Class FastaSearchSAXParser

  • All Implemented Interfaces:
    SearchContentHandler, XMLReader

    public class FastaSearchSAXParser
    extends Object
    implements SearchContentHandler

    FastaSearchSAXParser is a SAX2 compliant parser for '-m 10' format output from the the Fasta search program (see the Fasta documentation for details of this format).

    Versions of Fasta supported are as follows. Note that the compile time option -DM10_CONS should be used to allow correct reporting of the number of matches in HSPSummary elements

    • 33t07
    • 33t08 (current tests are against output from this version)

    The SAX2 events produced are as if the input to the parser was an XML file validating against the BioJava BlastLikeDataSetCollection DTD. There is no requirement for an intermediate conversion of native output to XML format.

    Keith James
    • Field Detail

      • tNamespaces

        protected boolean tNamespaces
      • tNamespacePrefixes

        protected boolean tNamespacePrefixes
      • oNamespacePrefix

        protected String oNamespacePrefix
      • oFullNamespacePrefix

        protected String oFullNamespacePrefix
      • iState

        protected int iState
    • Constructor Detail