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.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 and Description |
---|
ViewSequenceFactory() |
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. |
protected SequenceDBInstallation subjectDBs
protected SequenceDB querySeqHolder
protected java.lang.String databaseID
protected java.util.Map queryViewCache
protected java.util.Map subjectViewCache
public SequenceDB getQuerySeqHolder()
getQuerySeqHolder
returns the database of query
sequences used to retrieve sequences for creation of the
various result objects.SequenceDB
value.public void setQuerySeqHolder(SequenceDB querySeqHolder)
setQuerySeqHolder
sets the query sequence holder
to a specific database.querySeqHolder
- a SequenceDB
containing the
query sequence(s).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.SequenceDBInstallation
containing the
subject database(s).public void setSubjectDBInstallation(SequenceDBInstallation subjectDBs)
setSubjectDBInstallation
sets the subject database
holder to a specific installation.subjectDBs
- a SequenceDBInstallation
containing the subject database(s)public void setDatabaseID(java.lang.String databaseID)
protected Sequence makeQueryViewSequence(java.lang.String queryID) throws BioException
BioException
protected Sequence makeSubjectViewSequence(java.lang.String subjectID) throws BioException
BioException