org.dishevelled.bio.tools

Class FilterGaf

java.lang.Object

org.dishevelled.bio.tools.AbstractFilter

org.dishevelled.bio.tools.FilterGaf

All Implemented Interfaces:

Callable<Integer>

public final class FilterGaf
extends AbstractFilter

Filter alignments in GAF format.

Since:

1.4

Author:

Michael Heuer

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) static interface	FilterGaf.Filter Filter.
static class	FilterGaf.MappingQualityFilter Mapping quality filter.
static class	FilterGaf.QueryRangeFilter Query range filter.
static class	FilterGaf.ScriptFilter Script filter.

Constructor Summary

Constructors

Constructor and Description
FilterGaf(List<FilterGaf.Filter> filters, File inputGafFile, File outputGafFile) Filter alignments in GAF format.
FilterGaf(List<FilterGaf.Filter> filters, Path inputGafPath, File outputGafFile) Filter alignments in GAF format.

Method Summary

Modifier and Type	Method and Description
Integer	call()
static void	main(String[] args) Main.

Methods inherited from class org.dishevelled.bio.tools.AbstractFilter

createScriptEngine

Methods inherited from class java.lang.Object

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

Constructor Detail

FilterGaf

public FilterGaf(List<FilterGaf.Filter> filters,
                 File inputGafFile,
                 File outputGafFile)

Filter alignments in GAF format.

Parameters:

filters - list of filters, must not be null

inputGafFile - input GAF file, if any

outputGafFile - output GAF file, if any

FilterGaf

public FilterGaf(List<FilterGaf.Filter> filters,
                 Path inputGafPath,
                 File outputGafFile)

Filter alignments in GAF format.

Parameters:

filters - list of filters, must not be null

inputGafPath - input GAF path, if any

outputGafFile - output GAF file, if any

Since:

2.1

Method Detail

call

public Integer call()
             throws Exception

Throws:

Exception

main

public static void main(String[] args)

Main.

Parameters:

args - command line args