pal.alignment
Class StrippedAlignment
java.lang.Object
|
+--pal.alignment.AbstractAlignment
|
+--pal.alignment.StrippedAlignment
- All Implemented Interfaces:
- Alignment, IdGroup, Report, java.io.Serializable
- Direct Known Subclasses:
- StrippedAnnotatedAlignment
- public class StrippedAlignment
- extends AbstractAlignment
takes an alignment and repeatedly removes sites
- See Also:
- Serialized Form
Methods inherited from class pal.alignment.AbstractAlignment |
getAlignedSequenceString, getDataType, getFrequency, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getStates, guessDataType, isGap, report, setDataType, setFrequency, setIdentifier, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
rawAlignment
protected Alignment rawAlignment
rawNumSites
protected int rawNumSites
alias
protected int[] alias
notDropped
protected boolean[] notDropped
StrippedAlignment
public StrippedAlignment(Alignment raw)
- Constructor
- Parameters:
raw
- original alignment
getData
public char getData(int seq,
int site)
- sequence alignment at (sequence, site)
- Overrides:
getData
in class AbstractAlignment
dropSite
public void dropSite(int s)
- drop a site
- Parameters:
s
- site of original alignment
removeSites
public void removeSites(char c)
- remove site that contain a specified character
- Parameters:
c
- character that will cause the removal of a site
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