pal.alignment
Class ReadAlignment

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

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.

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
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, 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

ReadAlignment

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

ReadAlignment

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

getData

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