Uses of Class
baobab.util.BitList

Packages that use BitList
baobab.bio.permutation   
baobab.trace   
baobab.util   
 

Uses of BitList in baobab.bio.permutation
 

Methods in baobab.bio.permutation that return BitList
static BitList IntervalUtil.boundariesToList(PermutationBPGraph permutation, int start, int end)
          Generates a BitList from an interval
 BitList PermutationBPGraphIntervalFilter.getCoorientedInterval(int acceptedNumberOfInsertions, java.lang.String[] intervalAsListOfNames)
           
 BitList PermutationBPGraphIntervalFilter.getInterval(int acceptedNumberOfInsertions, java.lang.String[] intervalAsListOfNames)
           
static BitList IntervalUtil.unsortedToSortedList(int[] unsortedSegment, int permutationSize)
          Generates a BitList from an interval
 

Methods in baobab.bio.permutation that return types with arguments of type BitList
 java.util.TreeSet<BitList> PermutationBPGraphIntervalFilter.getCommonIntervals()
           
 java.util.TreeSet<BitList> PermutationBPGraphIntervalFilter.getCommonIntervals(boolean monoorientedIntervals)
           
 java.util.TreeSet<BitList> PerfectReversalConstraint.getIntervals()
           
 java.util.TreeSet<BitList> PermutationBPGraphIntervalFilter.getMonoorientedCommonIntervals()
           
 

Methods in baobab.bio.permutation with parameters of type BitList
static int[] IntervalUtil.listToBoundaries(PermutationBPGraph permutation, BitList segment)
          Generates a reversal from a trace element
 

Uses of BitList in baobab.trace
 

Methods in baobab.trace that return types with arguments of type BitList
 java.util.Vector<BitList> Trace.getElementsAsBitLists(int elementSize, int numberOfElements)
          Decode the trace as a Vector of elements (represented as arrays of bytes)
 java.util.Vector<BitList> SubTrace.getRepresentativeElementsAsBitLists(int elementSize, int numberOfElements)
          Decode the trace as a Vector of elements (represented as arrays of BitList)
 

Methods in baobab.trace with parameters of type BitList
 int Trace.getHeightOf(BitList element, int elementSize, int numberOfElements)
           
 

Method parameters in baobab.trace with type arguments of type BitList
 void DecomposedTrace.addElements(java.util.Vector<BitList> elements, int elementSize, int prevNumberOfElements)
          Adds a new element to this trace
 

Uses of BitList in baobab.util
 

Methods in baobab.util that return BitList
static BitList ByteSetUtil.bytesToBitList(byte[] elementValues, int nbits)
           
 BitList BitList.get(int start, int end)
           
 BitList BitList.get(int start, int end, boolean from1)
           
static BitList ByteSetUtil.intsToBitList(int[] elementValues, int nbits)
           
 

Methods in baobab.util with parameters of type BitList
 void BitList.and(BitList list)
           
static byte[] ByteSetUtil.bitListToBytes(BitList element)
           
static int[] ByteSetUtil.bitListToInts(BitList element)
           
static int BitList.compareBitLists(BitList list1, BitList list2)
           
 boolean BitList.intersects(BitList list)
           
static java.lang.String Util.listAsCondensedString(BitList list, int span, char sep)
           
static java.lang.String Util.listAsCondensedString(BitList list, java.lang.String[] mapIntToName, char sep, boolean condenseNames)
           
static java.lang.String Util.listAsCondensedString(BitList list, java.lang.String[] mapIntToName, java.util.Hashtable<java.lang.String,java.util.TreeSet<java.lang.String>> mapNamesToDescriptions, char sep, boolean condenseNames)
           
 void BitList.or(BitList list)
           
 boolean BitList.overlaps(BitList other)