pal.alignment
Class SimpleAlignment
java.lang.Object
|
+--pal.alignment.AbstractAlignment
|
+--pal.alignment.SimpleAlignment
- All Implemented Interfaces:
- Alignment, IdGroup, Report, java.io.Serializable
- Direct Known Subclasses:
- MultiLocusAnnotatedAlignment, SimpleAnnotatedAlignment
- public class SimpleAlignment
- extends AbstractAlignment
An alignment class that can be efficiently constructed
from an array of strings.
- See Also:
- Serialized Form
Constructor Summary |
SimpleAlignment()
parameterless constructor. |
SimpleAlignment(Alignment a)
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,
int sequenceToIgnore)
Clone constructor. |
SimpleAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps)
|
SimpleAlignment(Identifier id,
java.lang.String sequence,
DataType dataType_)
Constructor taking single identifier and sequence. |
SimpleAlignment(Identifier id,
java.lang.String sequence,
DataType dataType_,
boolean estFreqs)
Constructor taking single identifier and sequence. |
SimpleAlignment(IdGroup group,
char[][] cSequences)
|
SimpleAlignment(IdGroup group,
char[][] cSequences,
java.lang.String gaps)
|
SimpleAlignment(IdGroup group,
char[][] cSequences,
java.lang.String gaps,
DataType dataType_)
|
SimpleAlignment(IdGroup group,
java.lang.String[] sequences)
|
SimpleAlignment(IdGroup group,
java.lang.String[] sequences,
java.lang.String gaps)
|
Method Summary |
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 |
getDataType, getFrequency, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getStates, guessDataType, isGap, report, setDataType, setFrequency, setIdentifier, toString, whichIdNumber |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
SimpleAlignment
public SimpleAlignment()
- parameterless constructor.
SimpleAlignment
public SimpleAlignment(Alignment a)
- Clone constructor.
SimpleAlignment
public SimpleAlignment(Alignment a,
int sequenceToIgnore)
- Clone constructor.
- Parameters:
sequenceToIgnore
- Will not copy across specified sequence
SimpleAlignment
public SimpleAlignment(Identifier[] ids,
java.lang.String[] sequences,
java.lang.String gaps)
SimpleAlignment
public SimpleAlignment(IdGroup group,
java.lang.String[] sequences)
SimpleAlignment
public SimpleAlignment(IdGroup group,
java.lang.String[] sequences,
java.lang.String gaps)
SimpleAlignment
public SimpleAlignment(IdGroup group,
char[][] cSequences)
SimpleAlignment
public SimpleAlignment(IdGroup group,
char[][] cSequences,
java.lang.String gaps)
SimpleAlignment
public SimpleAlignment(IdGroup group,
char[][] cSequences,
java.lang.String gaps,
DataType dataType_)
SimpleAlignment
public SimpleAlignment(Identifier id,
java.lang.String sequence,
DataType dataType_)
- Constructor taking single identifier and sequence.
SimpleAlignment
public SimpleAlignment(Identifier id,
java.lang.String sequence,
DataType dataType_,
boolean estFreqs)
- Constructor taking single identifier and sequence.
SimpleAlignment
public SimpleAlignment(Alignment a,
Alignment b,
java.lang.String guide1,
java.lang.String guide2,
char gap)
- This constructor combines to alignments given two guide strings.
getData
public char getData(int seq,
int site)
- sequence alignment at (sequence, site)
- Overrides:
getData
in class AbstractAlignment
getAlignedSequenceString
public java.lang.String getAlignedSequenceString(int seq)
- Returns a string representing a single sequence (including gaps)
from this alignment.
- Overrides:
getAlignedSequenceString
in class AbstractAlignment