org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser
Class AnnotationParser

java.lang.Object
  org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser

All Implemented Interfaces:

java.io.Serializable

public class AnnotationParser
extends java.lang.Object
implements java.io.Serializable

Description:This Class is for retrieving probe annotation information from default annotation files provided by Affymetrix.

Version:

$Id: AnnotationParser.java 6776 2010-06-09 15:45:11Z zji $

Author:

Xuegong Wang, manjunath at genomecenter dot columbia dot edu

See Also:

Serialized Form

Field Summary

static java.lang.String	ABREV
static java.lang.String	ALIGNMENT
static java.lang.String	DESCRIPTION
static java.lang.String	GENE_ONTOLOGY_BIOLOGICAL_PROCESS
static java.lang.String	GENE_ONTOLOGY_CELLULAR_COMPONENT
static java.lang.String	GENE_ONTOLOGY_MOLECULAR_FUNCTION
static java.lang.String	GENE_SYMBOL
static java.lang.String	GENOME_VERSION
static java.lang.String	GOTERM
static java.lang.String	LOCUSLINK
static java.lang.String	MAIN_DELIMITER
static java.lang.String	PATHWAY
static java.lang.String	PROBE_SET_ID
static java.lang.String	REFSEQ
static java.lang.String	SCIENTIFIC_NAME
static java.lang.String	SWISSPROT
static java.lang.String	TRANSCRIPT
static java.lang.String	UNIGENE
static java.lang.String	UNIGENE_CLUSTER

Constructor Summary

AnnotationParser()

Method Summary

static void	cleanUpAnnotatioAfterUnload(DSDataSet<DSBioObject> dataset)
static java.lang.String	getChipType(DSDataSet<? extends DSBioObject> dataset)
static java.lang.String	getCurrentChipType()
static DSDataSet<? extends DSBioObject>	getCurrentDataSet()
static java.util.Set<java.lang.String>	getGeneIDs(java.lang.String markerID)
static org.apache.commons.collections15.MultiMap<java.lang.String,java.lang.Integer>	getGeneIdToMarkerIDMapping(DSMicroarraySet<? extends DSMicroarray> microarraySet)
static java.lang.String	getGeneName(java.lang.String id)
static java.util.Set<java.lang.String>	getGeneNames(java.lang.String markerID)
static java.lang.String[]	getInfo(java.lang.String affyID, java.lang.String fieldID) This method returns required annotation field for a given affymatrix marker ID .
static java.lang.String	getInfoAsString(java.lang.String affyID, java.lang.String fieldID)
static java.lang.String	getLastAnnotationFileName()
static APSerializable	getSerializable()
static java.util.Set<java.lang.String>	getSwissProtIDs(java.lang.String markerID)
static java.lang.String	matchChipType(DSDataSet<? extends DSBioObject> dataset, java.lang.String id, boolean askIfNotFound)
static void	openURL(java.lang.String url)
static void	setChipType(DSDataSet<? extends DSBioObject> dataset, java.lang.String chiptype)
static void	setCurrentDataSet(DSDataSet<DSBioObject> currentDataSet)
static void	setFromSerializable(APSerializable aps)
static boolean	showAnnotationsMessage()

Methods inherited from class java.lang.Object

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

Field Detail

GENE_ONTOLOGY_BIOLOGICAL_PROCESS

public static final java.lang.String GENE_ONTOLOGY_BIOLOGICAL_PROCESS

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Constant Field Values

GENE_ONTOLOGY_CELLULAR_COMPONENT

public static final java.lang.String GENE_ONTOLOGY_CELLULAR_COMPONENT

See Also:

Constant Field Values

GENE_ONTOLOGY_MOLECULAR_FUNCTION

public static final java.lang.String GENE_ONTOLOGY_MOLECULAR_FUNCTION

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Constant Field Values

GENE_SYMBOL

public static final java.lang.String GENE_SYMBOL

See Also:

Constant Field Values

PROBE_SET_ID

public static final java.lang.String PROBE_SET_ID

See Also:

Constant Field Values

MAIN_DELIMITER

public static final java.lang.String MAIN_DELIMITER

See Also:

Constant Field Values

DESCRIPTION

public static final java.lang.String DESCRIPTION

See Also:

Constant Field Values

ABREV

public static final java.lang.String ABREV

See Also:

Constant Field Values

PATHWAY

public static final java.lang.String PATHWAY

See Also:

Constant Field Values

GOTERM

public static final java.lang.String GOTERM

See Also:

Constant Field Values

UNIGENE

public static final java.lang.String UNIGENE

See Also:

Constant Field Values

UNIGENE_CLUSTER

public static final java.lang.String UNIGENE_CLUSTER

See Also:

Constant Field Values

LOCUSLINK

public static final java.lang.String LOCUSLINK

See Also:

Constant Field Values

SWISSPROT

public static final java.lang.String SWISSPROT

See Also:

Constant Field Values

REFSEQ

public static final java.lang.String REFSEQ

See Also:

Constant Field Values

TRANSCRIPT

public static final java.lang.String TRANSCRIPT

See Also:

Constant Field Values

SCIENTIFIC_NAME

public static final java.lang.String SCIENTIFIC_NAME

See Also:

Constant Field Values

GENOME_VERSION

public static final java.lang.String GENOME_VERSION

See Also:

Constant Field Values

ALIGNMENT

public static final java.lang.String ALIGNMENT

See Also:

Constant Field Values

Constructor Detail

AnnotationParser

public AnnotationParser()

Method Detail

getSerializable

public static APSerializable getSerializable()

setFromSerializable

public static void setFromSerializable(APSerializable aps)

getCurrentDataSet

public static DSDataSet<? extends DSBioObject> getCurrentDataSet()

setCurrentDataSet

public static void setCurrentDataSet(DSDataSet<DSBioObject> currentDataSet)

getCurrentChipType

public static java.lang.String getCurrentChipType()

getChipType

public static java.lang.String getChipType(DSDataSet<? extends DSBioObject> dataset)

setChipType

public static void setChipType(DSDataSet<? extends DSBioObject> dataset,
                               java.lang.String chiptype)

getLastAnnotationFileName

public static java.lang.String getLastAnnotationFileName()

getGeneName

public static java.lang.String getGeneName(java.lang.String id)

getInfo

public static java.lang.String[] getInfo(java.lang.String affyID,
                                         java.lang.String fieldID)

This method returns required annotation field for a given affymatrix marker ID .

Parameters:

affyid - affyID as string

fieldID -

getInfoAsString

public static java.lang.String getInfoAsString(java.lang.String affyID,
                                               java.lang.String fieldID)

getSwissProtIDs

public static java.util.Set<java.lang.String> getSwissProtIDs(java.lang.String markerID)

getGeneIDs

public static java.util.Set<java.lang.String> getGeneIDs(java.lang.String markerID)

getGeneIdToMarkerIDMapping

public static org.apache.commons.collections15.MultiMap<java.lang.String,java.lang.Integer> getGeneIdToMarkerIDMapping(DSMicroarraySet<? extends DSMicroarray> microarraySet)

getGeneNames

public static java.util.Set<java.lang.String> getGeneNames(java.lang.String markerID)

matchChipType

public static java.lang.String matchChipType(DSDataSet<? extends DSBioObject> dataset,
                                             java.lang.String id,
                                             boolean askIfNotFound)

showAnnotationsMessage

public static boolean showAnnotationsMessage()

openURL

public static void openURL(java.lang.String url)

cleanUpAnnotatioAfterUnload

public static void cleanUpAnnotatioAfterUnload(DSDataSet<DSBioObject> dataset)