public class SimpleAlignment extends AbstractAlignment
IdGroup.Utils
idGroup, numSeqs, numSites
Constructor and Description |
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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) |
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.
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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) |
Modifier and Type | Method and Description |
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java.lang.String |
getAlignedSequenceString(int seq)
Returns a string representing a single sequence (including gaps)
from this alignment.
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char |
getData(int seq,
int site)
sequence alignment at (sequence, site)
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getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber
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, 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 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