pal.alignment
Class StrippedAlignment

java.lang.Object
  |
  +--pal.alignment.AbstractAlignment
        |
        +--pal.alignment.StrippedAlignment
All Implemented Interfaces:
Alignment, IdGroup, Report, java.io.Serializable
Direct Known Subclasses:
StrippedAnnotatedAlignment

public class StrippedAlignment
extends AbstractAlignment

takes an alignment and repeatedly removes sites

See Also:
Serialized Form

Field Summary
protected  int[] alias
           
protected  boolean[] notDropped
           
protected  Alignment rawAlignment
           
protected  int rawNumSites
           
 
Fields inherited from class pal.alignment.AbstractAlignment
dataType, frequency, idGroup, numSeqs, numSites
 
Fields inherited from interface pal.alignment.Alignment
GAP
 
Constructor Summary
StrippedAlignment(Alignment raw)
          Constructor
 
Method Summary
 void dropSite(int s)
          drop a site
 char getData(int seq, int site)
          sequence alignment at (sequence, site)
 void removeConstantSites()
          remove constant sites
 void removeGaps()
          remove sites with gaps
 void removeNoninformativeSites()
          remove noninformative sites
 void removeSites(char c)
          remove site that contain a specified character
 void removeUnknowns()
          remove sites with unknowns
 
Methods inherited from class pal.alignment.AbstractAlignment
getAlignedSequenceString, getDataType, getFrequency, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getStates, guessDataType, isGap, report, setDataType, setFrequency, setIdentifier, toString, whichIdNumber
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

rawAlignment

protected Alignment rawAlignment

rawNumSites

protected int rawNumSites

alias

protected int[] alias

notDropped

protected boolean[] notDropped
Constructor Detail

StrippedAlignment

public StrippedAlignment(Alignment raw)
Constructor
Parameters:
raw - original alignment
Method Detail

getData

public char getData(int seq,
                    int site)
sequence alignment at (sequence, site)
Overrides:
getData in class AbstractAlignment

dropSite

public void dropSite(int s)
drop a site
Parameters:
s - site of original alignment

removeSites

public void removeSites(char c)
remove site that contain a specified character
Parameters:
c - character that will cause the removal of a site

removeGaps

public void removeGaps()
remove sites with gaps

removeUnknowns

public void removeUnknowns()
remove sites with unknowns

removeConstantSites

public void removeConstantSites()
remove constant sites

removeNoninformativeSites

public void removeNoninformativeSites()
remove noninformative sites