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java.lang.Objectorg.biojava.bio.program.ssbind.ViewSequenceFactory
org.biojava.bio.program.ssbind.SimilarityPairBuilder
public class SimilarityPairBuilder
SimilarityPairBuilder
annotates query and subject
Sequence
with SimilarityPairFeature
s
created from SAX events supplied via a
SeqSimilarityAdapter
. The objective is to describe a
simple pairwise relationship between the two sequences. This
differs slightly from using HomologyFeature
s which are
slightly heavier, have to contain a full alignment and don't have
an explicit distinction between query and subject sequences in the
alignment. 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.
The current implementation should be used with care on streams containing more than one search output. This is because the builder will not stop after each report has been processed and as a result all the subject sequences get instantiated and a large object network could be created during processing.
Field Summary | |
---|---|
static String |
SIMILARITY_PAIR_FEATURE_TYPE
Constant SIMILARITY_PAIR_FEATURE_TYPE the type
String used by SimilarityPairBuilder when creating
SimilarityPairFeature s. |
Fields inherited from class org.biojava.bio.program.ssbind.ViewSequenceFactory |
---|
databaseID, querySeqHolder, queryViewCache, subjectDBs, subjectViewCache |
Constructor Summary | |
---|---|
SimilarityPairBuilder()
|
Method Summary | |
---|---|
void |
addHitProperty(Object key,
Object value)
The addHitProperty method adds a key/value pair
containing some property of a particular hit. |
void |
addSearchProperty(Object key,
Object value)
The addSearchProperty method adds a key/value pair
containing some property of the overall search result. |
void |
addSubHitProperty(Object key,
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. |
Sequence |
getAnnotatedQuerySeq(String queryID)
|
Sequence |
getAnnotatedSubjectSeq(String subjectID)
|
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(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 String SIMILARITY_PAIR_FEATURE_TYPE
SIMILARITY_PAIR_FEATURE_TYPE
the type
String used by SimilarityPairBuilder
when creating
SimilarityPairFeature
s. This is the String which
is returned when a SimilarityPairFeature
's
getType()
method is called.
Constructor Detail |
---|
public SimilarityPairBuilder()
Method Detail |
---|
public Sequence getAnnotatedQuerySeq(String queryID) throws IllegalIDException
IllegalIDException
public Sequence getAnnotatedSubjectSeq(String subjectID) throws IllegalIDException
IllegalIDException
public void setQueryID(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(Object key, 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(Object key, 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(Object key, 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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