pal.alignment

Class SimpleAlignment

java.lang.Object

pal.alignment.AbstractAlignment

pal.alignment.SimpleAlignment

All Implemented Interfaces:

java.io.Serializable, Alignment, IdGroup, Report

Direct Known Subclasses:

MultiLocusAnnotatedAlignment, SimpleAnnotatedAlignment

public class SimpleAlignment
extends AbstractAlignment

An alignment class that can be efficiently constructed from an array of strings.

Version:

$Id: SimpleAlignment.java,v 1.26 2003/08/16 23:48:26 matt Exp $

Author:

Alexei Drummond

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
SimpleAlignment() parameterless constructor.
SimpleAlignment(Alignment a) Clone constructor.
SimpleAlignment(Alignment a, Alignment b, java.lang.String guide1, java.lang.String guide2, char gap) This constructor combines to alignments given two guide strings.
SimpleAlignment(Alignment a, int sequenceToIgnore) Clone constructor.
SimpleAlignment(Alignment a, LabelMapping lm) Clone constructor.
SimpleAlignment(Identifier[] ids, java.lang.String[] sequences, DataType dt)
SimpleAlignment(Identifier[] ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
SimpleAlignment(Identifier id, java.lang.String sequence, DataType dataType) Constructor taking single identifier and sequence.
SimpleAlignment(IdGroup group, char[][] cSequences, DataType dt)
SimpleAlignment(IdGroup group, char[][] cSequences, java.lang.String gaps, DataType dt)
SimpleAlignment(IdGroup group, DataType dt, int[][] sSequences)
SimpleAlignment(IdGroup ids, java.lang.String[] sequences, DataType dt)
SimpleAlignment(IdGroup ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	getAlignedSequenceString(int seq) Returns a string representing a single sequence (including gaps) from this alignment.
char	getData(int seq, int site) sequence alignment at (sequence, site)

Methods inherited from class pal.alignment.AbstractAlignment

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

SimpleAlignment

public SimpleAlignment()

parameterless constructor.

SimpleAlignment

public SimpleAlignment(Alignment a)

Clone constructor.

SimpleAlignment

public SimpleAlignment(Alignment a,
               LabelMapping lm)

Clone constructor.

SimpleAlignment

public SimpleAlignment(Alignment a,
               int sequenceToIgnore)

Clone constructor.

Parameters:

sequenceToIgnore - Will not copy across specified sequence

SimpleAlignment

public SimpleAlignment(Identifier[] ids,
               java.lang.String[] sequences,
               java.lang.String gaps,
               DataType dt)

SimpleAlignment

public SimpleAlignment(IdGroup ids,
               java.lang.String[] sequences,
               DataType dt)

SimpleAlignment

public SimpleAlignment(IdGroup ids,
               java.lang.String[] sequences,
               java.lang.String gaps,
               DataType dt)

SimpleAlignment

public SimpleAlignment(Identifier[] ids,
               java.lang.String[] sequences,
               DataType dt)

SimpleAlignment

public SimpleAlignment(IdGroup group,
               char[][] cSequences,
               DataType dt)

Parameters:

cSequences - sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]

SimpleAlignment

public SimpleAlignment(IdGroup group,
               DataType dt,
               int[][] sSequences)

Parameters:

cSequences - sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]

SimpleAlignment

public SimpleAlignment(IdGroup group,
               char[][] cSequences,
               java.lang.String gaps,
               DataType dt)

Parameters:

cSequences - sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]

SimpleAlignment

public SimpleAlignment(Identifier id,
               java.lang.String sequence,
               DataType dataType)

Constructor taking single identifier and sequence.

SimpleAlignment

public SimpleAlignment(Alignment a,
               Alignment b,
               java.lang.String guide1,
               java.lang.String guide2,
               char gap)

This constructor combines to alignments given two guide strings.

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

getAlignedSequenceString

public java.lang.String getAlignedSequenceString(int seq)

Returns a string representing a single sequence (including gaps) from this alignment.

Specified by:

getAlignedSequenceString in interface Alignment

Overrides:

getAlignedSequenceString in class AbstractAlignment