baobab.bio.permutation.colinearity
Class ColinearPermutation

java.lang.Object
  extended by baobab.bio.permutation.colinearity.ColinearPermutation

public class ColinearPermutation
extends java.lang.Object


Constructor Summary
ColinearPermutation(java.lang.String name, java.lang.String permAsString)
           
 
Method Summary
 void addPosToIgnore(int pos)
           
 int autoStart(boolean confirm, ColinearBlock block)
           
 LinkPermutationToColinearBlock closeColinearBlock(ColinearBlock b)
           
 void confirmPosition(int pos, ColinearBlock block)
           
 boolean containsValue(java.lang.String value)
           
 java.util.TreeSet<LinkPermutationToColinearBlock> getColinearBlocks()
           
 int getCurrentPos()
           
 java.lang.String getGroupedPermutation(int span)
           
 java.lang.String getName()
           
 java.lang.String getValue(int pos)
           
 boolean hasStartedBlock()
           
 boolean hasUnprocessedPositions()
           
 boolean ignore(int pos)
           
 void incrementCurrentPos()
           
 int indexOf(java.lang.String value)
           
 boolean isReversed(int pos)
           
 boolean isUnprocessed(int pos)
           
 boolean readAsReversed()
           
 void reset()
           
 int resume(int nextNum)
           
 void revert()
           
 void setCurrentPos(int pos)
           
 void setReadAsReversed(boolean readAsReversed)
           
 int size()
           
 boolean start(java.lang.String refValue, boolean isRefReversed, ColinearBlock block)
           
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ColinearPermutation

public ColinearPermutation(java.lang.String name,
                           java.lang.String permAsString)
Method Detail

size

public int size()

closeColinearBlock

public LinkPermutationToColinearBlock closeColinearBlock(ColinearBlock b)

getName

public java.lang.String getName()

getValue

public java.lang.String getValue(int pos)

isReversed

public boolean isReversed(int pos)

addPosToIgnore

public void addPosToIgnore(int pos)

ignore

public boolean ignore(int pos)

isUnprocessed

public boolean isUnprocessed(int pos)

incrementCurrentPos

public void incrementCurrentPos()

containsValue

public boolean containsValue(java.lang.String value)

indexOf

public int indexOf(java.lang.String value)

setCurrentPos

public void setCurrentPos(int pos)

getCurrentPos

public int getCurrentPos()

hasStartedBlock

public boolean hasStartedBlock()

hasUnprocessedPositions

public boolean hasUnprocessedPositions()

readAsReversed

public boolean readAsReversed()

setReadAsReversed

public void setReadAsReversed(boolean readAsReversed)

start

public boolean start(java.lang.String refValue,
                     boolean isRefReversed,
                     ColinearBlock block)

confirmPosition

public void confirmPosition(int pos,
                            ColinearBlock block)

autoStart

public int autoStart(boolean confirm,
                     ColinearBlock block)

reset

public void reset()

revert

public void revert()

getColinearBlocks

public java.util.TreeSet<LinkPermutationToColinearBlock> getColinearBlocks()

getGroupedPermutation

public java.lang.String getGroupedPermutation(int span)

resume

public int resume(int nextNum)