org.biojava.bio.search

Interface BlastLikeSearchFilter

All Superinterfaces:

Serializable

All Known Implementing Classes:

BlastLikeSearchFilter.AbstractBlastLikeSearchFilter, BlastLikeSearchFilter.ByHitProperty, BlastLikeSearchFilter.BySearchProperty, BlastLikeSearchFilter.BySubHitProperty, BlastLikeSearchFilter.Not

public interface BlastLikeSearchFilter
extends Serializable

A SearchContentHandler class that implements filtering in chains of SearchContentHandler instances.

The SearchContentHandler organise Blast-like searches as a hierarchy of search/hit/subhit. Each search is conducted with a single query sequence. Hits of the query sequence are reported against different target sequences. The hit is further subdivided into one of more subhits which represent the positions within the target sequence that alignments of the query sequence were achieved against the query sequence (e.g. HSPs).

This implementation depends on the a well ordered use of the SearchContentHandler interface. In particular, it requires that search/hit/subhit properties are reported immediately following the associated startSearch/startHit/startSubHit call. For example, search properties should not be reported following the corresponding startHit() call.

Semantics of this interface
BlastLikeSearchFilters test different levels of the SearchContentHandler property hierarchy and each filter should be seen as being applied when a full set of events from that level is received. So the ByHitProperty filter is applied when endHit() is called and determines whether all events received between startHit() and endHit() are to be passed on or discarded.

Some keys used by SearchContentHandlers
SearchProperties

KEY_QUERY_ID	String. Value from setQueryID
queryDescription	String. FASTA description line
program	String. variant of BLAST used
version	software version

HitProperties

subjectId	String. Identity of subject (target) sequence.
subjectSequenceLength	String representation of integer value
subjectDescription	String.

SubHitProperties

bitScore	String representation of real value
queryStrand	plus/minus
percentageIdentity	String representation of real value
querySequenceEnd	String representation of integer value
expectValue	String representation of real value
subjectStrand	plus/minus
subjectSequenceEnd	String representation of integer value
numberOfPositives	String representation of integer value
score	String representation of integer value
subjectSequence	String representation of sequence
alignmentSize	String representation of integer value
querySequenceStart	String representation of integer value
subjectSequenceStart	String representation of integer value
numberOfIdentities	String representation of integer value
querySequence	String representation of sequence

Author:

David Huen

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
static class	BlastLikeSearchFilter.And
static class	BlastLikeSearchFilter.ByHitProperty Applies test to the value specified by the key in hit properties.
static class	BlastLikeSearchFilter.BySearchProperty Applies test to the value specified by the key in search properties.
static class	BlastLikeSearchFilter.BySubHitProperty Applies test to the value specified by the key in subhit properties.
static interface	BlastLikeSearchFilter.Node
static class	BlastLikeSearchFilter.Not
static class	BlastLikeSearchFilter.Or

Field Summary

Fields

Modifier and Type	Field and Description
static String	KEY_QUERY_ID

Method Summary

Methods

Modifier and Type	Method and Description
TriState	accept() returns a TriState indicating the current outcome of evaluating this filter.
void	evaluate(BlastLikeSearchFilter.Node fch) computes the outcome of this filter on the specified node and stores it.
void	reset() resets the internal state of this filter including any cached evaluations.

Field Detail

KEY_QUERY_ID

static final String KEY_QUERY_ID

See Also:

Constant Field Values

Method Detail

accept

TriState accept()

returns a TriState indicating the current outcome of evaluating this filter. This is usually the outcome saved when evaluate(FilteringContentHandler fch) was called.

evaluate

void evaluate(BlastLikeSearchFilter.Node fch)

computes the outcome of this filter on the specified node and stores it. This method is only exposed to permit it to be included in an interface. Users should not use it.

reset

void reset()

resets the internal state of this filter including any cached evaluations. This method is only exposed to permit it to be included in an interface. Users should not use it.