Package pal.alignment
Class ReadAlignmentOld
java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.ReadAlignmentOld
- All Implemented Interfaces:
Serializable
,Alignment
,IdGroup
,Report
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:
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Nested Class Summary
Nested classes/interfaces inherited from interface pal.misc.IdGroup
IdGroup.Utils
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Field Summary
Fields inherited from class pal.alignment.AbstractAlignment
idGroup, numSeqs, numSites
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Constructor Summary
ConstructorsConstructorDescriptionReadAlignmentOld
(PushbackReader input) read from streamReadAlignmentOld
(String file) read from file -
Method Summary
Modifier and TypeMethodDescriptionchar
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
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Constructor Details
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ReadAlignmentOld
read from stream- Throws:
AlignmentParseException
IOException
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ReadAlignmentOld
read from file- Throws:
AlignmentParseException
IOException
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Method Details
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getData
public char getData(int seq, int site) sequence alignment at (sequence, site)- Specified by:
getData
in interfaceAlignment
- Specified by:
getData
in classAbstractAlignment
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