Package org.biojava.bio.program.ssbind
Class ViewSequenceFactory
java.lang.Object
org.biojava.bio.program.ssbind.ViewSequenceFactory
- Direct Known Subclasses:
BlastLikeHomologyBuilder
,SimilarityPairBuilder
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
FieldsModifier and TypeFieldDescriptionprotected String
protected SequenceDB
protected Map
protected SequenceDBInstallation
protected Map
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetQuerySeqHolder
returns the database of query sequences used to retrieve sequences for creation of the various result objects.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.
-
Field Details
-
subjectDBs
-
querySeqHolder
-
databaseID
-
queryViewCache
-
subjectViewCache
-
-
Constructor Details
-
ViewSequenceFactory
public ViewSequenceFactory()
-
-
Method Details
-
getQuerySeqHolder
getQuerySeqHolder
returns the database of query sequences used to retrieve sequences for creation of the various result objects.- Returns:
- a
SequenceDB
value.
-
setQuerySeqHolder
setQuerySeqHolder
sets the query sequence holder to a specific database.- Parameters:
querySeqHolder
- aSequenceDB
containing the query sequence(s).
-
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
setSubjectDBInstallation
sets the subject database holder to a specific installation.- Parameters:
subjectDBs
- aSequenceDBInstallation
containing the subject database(s)
-
setDatabaseID
-
makeQueryViewSequence
- Throws:
BioException
-
makeSubjectViewSequence
- Throws:
BioException
-