MultiLocusAnnotatedAlignment, SimpleAnnotatedAlignmentpublic class SimpleAlignment extends AbstractAlignment
IdGroup.UtilsidGroup, numSeqs, numSites| 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) |
| 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)
|
getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumberpublic 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 AlignmentgetData in class AbstractAlignmentpublic java.lang.String getAlignedSequenceString(int seq)
getAlignedSequenceString in interface AlignmentgetAlignedSequenceString in class AbstractAlignment