ubic.erminej.data

Class GeneAnnotationParser

java.lang.Object

ubic.erminej.data.GeneAnnotationParser

public class GeneAnnotationParser
extends Object

Reads tab-delimited file to create maps of probes to classes, classes to probes, probes to genes, genes to probes.

Version:

$Id: GeneAnnotationParser.java,v 1.22 2013/05/20 05:21:15 paul Exp $

Author:

paul

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GeneAnnotationParser.Format

Constructor Summary

Constructors

Constructor and Description
GeneAnnotationParser(GeneSetTerms geneSets)
GeneAnnotationParser(GeneSetTerms geneSets, StatusViewer messenger)

Method Summary

Methods

Modifier and Type	Method and Description
GeneAnnotations	read(InputStream i, GeneAnnotationParser.Format format, SettingsHolder settings)
GeneAnnotations	read(String fileName, GeneAnnotationParser.Format format, Settings settings)
protected GeneAnnotations	readAffyCsv(InputStream bis, Set<String> activeGenes, SettingsHolder settings) Parse affy formatted files (CSV or tabbed should be okay)
protected GeneAnnotations	readAgilent(InputStream bis, Set<String> activeGenes, SettingsHolder settings)
GeneAnnotations	readDefault(InputStream bis, Collection<Gene> activeGenes, SettingsHolder settings, boolean simple) Main default reading method.
GeneAnnotations	readDefault(String fileName, Collection<Gene> genes, SettingsHolder settings, boolean simple)
void	setFilterNonSpecific(boolean b)

Methods inherited from class java.lang.Object

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

Constructor Detail

GeneAnnotationParser

public GeneAnnotationParser(GeneSetTerms geneSets)

GeneAnnotationParser

public GeneAnnotationParser(GeneSetTerms geneSets,
                    StatusViewer messenger)

Method Detail

read

public GeneAnnotations read(InputStream i,
                   GeneAnnotationParser.Format format,
                   SettingsHolder settings)
                     throws IOException

Parameters:

i -

format -

settings -

Returns:

Throws:

IOException

read

public GeneAnnotations read(String fileName,
                   GeneAnnotationParser.Format format,
                   Settings settings)
                     throws IOException

Parameters:

fileName -

format -

settings -

Returns:

Throws:

IOException

readDefault

public GeneAnnotations readDefault(InputStream bis,
                          Collection<Gene> activeGenes,
                          SettingsHolder settings,
                          boolean simple)
                            throws IOException

Main default reading method. Because we want to be tolerant of file format variation, headers are not treated differently than other rows. This extra "gene" can be counted in things like rankings, so we do try to avoid it if we can, but doesn't directly effect most calculations.

Parameters:

bis -

genes -

settings -

simple - If true, assume two-column format with GO terms pipe-delimited in column 2, and only one gene per row (no ABC|ABC2 stuff)

Throws:

IOException

readDefault

public GeneAnnotations readDefault(String fileName,
                          Collection<Gene> genes,
                          SettingsHolder settings,
                          boolean simple)
                            throws IOException

Parameters:

fileName -

genes - Annotations for genes other than these will be ignored.

settings -

simple -

Returns:

Throws:

IOException

setFilterNonSpecific

public void setFilterNonSpecific(boolean b)

readAffyCsv

protected GeneAnnotations readAffyCsv(InputStream bis,
                          Set<String> activeGenes,
                          SettingsHolder settings)
                               throws IOException

Parse affy formatted files (CSV or tabbed should be okay)

Parameters:

bis -

object -

Throws:

IOException

readAgilent

protected GeneAnnotations readAgilent(InputStream bis,
                          Set<String> activeGenes,
                          SettingsHolder settings)
                               throws IOException

Parameters:

bis -

settings -

Throws:

IOException