public class BlastTabularParser extends java.lang.Object implements ResultFactory
Constructor and Description |
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BlastTabularParser() |
Modifier and Type | Method and Description |
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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.
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java.util.List<java.lang.String> |
getFileExtensions()
returns a list of file extensions associated to this ResultFactory
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void |
setDatabaseReferences(java.util.List<Sequence> sequences)
Intended for use with run module.
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void |
setFile(java.io.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.
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void |
setQueryReferences(java.util.List<Sequence> sequences)
Intended for use with run module.
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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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public java.util.List<java.lang.String> getFileExtensions()
ResultFactory
getFileExtensions
in interface ResultFactory
public void setFile(java.io.File f)
setFile
in interface ResultFactory
public java.util.List<Result> createObjects(double maxEScore) throws java.io.IOException, java.text.ParseException
ResultFactory
createObjects
in interface ResultFactory
java.io.IOException
java.text.ParseException
public void storeObjects(java.util.List<Result> results) throws java.io.IOException, java.text.ParseException
ResultFactory
storeObjects
in interface ResultFactory
java.io.IOException
java.text.ParseException
public void setQueryReferences(java.util.List<Sequence> sequences)
setQueryReferences
in interface ResultFactory
sequences
- public void setDatabaseReferences(java.util.List<Sequence> sequences)
setDatabaseReferences
in interface ResultFactory
sequences
- public void setParsingConsistency(org.biojava.nbio.core.search.io.blast.BlastTabularParser.PARSING_CONSISTENCY parsingConsistency)