pal.alignment
Class ReadAlignmentOld

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

public class ReadAlignmentOld
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
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
ReadAlignmentOld(java.io.PushbackReader input)
          read from stream
ReadAlignmentOld(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

ReadAlignmentOld

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

Throws:
AlignmentParseException
java.io.IOException

ReadAlignmentOld

public ReadAlignmentOld(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