Package pal.alignment
Class ReadAlignmentOld
- java.lang.Object
-
- pal.alignment.AbstractAlignment
-
- pal.alignment.ReadAlignmentOld
-
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
-
-
Constructor Summary
Constructors Constructor Description ReadAlignmentOld(java.io.PushbackReader input)
read from streamReadAlignmentOld(java.lang.String file)
read from file
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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
-
-
-
-
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 interfaceAlignment
- Specified by:
getData
in classAbstractAlignment
-
-