StrippedAnnotatedAlignmentpublic 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, whichIdNumberprotected 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 AlignmentgetData in class AbstractAlignmentpublic 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()