org.biojava.bio.search
Interface SearchContentHandler

All Known Subinterfaces:
SearchBuilder
All Known Implementing Classes:
BlastLikeHomologyBuilder, BlastLikeSearchBuilder, FastaSearchSAXParser, SearchContentAdapter, SearchContentFilter, SimilarityPairBuilder

public interface SearchContentHandler

SearchContentHandler is a notification interface for objects which listen to search stream parsers. This is applicable to all types of search results which are represented by flat files created by external programs e.g. Fasta, (T)BlastN/PX, EMBOSS programs. This is not limited to sequence similarity searches, but includes any format consisting of a header followed by hits, each of which may, or may not, have subhits.

Since:
1.1
Author:
Keith James

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.
 

Method Detail

getMoreSearches

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

Returns:
a boolean value.

setMoreSearches

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

Parameters:
value - a boolean value.

startSearch

public void startSearch()
The startSearch method indicates the start of useful search information.


endSearch

public void endSearch()
The endSearch method indicates the end of useful search information.


startHeader

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


endHeader

public void endHeader()
The endHeader method indicates the end of a formatted header.


startHit

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


endHit

public void endHit()
The endHit method indicates the end of a formatted hit.


startSubHit

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


endSubHit

public void endSubHit()
The endSubHit method indicates the end of a formatted subhit.


addSearchProperty

public 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.

Parameters:
key - an Object.
value - an Object.

addHitProperty

public 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.

Parameters:
key - an Object.
value - an Object.

addSubHitProperty

public 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.

Parameters:
key - an Object.
value - an Object.

setQueryID

public void setQueryID(java.lang.String queryID)
setQueryID identifies the query sequence by a name, ID or URN.

Parameters:
queryID - a String which should be an unique identifer for the sequence.

setDatabaseID

public void setDatabaseID(java.lang.String databaseID)
setDatabaseID identifies the database searched by a name, ID or URN.

Parameters:
databaseID - a String which should be an unique identifier for the database searched.