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

Nested Class Summary

Nested classes/interfaces inherited from interface pal.misc.IdGroup

IdGroup.Utils

Field Summary

Fields inherited from class pal.alignment.AbstractAlignment

idGroup, numSeqs, numSites

Fields inherited from interface pal.alignment.Alignment

GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA

Constructor Summary

Constructors

Constructor and Description
GapBalancedAlignment(Alignment base, int startingCodonPosition, boolean alignGap) The standard GapBalanced constructor
GapBalancedAlignment(Alignment base, int startingCodonPosition, boolean alignGap, int codonLength) GapBalanced power user constructor
GapBalancedAlignment(Alignment base, int startingCodonPosition, int codonLength) GapBalanced power user constructor

Method Summary

Methods

Modifier and Type	Method and Description
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

Constructor Detail

GapBalancedAlignment

public GapBalancedAlignment(Alignment base,
                    int startingCodonPosition,
                    boolean alignGap)

The standard GapBalanced constructor

Parameters:

Alignment - on which to based this gap balanced alignment

the - 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 alignment

startingCodonPosition - the starting codon position of the alignment

codonLength - 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 alignment

startingCodonPosition - the starting codon position of the alignment

alignGap - 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)

Method Detail

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