Package org.biojava.bio.program.ssbind
Class BlastLikeHomologyBuilder
java.lang.Object
org.biojava.bio.program.ssbind.ViewSequenceFactory
org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
- All Implemented Interfaces:
SearchContentHandler
BlastLikeHomologyBuilder
populates a
List
with Homology
instances created from
SAX events supplied via a SeqSimilarityAdapter
. The
SAX events should describe elements conforming to the BioJava
BlastLikeDataSetCollection DTD. Suitable sources are
BlastLikeSAXParser
or
FastaSAXParser
. Annotated ViewSequence
s
wrapping both query and subject sequences are created and populated
with HomologyFeature
s. See the documentation of
Homology
and HomologyFeature
.
As SimpleHomologyFeature
s are created on views of
the query and subject sequences, both query and subject should be
nucleotide sequences (SimpleHomologyFeature
extends
StrandedFeature
.). This limits the searches currently
handled to BLASTN, TBLASTX and Fasta DNA.
- Since:
- 1.2
- Author:
- Keith James, Greg Cox
-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
HOMOLOGY_FEATURE_TYPE
is the type String used byBlastLikeHomologyBuilder
when creatingHomologyFeature
s.Fields inherited from class org.biojava.bio.program.ssbind.ViewSequenceFactory
databaseID, querySeqHolder, queryViewCache, subjectDBs, subjectViewCache
-
Constructor Summary
ConstructorsConstructorDescriptionBlastLikeHomologyBuilder
(List target) Creates a newBlastLikeHomologyBuilder
which will instantiateHomology
objects into theList
target. -
Method Summary
Modifier and TypeMethodDescriptionvoid
addHitProperty
(Object key, Object value) TheaddHitProperty
method adds a key/value pair containing some property of a particular hit.void
addSearchProperty
(Object key, Object value) TheaddSearchProperty
method adds a key/value pair containing some property of the overall search result.void
addSubHitProperty
(Object key, Object value) TheaddSubHitProperty
method adds a key/value pair containing some property of a particular subhit.void
TheendHeader
method indicates the end of a formatted header.void
endHit()
TheendHit
method indicates the end of a formatted hit.void
TheendSearch
method indicates the end of useful search information.void
TheendSubHit
method indicates the end of a formatted subhit.boolean
getMoreSearches
returns the state of theSearchContentHandler
with respect to further searches from its data source.void
setMoreSearches
(boolean value) setMoreSearches
sets the state of theSearchContentHandler
's expectation of receiving more results.void
setQueryID
(String queryID) setQueryID
identifies the query sequence by a name, ID or URN.void
ThestartHeader
method indicates the start of a formatted header.void
startHit()
ThestartHit
method indicates the start of a formatted hit.void
ThestartSearch
method indicates the start of useful search information.void
ThestartSubHit
method indicates the start of a formatted subhit.Methods inherited from class org.biojava.bio.program.ssbind.ViewSequenceFactory
getQuerySeqHolder, getSubjectDBInstallation, makeQueryViewSequence, makeSubjectViewSequence, setDatabaseID, setQuerySeqHolder, setSubjectDBInstallation
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface org.biojava.bio.search.SearchContentHandler
setDatabaseID
-
Field Details
-
HOMOLOGY_FEATURE_TYPE
HOMOLOGY_FEATURE_TYPE
is the type String used byBlastLikeHomologyBuilder
when creatingHomologyFeature
s. This is the String which is returned when anHomologyFeature
'sgetType()
method is called.- See Also:
-
-
Constructor Details
-
BlastLikeHomologyBuilder
Creates a newBlastLikeHomologyBuilder
which will instantiateHomology
objects into theList
target.- Parameters:
target
- aList
.
-
-
Method Details
-
setQueryID
Description copied from interface:SearchContentHandler
setQueryID
identifies the query sequence by a name, ID or URN.- Specified by:
setQueryID
in interfaceSearchContentHandler
- Parameters:
queryID
- aString
which should be an unique identifer for the sequence.
-
getMoreSearches
Description copied from interface:SearchContentHandler
getMoreSearches
returns the state of theSearchContentHandler
with respect to further searches from its data source. Used for handling streams of search results.- Specified by:
getMoreSearches
in interfaceSearchContentHandler
- Returns:
- a
boolean
value.
-
setMoreSearches
Description copied from interface:SearchContentHandler
setMoreSearches
sets the state of theSearchContentHandler
's expectation of receiving more results. Used for handling streams of search results.- Specified by:
setMoreSearches
in interfaceSearchContentHandler
- Parameters:
value
- aboolean
value.
-
startSearch
Description copied from interface:SearchContentHandler
ThestartSearch
method indicates the start of useful search information.- Specified by:
startSearch
in interfaceSearchContentHandler
-
endSearch
Description copied from interface:SearchContentHandler
TheendSearch
method indicates the end of useful search information.- Specified by:
endSearch
in interfaceSearchContentHandler
-
startHeader
Description copied from interface:SearchContentHandler
ThestartHeader
method indicates the start of a formatted header. This usually contains information relevant to the search as a whole.- Specified by:
startHeader
in interfaceSearchContentHandler
-
endHeader
Description copied from interface:SearchContentHandler
TheendHeader
method indicates the end of a formatted header.- Specified by:
endHeader
in interfaceSearchContentHandler
-
startHit
Description copied from interface:SearchContentHandler
ThestartHit
method indicates the start of a formatted hit. This could be a single line, or a block of lines.- Specified by:
startHit
in interfaceSearchContentHandler
-
endHit
Description copied from interface:SearchContentHandler
TheendHit
method indicates the end of a formatted hit.- Specified by:
endHit
in interfaceSearchContentHandler
-
startSubHit
Description copied from interface:SearchContentHandler
ThestartSubHit
method indicates the start of a formatted subhit. There may be zero or more of these per hit.- Specified by:
startSubHit
in interfaceSearchContentHandler
-
endSubHit
Description copied from interface:SearchContentHandler
TheendSubHit
method indicates the end of a formatted subhit.- Specified by:
endSubHit
in interfaceSearchContentHandler
-
addSearchProperty
Description copied from interface:SearchContentHandler
TheaddSearchProperty
method adds a key/value pair containing some property of the overall search result.- Specified by:
addSearchProperty
in interfaceSearchContentHandler
- Parameters:
key
- anObject
.value
- anObject
.
-
addHitProperty
Description copied from interface:SearchContentHandler
TheaddHitProperty
method adds a key/value pair containing some property of a particular hit.- Specified by:
addHitProperty
in interfaceSearchContentHandler
- Parameters:
key
- anObject
.value
- anObject
.
-
addSubHitProperty
Description copied from interface:SearchContentHandler
TheaddSubHitProperty
method adds a key/value pair containing some property of a particular subhit.- Specified by:
addSubHitProperty
in interfaceSearchContentHandler
- Parameters:
key
- anObject
.value
- anObject
.
-