Class BlastTabularParser
- java.lang.Object
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- org.biojava.nbio.core.search.io.blast.BlastTabularParser
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- All Implemented Interfaces:
ResultFactory
public class BlastTabularParser extends Object implements 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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Constructor Summary
Constructors Constructor Description BlastTabularParser()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description List<Result>
createObjects(double maxEScore)
Launch the parsing and get back a list of Result objects representing the search result in the specified file.List<String>
getFileExtensions()
returns a list of file extensions associated to this ResultFactoryvoid
setDatabaseReferences(List<Sequence> sequences)
Intended for use with run module.void
setFile(File f)
void
setParsingConsistency(org.biojava.nbio.core.search.io.blast.BlastTabularParser.PARSING_CONSISTENCY parsingConsistency)
Tries to define a different level of consistency during parsing.void
setQueryReferences(List<Sequence> sequences)
Intended for use with run module.void
storeObjects(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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Constructor Detail
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BlastTabularParser
public BlastTabularParser()
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Method Detail
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getFileExtensions
public List<String> getFileExtensions()
Description copied from interface:ResultFactory
returns a list of file extensions associated to this ResultFactory- Specified by:
getFileExtensions
in interfaceResultFactory
- Returns:
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setFile
public void setFile(File f)
- Specified by:
setFile
in interfaceResultFactory
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createObjects
public List<Result> createObjects(double maxEScore) throws IOException, ParseException
Description copied from interface:ResultFactory
Launch the parsing and get back a list of Result objects representing the search result in the specified file.- Specified by:
createObjects
in interfaceResultFactory
- Returns:
- Throws:
IOException
ParseException
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storeObjects
public void storeObjects(List<Result> results) throws IOException, ParseException
Description copied from interface:ResultFactory
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.- Specified by:
storeObjects
in interfaceResultFactory
- Throws:
IOException
ParseException
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setQueryReferences
public void setQueryReferences(List<Sequence> sequences)
Intended for use with run module. Although possible, does not make a lot of sense to have it with limited information such those in tabular report- Specified by:
setQueryReferences
in interfaceResultFactory
- Parameters:
sequences
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setDatabaseReferences
public void setDatabaseReferences(List<Sequence> sequences)
Intended for use with run module. Although possible, does not make a lot of sense to have it with limited information such those in tabular report- Specified by:
setDatabaseReferences
in interfaceResultFactory
- Parameters:
sequences
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setParsingConsistency
public void setParsingConsistency(org.biojava.nbio.core.search.io.blast.BlastTabularParser.PARSING_CONSISTENCY parsingConsistency)
Tries to define a different level of consistency during parsing. LITERAL is intended a strict parsing much tight to the report. IMPROVED consistency tries to import data much tight to the data model (I hope you got the idea, if not, have a look to the code. I suggest to use improved unless you have reasons to do not)
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