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java.lang.Objectpal.alignment.AbstractAlignment
pal.alignment.SimpleAlignment
public class SimpleAlignment
An alignment class that can be efficiently constructed from an array of strings.
Nested Class Summary |
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Nested classes/interfaces inherited from interface pal.misc.IdGroup |
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IdGroup.Utils |
Field Summary |
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Fields inherited from class pal.alignment.AbstractAlignment |
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idGroup, numSeqs, numSites |
Fields inherited from interface pal.alignment.Alignment |
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GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA |
Constructor Summary | |
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SimpleAlignment()
parameterless constructor. |
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SimpleAlignment(Alignment a)
Clone constructor. |
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SimpleAlignment(Alignment a,
Alignment b,
java.lang.String guide1,
java.lang.String guide2,
char gap)
This constructor combines to alignments given two guide strings. |
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SimpleAlignment(Alignment a,
int sequenceToIgnore)
Clone constructor. |
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SimpleAlignment(Alignment a,
LabelMapping lm)
Clone constructor. |
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SimpleAlignment(Identifier[] ids,
java.lang.String[] sequences,
DataType dt)
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SimpleAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt)
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SimpleAlignment(Identifier id,
java.lang.String sequence,
DataType dataType)
Constructor taking single identifier and sequence. |
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SimpleAlignment(IdGroup group,
char[][] cSequences,
DataType dt)
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SimpleAlignment(IdGroup group,
char[][] cSequences,
java.lang.String gaps,
DataType dt)
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SimpleAlignment(IdGroup group,
DataType dt,
int[][] sSequences)
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SimpleAlignment(IdGroup ids,
java.lang.String[] sequences,
DataType dt)
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SimpleAlignment(IdGroup ids,
java.lang.String[] sequences,
java.lang.String gaps,
DataType dt)
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Method Summary | |
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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 |
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getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public SimpleAlignment()
public SimpleAlignment(Alignment a)
public SimpleAlignment(Alignment a, LabelMapping lm)
public SimpleAlignment(Alignment a, int sequenceToIgnore)
sequenceToIgnore
- Will not copy across specified sequencepublic SimpleAlignment(Identifier[] ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
public SimpleAlignment(IdGroup ids, java.lang.String[] sequences, DataType dt)
public SimpleAlignment(IdGroup ids, java.lang.String[] sequences, java.lang.String gaps, DataType dt)
public SimpleAlignment(Identifier[] ids, java.lang.String[] sequences, DataType dt)
public SimpleAlignment(IdGroup group, char[][] cSequences, DataType dt)
cSequences
- sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]public SimpleAlignment(IdGroup group, DataType dt, int[][] sSequences)
cSequences
- sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]public SimpleAlignment(IdGroup group, char[][] cSequences, java.lang.String gaps, DataType dt)
cSequences
- sequences as character matrix (assumes rectangular), laid out as cSequences[sequence][site]public SimpleAlignment(Identifier id, java.lang.String sequence, DataType dataType)
public SimpleAlignment(Alignment a, Alignment b, java.lang.String guide1, java.lang.String guide2, char gap)
Method Detail |
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public char getData(int seq, int site)
getData
in interface Alignment
getData
in class AbstractAlignment
public java.lang.String getAlignedSequenceString(int seq)
getAlignedSequenceString
in interface Alignment
getAlignedSequenceString
in class AbstractAlignment
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