public class StrippedAlignment extends AbstractAlignment
IdGroup.Utils
Modifier and Type | Field and Description |
---|---|
protected int[] |
alias |
protected boolean[] |
notDropped |
protected Alignment |
rawAlignment |
protected int |
rawNumSites |
idGroup, numSeqs, numSites
Constructor and Description |
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StrippedAlignment(Alignment raw)
Constructor
|
Modifier and Type | Method and Description |
---|---|
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
|
getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber
protected Alignment rawAlignment
protected int rawNumSites
protected int[] alias
protected boolean[] notDropped
public StrippedAlignment(Alignment raw)
raw
- original alignmentpublic 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()