Package org.biojava.nbio.core.search.io
Class SearchIO
- java.lang.Object
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- org.biojava.nbio.core.search.io.SearchIO
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- All Implemented Interfaces:
java.lang.Iterable<Result>
public class SearchIO extends java.lang.Object implements java.lang.Iterable<Result>
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 SearchIO(java.io.File f)
Build a SearchIO reader and tries to select the appropriate parser inspecting file extension.SearchIO(java.io.File f, ResultFactory factory)
Build a SearchIO reader and specify a ResultFactory object to be used for parsingSearchIO(java.io.File f, ResultFactory factory, double maxEvalue)
Build a SearchIO reader, specify a ResultFactory object to be used for parsing and filter hsp retrieved by a e-value threshold.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
getEvalueThreshold()
java.util.Iterator<Result>
iterator()
void
writeResults()
used to write a search report using the guessed or specified factory
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Constructor Detail
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SearchIO
public SearchIO(java.io.File f) throws java.io.IOException, java.text.ParseException
Build a SearchIO reader and tries to select the appropriate parser inspecting file extension.- Parameters:
f
-- Throws:
java.lang.Exception
java.io.IOException
java.text.ParseException
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SearchIO
public SearchIO(java.io.File f, ResultFactory factory) throws java.io.IOException, java.text.ParseException
Build a SearchIO reader and specify a ResultFactory object to be used for parsing- Parameters:
f
-factory
-- Throws:
java.io.IOException
- for file access related issuesjava.text.ParseException
- for file format related issues
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SearchIO
public SearchIO(java.io.File f, ResultFactory factory, double maxEvalue) throws java.io.IOException, java.text.ParseException
Build a SearchIO reader, specify a ResultFactory object to be used for parsing and filter hsp retrieved by a e-value threshold. This usually increase parsing speed- Parameters:
f
-factory
-maxEvalue
-- Throws:
java.io.IOException
- for file access related issuesjava.text.ParseException
- for file format related issues
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Method Detail
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writeResults
public void writeResults() throws java.io.IOException, java.text.ParseException
used to write a search report using the guessed or specified factory- Throws:
java.io.IOException
- for file access related issuesjava.text.ParseException
- for file format related issues
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getEvalueThreshold
public double getEvalueThreshold()
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