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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
subjectDBs
protected SequenceDBInstallation subjectDBs
querySeqHolder
protected SequenceDB querySeqHolder
queryViewCache
protected java.util.Map queryViewCache
subjectViewCache
protected java.util.Map subjectViewCache
ViewSequenceFactory
public ViewSequenceFactory()
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. SequenceDB
s 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)
makeQueryViewSequence
protected Sequence makeQueryViewSequence(java.lang.String queryID)
throws BioException
- Throws:
BioException
makeSubjectViewSequence
protected Sequence makeSubjectViewSequence(java.lang.String subjectID)
throws BioException
- Throws:
BioException