baobab.applogic.trace
Class TraceAppLogicUtil

java.lang.Object
  extended by baobab.applogic.AppLogicUtil
      extended by baobab.applogic.trace.TraceAppLogicUtil

public class TraceAppLogicUtil
extends AppLogicUtil


Field Summary
 
Fields inherited from class baobab.applogic.AppLogicUtil
WORK_DIR
 
Constructor Summary
TraceAppLogicUtil(java.lang.String outputDir, java.lang.String permName, java.lang.String permId)
           
TraceAppLogicUtil(java.lang.String workDir, java.lang.String permName, java.lang.String permId, boolean output)
           
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)
           
 
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)
           
 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)
           
 void close(boolean isSubTrace)
           
 void closeTraceInFile()
           
 void codeTraces(int elementSize, int numberOfElements, int numberOfConstraints, int x, int y, int z)
           
 void decodeTraces(int elementSize, int numberOfElements, int numberOfConstraints, int x, int y, int z, boolean printNames)
           
 void diffTraces(int numberOfElements, int elementSize, boolean isSubTrace, TraceSortedSet big, java.lang.String smallSuffix, java.lang.String diffSuffix)
           
 TraceSortedSet enumerateTraces(SignedPermutationBPGraph permutation, int reversalDistance, int x, int y, int z, int[] strata)
           
 void enumerateTracesByStrata(SignedPermutationBPGraph permutation, int reversalDistance, int lastBreakPoint, java.util.Vector<int[]> expectedReversals, int[] strataBoundaries, boolean strataOnly)
           
 void openTraceInFile(int numberOfElements, java.lang.String suffix)
           
 TraceSortedSet readCodedTraces(int elementSize, int numberOfElements, int numberOfConstraints, int x, int y, int z)
           
 Trace readTrace(int permutationSize, int numberOfElements, boolean isSubTrace)
           
 TraceSortedSet readTraces(SignedPermutationBPGraph permutation, int numberOfElements, boolean isSubTrace, int x, int y, int z)
           
 
Methods inherited from class baobab.applogic.AppLogicUtil
applyAllReversals, close, countAllSortingSequences, log
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

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)
Method Detail

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)