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java.lang.Objectpal.alignment.AbstractAlignment
pal.alignment.StrippedAlignment
public class StrippedAlignment
takes an alignment and repeatedly removes sites
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.IdGroup |
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IdGroup.Utils |
Field Summary | |
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protected int[] |
alias
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protected boolean[] |
notDropped
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protected Alignment |
rawAlignment
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protected int |
rawNumSites
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Fields inherited from class pal.alignment.AbstractAlignment |
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idGroup, numSeqs, numSites |
Fields inherited from interface pal.alignment.Alignment |
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GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA |
Constructor Summary | |
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StrippedAlignment(Alignment raw)
Constructor |
Method Summary | |
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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 |
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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 |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Field Detail |
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protected Alignment rawAlignment
protected int rawNumSites
protected int[] alias
protected boolean[] notDropped
Constructor Detail |
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public StrippedAlignment(Alignment raw)
raw
- original alignmentMethod Detail |
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public char getData(int seq, int site)
getData
in interface Alignment
getData
in class AbstractAlignment
public void dropSite(int s)
s
- site of original alignmentpublic void removeSites(char c)
c
- character that will cause the removal of a sitepublic void removeGaps()
public void removeUnknowns()
public void removeConstantSites()
public void removeNoninformativeSites()
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