StrippedAnnotatedAlignment
public class StrippedAlignment extends AbstractAlignment
IdGroup.Utils
Modifier and Type | Field | Description |
---|---|---|
protected int[] |
alias |
|
protected boolean[] |
notDropped |
|
protected Alignment |
rawAlignment |
|
protected int |
rawNumSites |
idGroup, numSeqs, numSites
Constructor | Description |
---|---|
StrippedAlignment(Alignment raw) |
Constructor
|
Modifier and Type | Method | 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()