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

Fields inherited from class pal.alignment.AbstractAlignment
dataType, frequency, idGroup, numSeqs, numSites
 
Fields inherited from interface pal.alignment.Alignment
GAP
 
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
 

Constructor Detail

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.
Method Detail

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