Package org.biojava.nbio.core.search.io
Class SearchIO
java.lang.Object
org.biojava.nbio.core.search.io.SearchIO
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
-
Constructor Summary
ConstructorsConstructorDescriptionBuild a SearchIO reader and tries to select the appropriate parser inspecting file extension.SearchIO(File f, ResultFactory factory) Build a SearchIO reader and specify a ResultFactory object to be used for parsingSearchIO(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. -
Method Summary
Modifier and TypeMethodDescriptiondoubleiterator()voidused to write a search report using the guessed or specified factoryMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface java.lang.Iterable
forEach, spliterator
-
Constructor Details
-
SearchIO
Build a SearchIO reader and tries to select the appropriate parser inspecting file extension.- Parameters:
f-- Throws:
ExceptionIOExceptionParseException
-
SearchIO
Build a SearchIO reader and specify a ResultFactory object to be used for parsing- Parameters:
f-factory-- Throws:
IOException- for file access related issuesParseException- for file format related issues
-
SearchIO
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:
IOException- for file access related issuesParseException- for file format related issues
-
-
Method Details
-
writeResults
used to write a search report using the guessed or specified factory- Throws:
IOException- for file access related issuesParseException- for file format related issues
-
getEvalueThreshold
public double getEvalueThreshold() -
iterator
-