pal.alignment
Class IndelAlignment
java.lang.Object
|
+--pal.alignment.AbstractAlignment
|
+--pal.alignment.IndelAlignment
- All Implemented Interfaces:
- Alignment, IdGroup, Report, java.io.Serializable
- Direct Known Subclasses:
- IndelAnnotatedAlignment
- public class IndelAlignment
- extends AbstractAlignment
This class extracts indels (insertion/deletion) out of an alignment, and creates
an alignment of indel polymorphisms. It uses the NumericDataType, so that the length
of each indel is recorded in the alignment. If anchored is true, then SSR-like
(microsatellites) indels
will be identified as the same indel locus. If anchored is false, then the same indel
start and end at the exact same position.
- See Also:
- Serialized Form
Method Summary |
char |
getData(int seq,
int site)
sequence alignment at (sequence, site) |
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 |
IndelAlignment
public IndelAlignment(Alignment a,
boolean anchored)
- Basic constructor.
- Parameters:
anchored
- sets to score anchored indels as same position
getData
public char getData(int seq,
int site)
- sequence alignment at (sequence, site)
- Overrides:
getData
in class AbstractAlignment