org.biojava.bio.program.ssbind

Class ViewSequenceFactory

java.lang.Object

org.biojava.bio.program.ssbind.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 Summary

Fields

Modifier and Type	Field and Description
protected java.lang.String	databaseID
protected SequenceDB	querySeqHolder
protected java.util.Map	queryViewCache
protected SequenceDBInstallation	subjectDBs
protected java.util.Map	subjectViewCache

Constructor Summary

Constructors

Constructor and Description
ViewSequenceFactory()

Method Summary

Modifier and Type	Method and 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(java.lang.String queryID)
protected Sequence	makeSubjectViewSequence(java.lang.String subjectID)
void	setDatabaseID(java.lang.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 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)

makeQueryViewSequence

protected Sequence makeQueryViewSequence(java.lang.String queryID)
                                  throws BioException

Throws:

BioException

makeSubjectViewSequence

protected Sequence makeSubjectViewSequence(java.lang.String subjectID)
                                    throws BioException

Throws:

BioException