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java.lang.Objectpal.alignment.AlignmentReaders
public final class AlignmentReaders
Temporary class for reading alignments... will fix up structure some time soon!
Nested Class Summary | |
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static class |
AlignmentReaders.PhylipClustalAlignment
|
static class |
AlignmentReaders.UnalignedAlignment
|
Constructor Summary | |
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AlignmentReaders()
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Method Summary | |
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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 sequences |
static Alignment |
readNewLineSeperatedSequences(java.io.Reader r,
DataType dt)
Read an a set of unaligned Fasta sequences |
static 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. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public AlignmentReaders()
Method Detail |
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public static final Alignment readFastaSequences(java.io.Reader r, DataType dt) throws java.io.IOException
java.io.IOException
public static final Alignment readNewLineSeperatedSequences(java.io.Reader r, DataType dt) throws java.io.IOException
java.io.IOException
public static final Alignment readPhylipClustalAlignment(java.io.Reader r, DataType dt) throws AlignmentParseException, java.io.IOException
AlignmentParseException
java.io.IOException
public static final Alignment[] readAllPhylipClustalAlignments(java.io.Reader r, DataType dt) throws AlignmentParseException, java.io.IOException
AlignmentParseException
java.io.IOException
public static final void readPhylipClustalAlignment(java.io.Reader r, DataType dt, AlignmentReceiver receiver) throws AlignmentParseException, java.io.IOException
AlignmentParseException
java.io.IOException
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