pal.alignment
Class SimpleAlignment

java.lang.Object
  extended by pal.alignment.AbstractAlignment
      extended by 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
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
 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