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java.lang.Objectorg.biojava.bio.program.ssbind.ViewSequenceFactory
org.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
public class BlastLikeHomologyBuilder
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.
Field Summary | |
---|---|
static java.lang.String |
HOMOLOGY_FEATURE_TYPE
HOMOLOGY_FEATURE_TYPE is the type String used by
BlastLikeHomologyBuilder when creating
HomologyFeature s. |
Fields inherited from class org.biojava.bio.program.ssbind.ViewSequenceFactory |
---|
databaseID, querySeqHolder, queryViewCache, subjectDBs, subjectViewCache |
Constructor Summary | |
---|---|
BlastLikeHomologyBuilder(java.util.List target)
Creates a new BlastLikeHomologyBuilder which will
instantiate Homology objects into the
List target. |
Method Summary | |
---|---|
void |
addHitProperty(java.lang.Object key,
java.lang.Object value)
The addHitProperty method adds a key/value pair
containing some property of a particular hit. |
void |
addSearchProperty(java.lang.Object key,
java.lang.Object value)
The addSearchProperty method adds a key/value pair
containing some property of the overall search result. |
void |
addSubHitProperty(java.lang.Object key,
java.lang.Object value)
The addSubHitProperty method adds a key/value pair
containing some property of a particular subhit. |
void |
endHeader()
The endHeader method indicates the end of a
formatted header. |
void |
endHit()
The endHit method indicates the end of a formatted
hit. |
void |
endSearch()
The endSearch method indicates the end of useful
search information. |
void |
endSubHit()
The endSubHit method indicates the end of a
formatted subhit. |
boolean |
getMoreSearches()
getMoreSearches returns the state of the
SearchContentHandler with respect to further
searches from its data source. |
void |
setMoreSearches(boolean value)
setMoreSearches sets the state of the
SearchContentHandler 's expectation of receiving
more results. |
void |
setQueryID(java.lang.String queryID)
setQueryID identifies the query sequence by a
name, ID or URN. |
void |
startHeader()
The startHeader method indicates the start of a
formatted header. |
void |
startHit()
The startHit method indicates the start of a
formatted hit. |
void |
startSearch()
The startSearch method indicates the start of
useful search information. |
void |
startSubHit()
The startSubHit 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 Detail |
---|
public static final java.lang.String HOMOLOGY_FEATURE_TYPE
HOMOLOGY_FEATURE_TYPE
is the type String used by
BlastLikeHomologyBuilder
when creating
HomologyFeature
s. This is the String which is
returned when an HomologyFeature
's
getType()
method is called.
Constructor Detail |
---|
public BlastLikeHomologyBuilder(java.util.List target)
BlastLikeHomologyBuilder
which will
instantiate Homology
objects into the
List
target.
target
- a List
.Method Detail |
---|
public void setQueryID(java.lang.String queryID)
SearchContentHandler
setQueryID
identifies the query sequence by a
name, ID or URN.
setQueryID
in interface SearchContentHandler
queryID
- a String
which should be an unique
identifer for the sequence.public boolean getMoreSearches()
SearchContentHandler
getMoreSearches
returns the state of the
SearchContentHandler
with respect to further
searches from its data source. Used for handling streams of
search results.
getMoreSearches
in interface SearchContentHandler
boolean
value.public void setMoreSearches(boolean value)
SearchContentHandler
setMoreSearches
sets the state of the
SearchContentHandler
's expectation of receiving
more results. Used for handling streams of search results.
setMoreSearches
in interface SearchContentHandler
value
- a boolean
value.public void startSearch()
SearchContentHandler
startSearch
method indicates the start of
useful search information.
startSearch
in interface SearchContentHandler
public void endSearch()
SearchContentHandler
endSearch
method indicates the end of useful
search information.
endSearch
in interface SearchContentHandler
public void startHeader()
SearchContentHandler
startHeader
method indicates the start of a
formatted header. This usually contains information relevant to
the search as a whole.
startHeader
in interface SearchContentHandler
public void endHeader()
SearchContentHandler
endHeader
method indicates the end of a
formatted header.
endHeader
in interface SearchContentHandler
public void startHit()
SearchContentHandler
startHit
method indicates the start of a
formatted hit. This could be a single line, or a block of
lines.
startHit
in interface SearchContentHandler
public void endHit()
SearchContentHandler
endHit
method indicates the end of a formatted
hit.
endHit
in interface SearchContentHandler
public void startSubHit()
SearchContentHandler
startSubHit
method indicates the start of a
formatted subhit. There may be zero or more of these per hit.
startSubHit
in interface SearchContentHandler
public void endSubHit()
SearchContentHandler
endSubHit
method indicates the end of a
formatted subhit.
endSubHit
in interface SearchContentHandler
public void addSearchProperty(java.lang.Object key, java.lang.Object value)
SearchContentHandler
addSearchProperty
method adds a key/value pair
containing some property of the overall search result.
addSearchProperty
in interface SearchContentHandler
key
- an Object
.value
- an Object
.public void addHitProperty(java.lang.Object key, java.lang.Object value)
SearchContentHandler
addHitProperty
method adds a key/value pair
containing some property of a particular hit.
addHitProperty
in interface SearchContentHandler
key
- an Object
.value
- an Object
.public void addSubHitProperty(java.lang.Object key, java.lang.Object value)
SearchContentHandler
addSubHitProperty
method adds a key/value pair
containing some property of a particular subhit.
addSubHitProperty
in interface SearchContentHandler
key
- an Object
.value
- an Object
.
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