org.biojava.bio.program.ssbind

Class SimilarityPairBuilder

java.lang.Object

org.biojava.bio.program.ssbind.ViewSequenceFactory

org.biojava.bio.program.ssbind.SimilarityPairBuilder

All Implemented Interfaces:

SearchContentHandler

public class SimilarityPairBuilder
extends ViewSequenceFactory
implements SearchContentHandler

SimilarityPairBuilder annotates query and subject Sequence with SimilarityPairFeatures 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 HomologyFeatures 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 ViewSequences 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.

Since:

1.2

Author:

Keith James, Greg Cox

Field Summary

Fields

Modifier and Type	Field and Description
static String	SIMILARITY_PAIR_FEATURE_TYPE Constant SIMILARITY_PAIR_FEATURE_TYPE the type String used by SimilarityPairBuilder when creating SimilarityPairFeatures.

Fields inherited from class org.biojava.bio.program.ssbind.ViewSequenceFactory

databaseID, querySeqHolder, queryViewCache, subjectDBs, subjectViewCache

Constructor Summary

Constructors

Constructor and Description
SimilarityPairBuilder()

Method Summary

Methods

Modifier and Type	Method and Description
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

SIMILARITY_PAIR_FEATURE_TYPE

public static final String SIMILARITY_PAIR_FEATURE_TYPE

Constant SIMILARITY_PAIR_FEATURE_TYPE the type String used by SimilarityPairBuilder when creating SimilarityPairFeatures. This is the String which is returned when a SimilarityPairFeature's getType() method is called.

See Also:

Constant Field Values

Constructor Detail

SimilarityPairBuilder

public SimilarityPairBuilder()

Method Detail

getAnnotatedQuerySeq

public Sequence getAnnotatedQuerySeq(String queryID)
                              throws IllegalIDException

Throws:

IllegalIDException

getAnnotatedSubjectSeq

public Sequence getAnnotatedSubjectSeq(String subjectID)
                                throws IllegalIDException

Throws:

IllegalIDException

setQueryID

public void setQueryID(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.

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(Object key,
                     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(Object key,
                  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(Object key,
                     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.