baobab.bio.permutation.colinearity
Class ColinearPermutation
java.lang.Object
baobab.bio.permutation.colinearity.ColinearPermutation
public class ColinearPermutation
- extends java.lang.Object
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
ColinearPermutation
public ColinearPermutation(java.lang.String name,
java.lang.String permAsString)
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)