pal.alignment
Class AlignmentReaders

java.lang.Object
  extended by pal.alignment.AlignmentReaders

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

Nested Class Summary
static class AlignmentReaders.PhylipClustalAlignment
           
static class AlignmentReaders.UnalignedAlignment
           
 
Constructor Summary
AlignmentReaders()
           
 
Method Summary
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
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

AlignmentReaders

public AlignmentReaders()
Method Detail

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

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

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

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

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