Package pal.alignment
Class AlignmentReaders
- java.lang.Object
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- pal.alignment.AlignmentReaders
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public final class AlignmentReaders extends java.lang.Object
Temporary class for reading alignments... will fix up structure some time soon!- Version:
- $Id: AlignmentReaders.java,v 1.11 2004/10/14 02:01:42 matt Exp $
- Author:
- Matthew Goode
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
AlignmentReaders.PhylipClustalAlignment
static class
AlignmentReaders.UnalignedAlignment
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Constructor Summary
Constructors Constructor Description AlignmentReaders()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static Alignment[]
readAllPhylipClustalAlignments(java.io.Reader r, DataType dt)
Read an alignment in phylip/clustal/simple format.static Alignment
readFastaSequences(java.io.Reader r, DataType dt)
Read an a set of unaligned Fasta sequencesstatic Alignment
readNewLineSeperatedSequences(java.io.Reader r, DataType dt)
Read an a set of unaligned Fasta sequencesstatic Alignment
readPhylipClustalAlignment(java.io.Reader r, DataType dt)
Read an alignment in phylip/clustal/simple format.static void
readPhylipClustalAlignment(java.io.Reader r, DataType dt, AlignmentReceiver receiver)
Read an alignment in phylip/clustal/simple format.
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Method Detail
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readFastaSequences
public static final Alignment readFastaSequences(java.io.Reader r, DataType dt) throws java.io.IOException
Read an a set of unaligned Fasta sequences- Throws:
java.io.IOException
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readNewLineSeperatedSequences
public static final Alignment readNewLineSeperatedSequences(java.io.Reader r, DataType dt) throws java.io.IOException
Read an a set of unaligned Fasta sequences- Throws:
java.io.IOException
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readPhylipClustalAlignment
public static final Alignment readPhylipClustalAlignment(java.io.Reader r, DataType dt) throws AlignmentParseException, java.io.IOException
Read an alignment in phylip/clustal/simple format. Handles interleaved/sequential - with the name repeated, or with the name only given once for each sequence Aims to be as general as possible (possibly causeing problems with some formats).- Throws:
AlignmentParseException
java.io.IOException
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readAllPhylipClustalAlignments
public static final Alignment[] readAllPhylipClustalAlignments(java.io.Reader r, DataType dt) throws AlignmentParseException, java.io.IOException
Read an alignment in phylip/clustal/simple format. Handles interleaved/sequential - with the name repeated, or with the name only given once for each sequence Aims to be as general as possible (possibly causeing problems with some formats).- Throws:
AlignmentParseException
java.io.IOException
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readPhylipClustalAlignment
public static final void readPhylipClustalAlignment(java.io.Reader r, DataType dt, AlignmentReceiver receiver) throws AlignmentParseException, java.io.IOException
Read an alignment in phylip/clustal/simple format. Handles interleaved/sequential - with the name repeated, or with the name only given once for each sequence Aims to be as general as possible (possibly causeing problems with some formats).- Throws:
AlignmentParseException
java.io.IOException
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