Package pal.alignment
Class StrippedAlignment
java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.StrippedAlignment
- All Implemented Interfaces:
Serializable
,Alignment
,IdGroup
,Report
- Direct Known Subclasses:
StrippedAnnotatedAlignment
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:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected int[]
protected boolean[]
protected Alignment
protected int
Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
dropSite
(int s) drop a sitechar
getData
(int seq, int site) sequence alignment at (sequence, site)void
remove constant sitesvoid
remove sites with gapsvoid
remove noninformative sitesvoid
removeSites
(char c) remove site that contain a specified charactervoid
remove sites with unknownsMethods 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 Details
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rawAlignment
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rawNumSites
protected int rawNumSites -
alias
protected int[] alias -
notDropped
protected boolean[] notDropped
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Constructor Details
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StrippedAlignment
Constructor- Parameters:
raw
- original alignment
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Method Details
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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 -
removeUnknowns
public void removeUnknowns()remove sites with unknowns -
removeConstantSites
public void removeConstantSites()remove constant sites -
removeNoninformativeSites
public void removeNoninformativeSites()remove noninformative sites
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