pal.alignment
Class GapBalancedAlignment
java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.GapBalancedAlignment
- All Implemented Interfaces:
- java.io.Serializable, Alignment, IdGroup, Report
public class GapBalancedAlignment
- extends AbstractAlignment
- implements java.io.Serializable
Creates a "Gap-Balanced" alignment.
- Version:
- $Id: GapBalancedAlignment.java,v 1.14 2003/04/10 05:53:47 matt Exp $
- Author:
- Matthew Goode
- 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, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
GapBalancedAlignment
public GapBalancedAlignment(Alignment base,
int startingCodonPosition,
boolean alignGap)
- The standard GapBalanced constructor
- Parameters:
Alignment
- on which to based this gap balanced alignmentthe
- estimated startingCodonPosition of the alignment
GapBalancedAlignment
public GapBalancedAlignment(Alignment base,
int startingCodonPosition,
int codonLength)
- GapBalanced power user constructor
- Parameters:
Alignment
- on which to based this gap balanced alignmentstartingCodonPosition
- the starting codon position of the alignmentcodonLength
- the length of a codon (to make things general,
- the author is a Computer Scientist)
GapBalancedAlignment
public GapBalancedAlignment(Alignment base,
int startingCodonPosition,
boolean alignGap,
int codonLength)
- GapBalanced power user constructor
- Parameters:
Alignment
- on which to based this gap balanced alignmentstartingCodonPosition
- the starting codon position of the alignmentalignGap
- sometimes a large cap may occur in the middle of a sequence's codon. If this is true than no
columns can match up in this area (it's hard to explain - for safety choose true!)codonLength
- the length of a codon (to make things general,
- the author is a Computer Scientist)
getData
public char getData(int seq,
int site)
- sequence alignment at (sequence, site)
- Specified by:
getData
in interface Alignment
- Specified by:
getData
in class AbstractAlignment