Package org.biojava.bio.program.ssbind
Class BlastLikeSearchBuilder
java.lang.Object
org.biojava.bio.program.ssbind.BlastLikeSearchBuilder
- All Implemented Interfaces:
SearchBuilder
,SearchContentHandler
BlastLikeSearchBuilder
will create
SeqSimilaritySearchResult
s from SAX events via a
SeqSimilarityAdapter
. The SAX events should describe
elements conforming to the BioJava BlastLikeDataSetCollection
DTD. Suitable sources are BlastLikeSAXParser
or
FastaSearchSAXParser
. The result objects are placed in
the List
supplied to the constructor.
The start/end/strand of SeqSimilaritySearchHit
s are
calculated from their constituent
SeqSimilaritySearchSubHit
s as follows:
- The query start is the lowest query start coordinate of its sub-hits, regardless of strand
- The query end is the highest query end coordinate of its sub-hits, regardless of strand
- The hit start is the lowest hit start coordinate of its sub-hits, regardless of strand
- The hit end is the highest hit end coordinate of its sub-hits, regardless of strand
- The query strand is null for protein sequences. Otherwise it is
equal to the query strand of its sub-hits if they are all on the
same strand, or
StrandedFeature.UNKNOWN
if the sub-hits have mixed query strands - The hit strand is null for protein sequences. Otherwise it is
equal to the hit strand of its sub-hits if they are all on the same
strand, or
StrandedFeature.UNKNOWN
if the sub-hits have mixed hit strands
This class has special meanings for particular keys: if you want to adapt this class for another parser, you will need to be aware of this. These originate from and are fully described in the BlastLikeDataSetCollection DTD.
Key | Meaning |
---|---|
program | either this value or the subjectSequenceType value must be set. This can take values acceptable to AlphabetResolver. These are BLASTN, BLASTP, BLASTX, TBLASTN, TBLASTX, DNA and PROTEIN. |
databaseId | Identifier of database searched (in SequenceDBInstallation). |
subjectSequenceType | type of sequence that hit is. Can be DNA or PROTEIN. |
subjectId | id of sequence that is hit |
subjectDescription | description of sequence that is hit |
queryStrand | Strandedness of query in alignment. Takes values of "plus" and "minus" |
subjectStrand | Strandedness of query in alignment. Takes values of "plus" and "minus" |
queryFrame | self-evident |
subjectFrame | self-evident |
querySequenceStart | self-evident |
querySequenceEnd | self-evident |
subjectSequenceStart | self-evident |
subjectSequenceEnd | self-evident |
score | self-evident |
expectValue | self-evident |
pValue | self-evident |
- Since:
- 1.2
- Author:
- Keith James, Greg Cox
-
Constructor Summary
ConstructorsConstructorDescriptionBlastLikeSearchBuilder
(List target) Creates a newBlastLikeSearchBuilder
which will instantiate results into theList
target.BlastLikeSearchBuilder
(List target, SequenceDB querySeqHolder, SequenceDBInstallation subjectDBs) Creates a newBlastLikeSearchBuilder
which will instantiate results 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.ThemakeSearchResult
method returns aSeqSimilaritySearchResult
instance created from accumulated data.void
setDatabaseID
(String databaseID) setDatabaseID
identifies the database searched by a name, ID or URN.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
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.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.
-
Constructor Details
-
BlastLikeSearchBuilder
Creates a newBlastLikeSearchBuilder
which will instantiate results into theList
target.- Parameters:
target
- aList
.
-
BlastLikeSearchBuilder
public BlastLikeSearchBuilder(List target, SequenceDB querySeqHolder, SequenceDBInstallation subjectDBs) Creates a newBlastLikeSearchBuilder
which will instantiate results into theList
target.- Parameters:
target
- aList
.querySeqHolder
- aSequenceDB
of query sequences.subjectDBs
- aSequenceDBInstallation
of databases searched.
-
-
Method Details
-
makeSearchResult
Description copied from interface:SearchBuilder
ThemakeSearchResult
method returns aSeqSimilaritySearchResult
instance created from accumulated data.- Specified by:
makeSearchResult
in interfaceSearchBuilder
- Returns:
- a
SeqSimilaritySearchResult
. - Throws:
BioException
- if an error occurs.
-
setQuerySeqHolder
setQuerySeqHolder
sets the query sequence holder to a specific database.- Parameters:
querySeqHolder
- aSequenceDB
containing the query sequence(s).
-
setSubjectDBInstallation
setSubjectDBInstallation
sets the subject database holder to a specific installation.- Parameters:
subjectDBs
- aSequenceDBInstallation
containing the subject database(s)
-
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.
-
setDatabaseID
Description copied from interface:SearchContentHandler
setDatabaseID
identifies the database searched by a name, ID or URN.- Specified by:
setDatabaseID
in interfaceSearchContentHandler
- Parameters:
databaseID
- aString
which should be an unique identifier for the database searched.
-
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
.
-