Package org.biojava.nbio.core.search.io

Class SearchIO

java.lang.Object

org.biojava.nbio.core.search.io.SearchIO

All Implemented Interfaces:

Iterable<Result>

public class SearchIO
extends Object
implements 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

Constructor Summary

Constructors

Constructor	Description
SearchIO(File f)	Build 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 parsing
SearchIO(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 Type	Method	Description
double	getEvalueThreshold()
Iterator<Result>	iterator()
void	writeResults()	used to write a search report using the guessed or specified factory

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Details

SearchIO

public SearchIO(File f)
         throws IOException,
ParseException

Build a SearchIO reader and tries to select the appropriate parser inspecting file extension.

Parameters:

f -

Throws:

IOException

ParseException

SearchIO

public SearchIO(File f,
 ResultFactory factory)
         throws IOException,
ParseException

Build a SearchIO reader and specify a ResultFactory object to be used for parsing

Parameters:

f -

factory -

Throws:

IOException - for file access related issues

ParseException - for file format related issues

SearchIO

public SearchIO(File f,
 ResultFactory factory,
 double maxEvalue)
         throws IOException,
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:

IOException - for file access related issues

ParseException - for file format related issues

Method Details

writeResults

public void writeResults()
                  throws IOException,
ParseException

used to write a search report using the guessed or specified factory

Throws:

IOException - for file access related issues

ParseException - for file format related issues

getEvalueThreshold

public double getEvalueThreshold()

iterator

public Iterator<Result> iterator()

Specified by:

iterator in interface Iterable<Result>