Package pal.alignment
Class SimpleAlignment
- java.lang.Object
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- pal.alignment.AbstractAlignment
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- pal.alignment.SimpleAlignment
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
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Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
Constructors Constructor Description SimpleAlignment()
parameterless constructor.SimpleAlignment(Alignment a)
Clone constructor.SimpleAlignment(Alignment a, int sequenceToIgnore)
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, LabelMapping lm)
Clone constructor.SimpleAlignment(Identifier[] ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
SimpleAlignment(Identifier[] ids, java.lang.String[] sequences, DataType dt)
SimpleAlignment(Identifier id, java.lang.String sequence, DataType dataType)
Constructor taking single identifier and sequence.SimpleAlignment(IdGroup group, char[][] cSequences, java.lang.String gaps, DataType dt)
SimpleAlignment(IdGroup group, char[][] cSequences, DataType dt)
SimpleAlignment(IdGroup ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
SimpleAlignment(IdGroup ids, java.lang.String[] sequences, DataType dt)
SimpleAlignment(IdGroup group, DataType dt, int[][] sSequences)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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
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Constructor Detail
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SimpleAlignment
public SimpleAlignment()
parameterless constructor.
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SimpleAlignment
public SimpleAlignment(Alignment a)
Clone constructor.
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SimpleAlignment
public SimpleAlignment(Alignment a, LabelMapping lm)
Clone constructor.
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SimpleAlignment
public SimpleAlignment(Alignment a, int sequenceToIgnore)
Clone constructor.- Parameters:
sequenceToIgnore
- Will not copy across specified sequence
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SimpleAlignment
public SimpleAlignment(Identifier[] ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
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SimpleAlignment
public SimpleAlignment(IdGroup ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
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SimpleAlignment
public SimpleAlignment(Identifier[] ids, java.lang.String[] sequences, DataType dt)
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SimpleAlignment
public SimpleAlignment(IdGroup group, char[][] cSequences, DataType dt)
- Parameters:
cSequences
- sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]
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SimpleAlignment
public SimpleAlignment(IdGroup group, DataType dt, int[][] sSequences)
- Parameters:
cSequences
- sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]
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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]
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SimpleAlignment
public SimpleAlignment(Identifier id, java.lang.String sequence, DataType dataType)
Constructor taking single identifier and sequence.
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Method Detail
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getData
public char getData(int seq, int site)
sequence alignment at (sequence, site)- Specified by:
getData
in interfaceAlignment
- Specified by:
getData
in classAbstractAlignment
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getAlignedSequenceString
public java.lang.String getAlignedSequenceString(int seq)
Returns a string representing a single sequence (including gaps) from this alignment.- Specified by:
getAlignedSequenceString
in interfaceAlignment
- Overrides:
getAlignedSequenceString
in classAbstractAlignment
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