baobab.applogic.trace
Class TraceAppLogicUtil
java.lang.Object
baobab.applogic.AppLogicUtil
baobab.applogic.trace.TraceAppLogicUtil
public class TraceAppLogicUtil
- extends AppLogicUtil
Constructor Summary |
TraceAppLogicUtil(java.lang.String outputDir,
java.lang.String permName,
java.lang.String permId)
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TraceAppLogicUtil(java.lang.String workDir,
java.lang.String permName,
java.lang.String permId,
boolean output)
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TraceAppLogicUtil(java.lang.String workDir,
java.lang.String permName,
java.lang.String permId,
boolean output,
java.lang.String[] mapIntToNames,
java.util.Hashtable<java.lang.String,java.util.TreeSet<java.lang.String>> mapNamesToDescriptions,
boolean condenseNames)
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Method Summary |
TraceSortedSet |
analyzeDecomposedTraces(ComplexSignedPermutationBPGraph permutation,
int reversalDistance,
boolean removePrevious,
int baseStep,
int prevSize,
boolean isFragmented,
int x,
int y,
int z,
java.lang.String thisWorkDir,
int[] decompose,
int maxNonPerfectReversalScore,
boolean doProgressiveDetection,
TerminusSymmetryReversalConstraint symmetry)
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TraceSortedSet |
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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void |
close(boolean isSubTrace)
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void |
closeTraceInFile()
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void |
codeTraces(int elementSize,
int numberOfElements,
int numberOfConstraints,
int x,
int y,
int z)
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void |
decodeTraces(int elementSize,
int numberOfElements,
int numberOfConstraints,
int x,
int y,
int z,
boolean printNames)
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void |
diffTraces(int numberOfElements,
int elementSize,
boolean isSubTrace,
TraceSortedSet big,
java.lang.String smallSuffix,
java.lang.String diffSuffix)
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TraceSortedSet |
enumerateTraces(SignedPermutationBPGraph permutation,
int reversalDistance,
int x,
int y,
int z,
int[] strata)
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void |
enumerateTracesByStrata(SignedPermutationBPGraph permutation,
int reversalDistance,
int lastBreakPoint,
java.util.Vector<int[]> expectedReversals,
int[] strataBoundaries,
boolean strataOnly)
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void |
openTraceInFile(int numberOfElements,
java.lang.String suffix)
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TraceSortedSet |
readCodedTraces(int elementSize,
int numberOfElements,
int numberOfConstraints,
int x,
int y,
int z)
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Trace |
readTrace(int permutationSize,
int numberOfElements,
boolean isSubTrace)
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TraceSortedSet |
readTraces(SignedPermutationBPGraph permutation,
int numberOfElements,
boolean isSubTrace,
int x,
int y,
int z)
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Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
TraceAppLogicUtil
public TraceAppLogicUtil(java.lang.String workDir,
java.lang.String permName,
java.lang.String permId,
boolean output,
java.lang.String[] mapIntToNames,
java.util.Hashtable<java.lang.String,java.util.TreeSet<java.lang.String>> mapNamesToDescriptions,
boolean condenseNames)
TraceAppLogicUtil
public TraceAppLogicUtil(java.lang.String workDir,
java.lang.String permName,
java.lang.String permId,
boolean output)
TraceAppLogicUtil
public TraceAppLogicUtil(java.lang.String outputDir,
java.lang.String permName,
java.lang.String permId)
close
public void close(boolean isSubTrace)
closeTraceInFile
public void closeTraceInFile()
openTraceInFile
public void openTraceInFile(int numberOfElements,
java.lang.String suffix)
readTrace
public Trace readTrace(int permutationSize,
int numberOfElements,
boolean isSubTrace)
analyzeTraces
public TraceSortedSet 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)
analyzeDecomposedTraces
public TraceSortedSet analyzeDecomposedTraces(ComplexSignedPermutationBPGraph permutation,
int reversalDistance,
boolean removePrevious,
int baseStep,
int prevSize,
boolean isFragmented,
int x,
int y,
int z,
java.lang.String thisWorkDir,
int[] decompose,
int maxNonPerfectReversalScore,
boolean doProgressiveDetection,
TerminusSymmetryReversalConstraint symmetry)
enumerateTraces
public TraceSortedSet enumerateTraces(SignedPermutationBPGraph permutation,
int reversalDistance,
int x,
int y,
int z,
int[] strata)
enumerateTracesByStrata
public void enumerateTracesByStrata(SignedPermutationBPGraph permutation,
int reversalDistance,
int lastBreakPoint,
java.util.Vector<int[]> expectedReversals,
int[] strataBoundaries,
boolean strataOnly)
diffTraces
public void diffTraces(int numberOfElements,
int elementSize,
boolean isSubTrace,
TraceSortedSet big,
java.lang.String smallSuffix,
java.lang.String diffSuffix)
readTraces
public TraceSortedSet readTraces(SignedPermutationBPGraph permutation,
int numberOfElements,
boolean isSubTrace,
int x,
int y,
int z)
readCodedTraces
public TraceSortedSet readCodedTraces(int elementSize,
int numberOfElements,
int numberOfConstraints,
int x,
int y,
int z)
decodeTraces
public void decodeTraces(int elementSize,
int numberOfElements,
int numberOfConstraints,
int x,
int y,
int z,
boolean printNames)
codeTraces
public void codeTraces(int elementSize,
int numberOfElements,
int numberOfConstraints,
int x,
int y,
int z)