pal.alignment
Class ReadAlignmentOld

java.lang.Object
  pal.alignment.AbstractAlignment
      pal.alignment.ReadAlignmentOld

All Implemented Interfaces:

Alignment, IdGroup, Report, java.io.Serializable

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.

See Also:

Serialized Form

Nested Class Summary

Nested classes inherited from class 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

ReadAlignmentOld

public ReadAlignmentOld(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)

Specified by:

getData in interface Alignment

Specified by:

getData in class AbstractAlignment