Package pal.alignment
Class StrippedAlignment
- java.lang.Object
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- pal.alignment.AbstractAlignment
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- pal.alignment.StrippedAlignment
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
Fields Modifier and Type Field Description protected int[]
alias
protected boolean[]
notDropped
protected Alignment
rawAlignment
protected int
rawNumSites
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Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
Constructors Constructor Description StrippedAlignment(Alignment raw)
Constructor
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
dropSite(int s)
drop a sitechar
getData(int seq, int site)
sequence alignment at (sequence, site)void
removeConstantSites()
remove constant sitesvoid
removeGaps()
remove sites with gapsvoid
removeNoninformativeSites()
remove noninformative sitesvoid
removeSites(char c)
remove site that contain a specified charactervoid
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
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Field Detail
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rawAlignment
protected Alignment rawAlignment
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rawNumSites
protected int rawNumSites
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alias
protected int[] alias
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notDropped
protected boolean[] notDropped
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Constructor Detail
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StrippedAlignment
public StrippedAlignment(Alignment raw)
Constructor- Parameters:
raw
- original alignment
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Method Detail
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getData
public char getData(int seq, int site)
sequence alignment at (sequence, site)- Specified by:
getData
in interfaceAlignment
- Specified by:
getData
in classAbstractAlignment
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dropSite
public void dropSite(int s)
drop a site- Parameters:
s
- site of original alignment
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removeSites
public void removeSites(char c)
remove site that contain a specified character- Parameters:
c
- character that will cause the removal of a site
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removeGaps
public void removeGaps()
remove sites with gaps
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removeUnknowns
public void removeUnknowns()
remove sites with unknowns
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removeConstantSites
public void removeConstantSites()
remove constant sites
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removeNoninformativeSites
public void removeNoninformativeSites()
remove noninformative sites
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