Class ViewSequenceFactory

  • Direct Known Subclasses:
    BlastLikeHomologyBuilder, SimilarityPairBuilder

    public abstract class ViewSequenceFactory
    extends java.lang.Object
    ViewSequenceFactory is a base class for creating search handlers which create and cache views on the query and subject sequences.
    Author:
    Keith James
    • Field Detail

      • querySeqHolder

        protected SequenceDB querySeqHolder
      • databaseID

        protected java.lang.String databaseID
      • queryViewCache

        protected java.util.Map queryViewCache
      • subjectViewCache

        protected java.util.Map subjectViewCache
    • Constructor Detail

      • ViewSequenceFactory

        public ViewSequenceFactory()
    • Method Detail

      • getQuerySeqHolder

        public SequenceDB getQuerySeqHolder()
        getQuerySeqHolder returns the database of query sequences used to retrieve sequences for creation of the various result objects.
        Returns:
        a SequenceDB value.
      • setQuerySeqHolder

        public void setQuerySeqHolder​(SequenceDB querySeqHolder)
        setQuerySeqHolder sets the query sequence holder to a specific database.
        Parameters:
        querySeqHolder - a SequenceDB containing the query sequence(s).
      • getSubjectDBInstallation

        public SequenceDBInstallation getSubjectDBInstallation()
        getSubjectDBInstallation returns the installation in which all the databases searched may be found. SequenceDBs are retrieved for creation of the various result objects.
        Returns:
        a SequenceDBInstallation containing the subject database(s).
      • setSubjectDBInstallation

        public void setSubjectDBInstallation​(SequenceDBInstallation subjectDBs)
        setSubjectDBInstallation sets the subject database holder to a specific installation.
        Parameters:
        subjectDBs - a SequenceDBInstallation containing the subject database(s)
      • setDatabaseID

        public void setDatabaseID​(java.lang.String databaseID)