org.biojava.bio.program.ssbind.ViewSequenceFactory

org.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

Fields

Modifier and Type

Field

Description

static final 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
databaseID, querySeqHolder, queryViewCache, subjectDBs, subjectViewCache
Constructor Summary

Constructors

Constructor

Description

BlastLikeHomologyBuilder(List target)

Creates a new BlastLikeHomologyBuilder which will instantiate Homology objects into the List target.
Method Summary

Modifier and Type

Method

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.

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 Details
- HOMOLOGY_FEATURE_TYPE
  
  public static final 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 Details
- BlastLikeHomologyBuilder
  
  public BlastLikeHomologyBuilder(List target)
  
  Creates a new BlastLikeHomologyBuilder which will instantiate Homology objects into the List target.
  
  Parameters:
  
  target - a List.
Method Details
- 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.

Class BlastLikeHomologyBuilder

Field Summary

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

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Methods inherited from interface org.biojava.bio.search.SearchContentHandler

Field Details

HOMOLOGY_FEATURE_TYPE

Constructor Details

BlastLikeHomologyBuilder

Method Details

setQueryID

getMoreSearches

setMoreSearches

startSearch

endSearch

startHeader

endHeader

startHit

endHit

startSubHit

endSubHit

addSearchProperty

addHitProperty

addSubHitProperty