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objects of this type represent one particular installation (not just implementation) of a sequence similarity searcher such as BLASTP. Objects of this type must be immutable such that all parameters affecting the outcome of a search must be passed as an argument to the search() method.
Method Summary | |
java.lang.Object |
clone()
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java.util.Set |
getSearchableDBs()
return a set of all databases that can be searched with this sequence similarity searcher. |
SeqSimilaritySearchResult |
search(SymbolList querySeq,
SequenceDB db,
java.util.Map searchParameters)
using this sequence similarity searcher, search with the given sequence against the given sequence database. |
Method Detail |
public java.util.Set getSearchableDBs()
public SeqSimilaritySearchResult search(SymbolList querySeq, SequenceDB db, java.util.Map searchParameters) throws BioException
Particular implementations of a searcher will differ in the number and kind of parameters that can be used to customize a search. All these parameters must be passed as an argument to this method, i.e. these parameters are not part of the state of this searcher.
This method performs a synchronous search, i.e. it will block until the search result becomes available.
querySeq
- the sequence with which to search.
May not be null otherwise an IllegalArgumentException is thrown.db
- the sequence database against which the similarity search will be performed.
May not be null otherwise an IllegalArgumentException is thrown. Must also be an element of the set of
searchable dbs returnes by getSearchableDBs().searchParameters
- parameters that customize the search. Null must always be a legal value
for this argument and results in a default search being performed. If this
map contains keys and/or values that are not supported by a particular implementation of
this interface, an IllegalArgumentException is thrown.public java.lang.Object clone()
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