pal.alignment
Class StrippedAlignment

java.lang.Object
  pal.alignment.AbstractAlignment
      pal.alignment.StrippedAlignment

All Implemented Interfaces:

java.io.Serializable, Alignment, IdGroup, Report

Direct Known Subclasses:

StrippedAnnotatedAlignment

public class StrippedAlignment
extends AbstractAlignment

takes an alignment and repeatedly removes sites

Version:

$Id: StrippedAlignment.java,v 1.6 2002/02/27 22:25:59 matt Exp $

Author:

Korbinian Strimmer

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.IdGroup

IdGroup.Utils

Field Summary

protected int[]	alias
protected boolean[]	notDropped
protected Alignment	rawAlignment
protected int	rawNumSites

Fields inherited from class pal.alignment.AbstractAlignment

idGroup, numSeqs, numSites

Fields inherited from interface pal.alignment.Alignment

GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA

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, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, 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)

Specified by:

getData in interface Alignment

Specified by:

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