ReadAlignmentOld

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java.lang.Object
- pal.alignment.AbstractAlignment
- - 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
  
  Constructors
  Constructor and Description
  
  ReadAlignmentOld(java.io.PushbackReader input)
  read from stream
  
  ReadAlignmentOld(java.lang.String file)
  read from file
- Method Summary
  
  All Methods Instance Methods Concrete Methods
  Modifier and Type Method and Description
  
  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

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