.util.Vector<int[]> performedReversals,
int[] strataBoundaries,
boolean ascendingStratification,
long seed)
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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()
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SignedPermutationBPGraph |
SignedPermutationBPGraphReversalFilter.getPermutation()
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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 | |
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boolean |
SignedPermutationBPGraph.equals(SignedPermutationBPGraph perm)
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java.util.Vector<int[]> |
StrataReversalConstraint.getNextReversals(SignedPermutationBPGraph permutation)
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int |
TerminusSymmetryReversalConstraint.qualifyInterval(SignedPermutationBPGraph permutation,
int start,
int end)
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void |
PerfectReversalConstraint.update(SignedPermutationBPGraph permutation)
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Constructors in baobab.bio.permutation with parameters of type SignedPermutationBPGraph | |
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ComplexSignedPermutationBPGraph(SignedPermutationBPGraph other)
Creates a complex signed permutation over a simple signed permutation |
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PerfectReversalConstraint(SignedPermutationBPGraph permutation,
boolean progressiveDetection,
int maxNonPerfectReversalScore)
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ReversalConstraint(SignedPermutationBPGraph permutation,
int priority)
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SignedBPGraphReversalBlock(SignedPermutationBPGraph permutation,
BPGraphPoint start,
BPGraphPoint end)
Creates a new block |
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SignedBPGraphReversalBlock(SignedPermutationBPGraph permutation,
int start,
int end)
Creates a new block |
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