Package pal.alignment
Class SimpleAlignment
java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.SimpleAlignment
- All Implemented Interfaces:
Serializable
,Alignment
,IdGroup
,Report
- Direct Known Subclasses:
MultiLocusAnnotatedAlignment
,SimpleAnnotatedAlignment
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:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
ConstructorsConstructorDescriptionparameterless constructor.Clone constructor.SimpleAlignment
(Alignment a, int sequenceToIgnore) Clone constructor.SimpleAlignment
(Alignment a, Alignment b, String guide1, String guide2, char gap) This constructor combines to alignments given two guide strings.SimpleAlignment
(Alignment a, LabelMapping lm) Clone constructor.SimpleAlignment
(Identifier[] ids, String[] sequences, String gaps, DataType dt) SimpleAlignment
(Identifier[] ids, String[] sequences, DataType dt) SimpleAlignment
(Identifier id, String sequence, DataType dataType) Constructor taking single identifier and sequence.SimpleAlignment
(IdGroup group, char[][] cSequences, String gaps, DataType dt) SimpleAlignment
(IdGroup group, char[][] cSequences, DataType dt) SimpleAlignment
(IdGroup ids, String[] sequences, String gaps, DataType dt) SimpleAlignment
(IdGroup ids, String[] sequences, DataType dt) SimpleAlignment
(IdGroup group, DataType dt, int[][] sSequences) -
Method Summary
Modifier and TypeMethodDescriptiongetAlignedSequenceString
(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 Details
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SimpleAlignment
public SimpleAlignment()parameterless constructor. -
SimpleAlignment
Clone constructor. -
SimpleAlignment
Clone constructor. -
SimpleAlignment
Clone constructor.- Parameters:
sequenceToIgnore
- Will not copy across specified sequence
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SimpleAlignment
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SimpleAlignment
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SimpleAlignment
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SimpleAlignment
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SimpleAlignment
- Parameters:
cSequences
- sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]
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SimpleAlignment
- Parameters:
cSequences
- sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]
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SimpleAlignment
- Parameters:
cSequences
- sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]
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SimpleAlignment
Constructor taking single identifier and sequence. -
SimpleAlignment
This constructor combines to alignments given two guide strings.
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Method Details
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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
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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