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ViewSequenceFactory (biojava-legacy 1.9.5 API)

  • java.lang.Object
    • org.biojava.bio.program.ssbind.ViewSequenceFactory
  • Direct Known Subclasses:
    BlastLikeHomologyBuilder, SimilarityPairBuilder
    public abstract class ViewSequenceFactory
extends 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 Summary

      Fields 
      Modifier and Type Field Description
      protected String databaseID  
      protected SequenceDB querySeqHolder  
      protected Map queryViewCache  
      protected SequenceDBInstallation subjectDBs  
      protected Map subjectViewCache  

    • Constructor Summary

      Constructors 
      Constructor Description
      ViewSequenceFactory()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      SequenceDB getQuerySeqHolder()

      getQuerySeqHolder returns the database of query sequences used to retrieve sequences for creation of the various result objects.
      SequenceDBInstallation getSubjectDBInstallation()

      getSubjectDBInstallation returns the installation in which all the databases searched may be found.
      protected Sequence makeQueryViewSequence​(String queryID)  
      protected Sequence makeSubjectViewSequence​(String subjectID)  
      void setDatabaseID​(String databaseID)  
      void setQuerySeqHolder​(SequenceDB querySeqHolder)

      setQuerySeqHolder sets the query sequence holder to a specific database.
      void setSubjectDBInstallation​(SequenceDBInstallation subjectDBs)

      setSubjectDBInstallation sets the subject database holder to a specific installation.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • subjectDBs

        protected SequenceDBInstallation subjectDBs

      • querySeqHolder

        protected SequenceDB querySeqHolder

      • databaseID

        protected String databaseID

      • queryViewCache

        protected Map queryViewCache

      • subjectViewCache

        protected 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​(String databaseID)

      • makeQueryViewSequence

        protected Sequence makeQueryViewSequence​(String queryID)
                                  throws BioException
        Throws:
        BioException

      • makeSubjectViewSequence

        protected Sequence makeSubjectViewSequence​(String subjectID)
                                    throws BioException
        Throws:
        BioException