pal.alignment
Class ReadAlignment

java.lang.Object
  extended by pal.alignment.AbstractAlignment
      extended by pal.alignment.ReadAlignment
All Implemented Interfaces:
java.io.Serializable, Alignment, IdGroup, Report

public class ReadAlignment
extends AbstractAlignment

reads aligned sequence data from plain text files.

recognizes PHYLIP 3.4 INTERLEAVED, PHYLIP SEQUENTIAL, CLUSTAL and derived formats.

Other features: - the dot as "copy character" is recognized, - all base characters are capitalized, - automatic data type estimation - determination of corresponding base frequencies.

Version:
$Id: ReadAlignment.java,v 1.7 2003/09/04 03:22:34 matt Exp $
Author:
Korbinian Strimmer, Alexei Drummond, Alex Moore a.d.moore@ex.ac.uk
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
 
Field Summary
 
Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
 
Fields inherited from interface pal.alignment.Alignment
GAP, GAP_TLA, GAPS, UNKNOWN, UNKNOWN_TLA
 
Constructor Summary
ReadAlignment(java.io.PushbackReader input)
          read from stream
ReadAlignment(java.lang.String file)
          read from file
 
Method Summary
 char getData(int seq, int site)
          sequence alignment at (sequence, site)
 
Methods inherited from class pal.alignment.AbstractAlignment
getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

ReadAlignment

public ReadAlignment(java.io.PushbackReader input)
              throws AlignmentParseException,
                     java.io.IOException
read from stream

Throws:
AlignmentParseException
java.io.IOException

ReadAlignment

public ReadAlignment(java.lang.String file)
              throws AlignmentParseException,
                     java.io.IOException
read from file

Throws:
AlignmentParseException
java.io.IOException
Method Detail

getData

public char getData(int seq,
                    int site)
sequence alignment at (sequence, site)

Specified by:
getData in interface Alignment
Specified by:
getData in class AbstractAlignment