Package pal.alignment
Class AlignmentReaders
java.lang.Object
pal.alignment.AlignmentReaders
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 ClassesModifier and TypeClassDescriptionstatic class
static class
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionstatic final Alignment[]
Read an alignment in phylip/clustal/simple format.static final Alignment
readFastaSequences
(Reader r, DataType dt) Read an a set of unaligned Fasta sequencesstatic final Alignment
Read an a set of unaligned Fasta sequencesstatic final Alignment
Read an alignment in phylip/clustal/simple format.static final void
readPhylipClustalAlignment
(Reader r, DataType dt, AlignmentReceiver receiver) Read an alignment in phylip/clustal/simple format.
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Constructor Details
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AlignmentReaders
public AlignmentReaders()
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Method Details
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readFastaSequences
Read an a set of unaligned Fasta sequences- Throws:
IOException
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readNewLineSeperatedSequences
public static final Alignment readNewLineSeperatedSequences(Reader r, DataType dt) throws IOException Read an a set of unaligned Fasta sequences- Throws:
IOException
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readPhylipClustalAlignment
public static final Alignment readPhylipClustalAlignment(Reader r, DataType dt) throws AlignmentParseException, 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
IOException
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readAllPhylipClustalAlignments
public static final Alignment[] readAllPhylipClustalAlignments(Reader r, DataType dt) throws AlignmentParseException, 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
IOException
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readPhylipClustalAlignment
public static final void readPhylipClustalAlignment(Reader r, DataType dt, AlignmentReceiver receiver) throws AlignmentParseException, 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
IOException
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