public class ReadAlignmentOld extends AbstractAlignment
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.
IdGroup.Utils
idGroup, numSeqs, numSites
Constructor and Description |
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ReadAlignmentOld(java.io.PushbackReader input)
read from stream
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ReadAlignmentOld(java.lang.String file)
read from file
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Modifier and Type | Method and Description |
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char |
getData(int seq,
int site)
sequence alignment at (sequence, site)
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getAlignedSequenceString, getChar, getDataType, getIdCount, getIdentifier, getLength, getSequenceCount, getSiteCount, getState, getStates, guessDataType, isGap, isUnknownState, report, setDataType, setIdentifier, toString, whichIdNumber
public ReadAlignmentOld(java.io.PushbackReader input) throws AlignmentParseException, java.io.IOException
AlignmentParseException
java.io.IOException
public ReadAlignmentOld(java.lang.String file) throws AlignmentParseException, java.io.IOException
AlignmentParseException
java.io.IOException
public char getData(int seq, int site)
getData
in interface Alignment
getData
in class AbstractAlignment