Package org.biojava.bio.search

Class FilteringContentHandler

java.lang.Object

org.biojava.bio.search.SearchContentAdapter

org.biojava.bio.search.FilteringContentHandler

All Implemented Interfaces:

BlastLikeSearchFilter.Node, SearchContentHandler

public class FilteringContentHandler
extends SearchContentAdapter
implements BlastLikeSearchFilter.Node

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	FilteringContentHandler.FilterVisitor	Visitor class that parses the filter tree

Constructor Summary

Constructors

Constructor	Description
FilteringContentHandler(BlastLikeSearchFilter filter)
FilteringContentHandler(BlastLikeSearchFilter filter, SearchContentHandler delegate)

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.
Object	getHitProperty(Object key)
Object	getSearchProperty(Object key)
Object	getSubHitProperty(Object key)
void	setDatabaseID(String id)	setDatabaseID identifies the database searched by a name, ID or URN.
void	setQueryID(String queryID)	setQueryID identifies the query sequence by a name, ID or URN.
void	setSearchContentHandler(SearchContentHandler delegate)
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.search.SearchContentAdapter

getMoreSearches, setMoreSearches

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

FilteringContentHandler

public FilteringContentHandler(BlastLikeSearchFilter filter,
                               SearchContentHandler delegate)
                        throws BioException

Throws:

BioException

FilteringContentHandler

public FilteringContentHandler(BlastLikeSearchFilter filter)
                        throws BioException

Throws:

BioException

Method Detail

getSearchProperty

public Object getSearchProperty(Object key)

Specified by:

getSearchProperty in interface BlastLikeSearchFilter.Node

getHitProperty

public Object getHitProperty(Object key)

Specified by:

getHitProperty in interface BlastLikeSearchFilter.Node

getSubHitProperty

public Object getSubHitProperty(Object key)

Specified by:

getSubHitProperty in interface BlastLikeSearchFilter.Node

setSearchContentHandler

public void setSearchContentHandler(SearchContentHandler delegate)

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

Overrides:

startHeader in class SearchContentAdapter

setDatabaseID

public void setDatabaseID(String id)

Description copied from interface: SearchContentHandler

setDatabaseID identifies the database searched by a name, ID or URN.

Specified by:

setDatabaseID in interface SearchContentHandler

Overrides:

setDatabaseID in class SearchContentAdapter

Parameters:

id - a String which should be an unique identifier for the database searched.

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

Overrides:

endHeader in class SearchContentAdapter

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

Overrides:

startSearch in class SearchContentAdapter

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

Overrides:

setQueryID in class SearchContentAdapter

Parameters:

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

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

Overrides:

addSearchProperty in class SearchContentAdapter

Parameters:

key - an Object.

value - an Object.

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

Overrides:

startHit in class SearchContentAdapter

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

Overrides:

addHitProperty in class SearchContentAdapter

Parameters:

key - an Object.

value - an Object.

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

Overrides:

startSubHit in class SearchContentAdapter

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

Overrides:

addSubHitProperty in class SearchContentAdapter

Parameters:

key - an Object.

value - an Object.

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

Overrides:

endSubHit in class SearchContentAdapter

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

Overrides:

endHit in class SearchContentAdapter

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

Overrides:

endSearch in class SearchContentAdapter