Package pal.alignment

Class 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

    • 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