Package org.biojava.nbio.core.search.io
Interface ResultFactory
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- All Known Implementing Classes:
BlastTabularParser
,BlastXMLParser
public interface ResultFactory
Designed by Paolo Pavan. You may want to find my contacts on Github and LinkedIn for code info or discuss major changes. https://github.com/paolopavan- Author:
- Paolo Pavan
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description java.util.List<Result>
createObjects(double maxEScore)
Launch the parsing and get back a list of Result objects representing the search result in the specified file.java.util.List<java.lang.String>
getFileExtensions()
returns a list of file extensions associated to this ResultFactoryvoid
setDatabaseReferences(java.util.List<Sequence> sequences)
Specify the collection of sequences objects used as database in the Search run.void
setFile(java.io.File f)
void
setQueryReferences(java.util.List<Sequence> sequences)
Specify the collection of sequences objects used as queries in the Search run.void
storeObjects(java.util.List<Result> results)
The factory that implements this method will be able to save the Search results to a file in the same format that it is able to read.
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Method Detail
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getFileExtensions
java.util.List<java.lang.String> getFileExtensions()
returns a list of file extensions associated to this ResultFactory- Returns:
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setFile
void setFile(java.io.File f)
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createObjects
java.util.List<Result> createObjects(double maxEScore) throws java.io.IOException, java.text.ParseException
Launch the parsing and get back a list of Result objects representing the search result in the specified file.- Parameters:
maxEScore
-- Returns:
- Throws:
java.lang.Exception
java.io.IOException
java.text.ParseException
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storeObjects
void storeObjects(java.util.List<Result> results) throws java.io.IOException, java.text.ParseException
The factory that implements this method will be able to save the Search results to a file in the same format that it is able to read.- Parameters:
results
-- Throws:
java.lang.Exception
java.io.IOException
java.text.ParseException
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setQueryReferences
void setQueryReferences(java.util.List<Sequence> sequences)
Specify the collection of sequences objects used as queries in the Search run. They will be associated back to the query during the construction of the Result object.- Parameters:
sequences
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setDatabaseReferences
void setDatabaseReferences(java.util.List<Sequence> sequences)
Specify the collection of sequences objects used as database in the Search run. They will be associated back to the Hit during the construction of the Hit object.- Parameters:
sequences
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