org.biojava.bio.program.ssbind
Class ViewSequenceFactory

java.lang.Object
  extended by 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
protected  String databaseID
           
protected  SequenceDB querySeqHolder
           
protected  Map queryViewCache
           
protected  SequenceDBInstallation subjectDBs
           
protected  Map subjectViewCache
           
 
Constructor Summary
ViewSequenceFactory()
           
 
Method Summary
 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


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