Class IndexTools


  • public class IndexTools
    extends java.lang.Object
    IndexTools contains static utility methods for creating flatfile indices according to the OBDA standard.
    Author:
    Keith James, Matthew Pocock
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static void indexEmbl​(java.lang.String name, java.io.File location, java.io.File[] seqFiles, int alphabetIdentifier)
      indexEmbl indexes DNA, RNA or protein EMBL format sequence files on ID as primary identifier and AC as secondary.
      static void indexFasta​(java.lang.String name, java.io.File location, java.io.File[] seqFiles, int alphabetIdentifier)
      indexFasta indexes DNA, RNA or protein Fasta format sequence files on primary identifier.
      static void indexGenbank​(java.lang.String name, java.io.File location, java.io.File[] seqFiles, int alphabetIdentifier)
      indexGenbank indexes DNA, RNA or protein Genbank format sequence files on LOCUS as primary identifier and ACCESSION as secondary.
      static void indexSwissprot​(java.lang.String name, java.io.File location, java.io.File[] seqFiles)
      indexSwissprot indexes Swissprot format protein sequence files on ID as primary identifier.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Method Detail

      • indexFasta

        public static void indexFasta​(java.lang.String name,
                                      java.io.File location,
                                      java.io.File[] seqFiles,
                                      int alphabetIdentifier)
                               throws java.io.FileNotFoundException,
                                      java.io.IOException,
                                      ParserException,
                                      BioException
        indexFasta indexes DNA, RNA or protein Fasta format sequence files on primary identifier.
        Parameters:
        location - a File directory which will contain the indices.
        seqFiles - a File [] array of files to index.
        alphabetIdentifier - an int indicating the type of sequence to be indexed. May be one of SeqIOConstants.DNA SeqIOConstants.RNA SeqIOConstants.AA.
        name - a String arbitrary database name.
        Throws:
        java.io.FileNotFoundException - if an error occurs.
        java.io.IOException - if an error occurs.
        ParserException - if an error occurs.
        BioException - if an error occurs.
      • indexEmbl

        public static void indexEmbl​(java.lang.String name,
                                     java.io.File location,
                                     java.io.File[] seqFiles,
                                     int alphabetIdentifier)
                              throws java.io.FileNotFoundException,
                                     java.io.IOException,
                                     ParserException,
                                     BioException
        indexEmbl indexes DNA, RNA or protein EMBL format sequence files on ID as primary identifier and AC as secondary.
        Parameters:
        location - a File directory which will contain the indices.
        seqFiles - a File [] array of files to index.
        alphabetIdentifier - an int indicating the type of sequence to be indexed. May be one of SeqIOConstants.DNA SeqIOConstants.RNA SeqIOConstants.AA.
        name - a String arbitrary database name.
        Throws:
        java.io.FileNotFoundException - if an error occurs.
        java.io.IOException - if an error occurs.
        ParserException - if an error occurs.
        BioException - if an error occurs.
      • indexGenbank

        public static void indexGenbank​(java.lang.String name,
                                        java.io.File location,
                                        java.io.File[] seqFiles,
                                        int alphabetIdentifier)
                                 throws java.io.FileNotFoundException,
                                        java.io.IOException,
                                        ParserException,
                                        BioException
        indexGenbank indexes DNA, RNA or protein Genbank format sequence files on LOCUS as primary identifier and ACCESSION as secondary.
        Parameters:
        location - a File directory which will contain the indices.
        seqFiles - a File [] array of files to index.
        alphabetIdentifier - an int indicating the type of sequence to be indexed. May be one of SeqIOConstants.DNA SeqIOConstants.RNA SeqIOConstants.AA.
        name - a String arbitrary database name.
        Throws:
        java.io.FileNotFoundException - if an error occurs.
        java.io.IOException - if an error occurs.
        ParserException - if an error occurs.
        BioException - if an error occurs.
      • indexSwissprot

        public static void indexSwissprot​(java.lang.String name,
                                          java.io.File location,
                                          java.io.File[] seqFiles)
                                   throws java.io.FileNotFoundException,
                                          java.io.IOException,
                                          ParserException,
                                          BioException
        indexSwissprot indexes Swissprot format protein sequence files on ID as primary identifier.
        Parameters:
        location - a File directory which will contain the indices.
        seqFiles - a File [] array of files to index.
        Throws:
        java.io.FileNotFoundException - if an error occurs.
        java.io.IOException - if an error occurs.
        ParserException - if an error occurs.
        BioException - if an error occurs.