pal.alignment
Class AminoAcidAlignment

java.lang.Object
  |
  +--pal.alignment.AbstractAlignment
        |
        +--pal.alignment.AminoAcidAlignment
All Implemented Interfaces:
Alignment, IdGroup, Report, java.io.Serializable

public class AminoAcidAlignment
extends AbstractAlignment

generates an amino acid alignment from a nucleotide alignment. Is designed to translate from nucleotide alignments that do not have gaps. Codons that include one or more gaps will be translated as a '?'.

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
AminoAcidAlignment(Alignment raw)
          Constructs an AminoAcidAlignment from a given alignment (which should be a nucleotide alignment), from codon position 0.
AminoAcidAlignment(Alignment raw, int startingCodonPosition)
          Constructor
AminoAcidAlignment(Alignment raw, int startingCodonPosition, CodonTable trans)
          Constructor
 
Method Summary
 char getData(int seq, int site)
          sequence alignment at (sequence, site)
 
Methods inherited from class pal.alignment.AbstractAlignment
getAlignedSequenceString, 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

AminoAcidAlignment

public AminoAcidAlignment(Alignment raw)
Constructs an AminoAcidAlignment from a given alignment (which should be a nucleotide alignment), from codon position 0.
Parameters:
raw - original alignment
if - a codon contains a gap or uses non nucleotide characters resulting amino acid will be marked as a '?'

AminoAcidAlignment

public AminoAcidAlignment(Alignment raw,
                          int startingCodonPosition)
Constructor
Parameters:
raw - original alignment
startingCodonPosition - - the starting codon position (0,1,2)
if - a codon contains a gap or uses non nucleotide characters resulting amino acid will be marked as a '?'

AminoAcidAlignment

public AminoAcidAlignment(Alignment raw,
                          int startingCodonPosition,
                          CodonTable trans)
Constructor
Parameters:
raw - original alignment
startingCodonPosition - - the starting codon position (0,1,2)
trans - - the CodonTable to use to convert nucleotides to amino acids
if - a codon contains a gap or uses non nucleotide characters resulting amino acid will be marked as a '?'
Method Detail

getData

public char getData(int seq,
                    int site)
sequence alignment at (sequence, site)
Overrides:
getData in class AbstractAlignment