org.biojava.bio.program.ssbind
Class BlastLikeHomologyBuilder

java.lang.Object
  extended byorg.biojava.bio.program.ssbind.ViewSequenceFactory
      extended byorg.biojava.bio.program.ssbind.BlastLikeHomologyBuilder
All Implemented Interfaces:
SearchContentHandler

public class BlastLikeHomologyBuilder
extends ViewSequenceFactory
implements 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 ViewSequences wrapping both query and subject sequences are created and populated with HomologyFeatures. See the documentation of Homology and HomologyFeature.

As SimpleHomologyFeatures 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
static java.lang.String HOMOLOGY_FEATURE_TYPE
          HOMOLOGY_FEATURE_TYPE is the type String used by BlastLikeHomologyBuilder when creating HomologyFeatures.
 
Fields inherited from class org.biojava.bio.program.ssbind.ViewSequenceFactory
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 setDatabaseID(java.lang.String databaseID)
          setDatabaseID identifies the database searched by a name, ID or URN.
 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, setQuerySeqHolder, setSubjectDBInstallation
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

HOMOLOGY_FEATURE_TYPE

public static final java.lang.String HOMOLOGY_FEATURE_TYPE
HOMOLOGY_FEATURE_TYPE is the type String used by BlastLikeHomologyBuilder when creating HomologyFeatures. This is the String which is returned when an HomologyFeature's getType() method is called.

See Also:
Constant Field Values
Constructor Detail

BlastLikeHomologyBuilder

public BlastLikeHomologyBuilder(java.util.List target)
Creates a new BlastLikeHomologyBuilder which will instantiate Homology objects into the List target.

Parameters:
target - a List.
Method Detail

setQueryID

public void setQueryID(java.lang.String queryID)
Description copied from interface: SearchContentHandler
setQueryID identifies the query sequence by a name, ID or URN.

Specified by:
setQueryID in interface SearchContentHandler
Parameters:
queryID - a String which should be an unique identifer for the sequence.

setDatabaseID

public void setDatabaseID(java.lang.String databaseID)
Description copied from interface: SearchContentHandler
setDatabaseID identifies the database searched by a name, ID or URN.

Specified by:
setDatabaseID in interface SearchContentHandler
Parameters:
databaseID - a String which should be an unique identifier for the database searched.

getMoreSearches

public boolean getMoreSearches()
Description copied from interface: SearchContentHandler
getMoreSearches returns the state of the SearchContentHandler with respect to further searches from its data source. Used for handling streams of search results.

Specified by:
getMoreSearches in interface SearchContentHandler
Returns:
a boolean value.

setMoreSearches

public void setMoreSearches(boolean value)
Description copied from interface: SearchContentHandler
setMoreSearches sets the state of the SearchContentHandler's expectation of receiving more results. Used for handling streams of search results.

Specified by:
setMoreSearches in interface SearchContentHandler
Parameters:
value - a boolean value.

startSearch

public void startSearch()
Description copied from interface: SearchContentHandler
The startSearch method indicates the start of useful search information.

Specified by:
startSearch in interface SearchContentHandler

endSearch

public void endSearch()
Description copied from interface: SearchContentHandler
The endSearch method indicates the end of useful search information.

Specified by:
endSearch in interface SearchContentHandler

startHeader

public void startHeader()
Description copied from interface: SearchContentHandler
The startHeader method indicates the start of a formatted header. This usually contains information relevant to the search as a whole.

Specified by:
startHeader in interface SearchContentHandler

endHeader

public void endHeader()
Description copied from interface: SearchContentHandler
The endHeader method indicates the end of a formatted header.

Specified by:
endHeader in interface SearchContentHandler

startHit

public void startHit()
Description copied from interface: SearchContentHandler
The startHit method indicates the start of a formatted hit. This could be a single line, or a block of lines.

Specified by:
startHit in interface SearchContentHandler

endHit

public void endHit()
Description copied from interface: SearchContentHandler
The endHit method indicates the end of a formatted hit.

Specified by:
endHit in interface SearchContentHandler

startSubHit

public void startSubHit()
Description copied from interface: SearchContentHandler
The startSubHit method indicates the start of a formatted subhit. There may be zero or more of these per hit.

Specified by:
startSubHit in interface SearchContentHandler

endSubHit

public void endSubHit()
Description copied from interface: SearchContentHandler
The endSubHit method indicates the end of a formatted subhit.

Specified by:
endSubHit in interface SearchContentHandler

addSearchProperty

public void addSearchProperty(java.lang.Object key,
                              java.lang.Object value)
Description copied from interface: SearchContentHandler
The addSearchProperty method adds a key/value pair containing some property of the overall search result.

Specified by:
addSearchProperty in interface SearchContentHandler
Parameters:
key - an Object.
value - an Object.

addHitProperty

public void addHitProperty(java.lang.Object key,
                           java.lang.Object value)
Description copied from interface: SearchContentHandler
The addHitProperty method adds a key/value pair containing some property of a particular hit.

Specified by:
addHitProperty in interface SearchContentHandler
Parameters:
key - an Object.
value - an Object.

addSubHitProperty

public void addSubHitProperty(java.lang.Object key,
                              java.lang.Object value)
Description copied from interface: SearchContentHandler
The addSubHitProperty method adds a key/value pair containing some property of a particular subhit.

Specified by:
addSubHitProperty in interface SearchContentHandler
Parameters:
key - an Object.
value - an Object.