Interface BlastLikeSearchFilter
- All Superinterfaces:
Serializable
- All Known Implementing Classes:
BlastLikeSearchFilter.AbstractBlastLikeSearchFilter
,BlastLikeSearchFilter.ByHitProperty
,BlastLikeSearchFilter.BySearchProperty
,BlastLikeSearchFilter.BySubHitProperty
,BlastLikeSearchFilter.Not
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
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Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic class
static final class
static final class
Applies test to the value specified by the key in hit properties.static final class
Applies test to the value specified by the key in search properties.static final class
Applies test to the value specified by the key in subhit properties.static interface
static final class
static final class
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Field Summary
Fields -
Method Summary
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Field Details
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KEY_QUERY_ID
- See Also:
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Method Details
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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
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.
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