Package pal.alignment
Class ReadAlignment
java.lang.Object
pal.alignment.AbstractAlignment
pal.alignment.ReadAlignment
- 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, Alex Moore a.d.moore@ex.ac.uk
- 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
ConstructorsConstructorDescriptionReadAlignment
(PushbackReader input) read from streamReadAlignment
(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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ReadAlignment
read from stream- Throws:
AlignmentParseException
IOException
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ReadAlignment
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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