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

java.lang.Object
  extended by 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 10020 2012-10-10 18:06:22Z youmi $
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 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 GOTERM
           
static java.lang.String LOCUSLINK
           
static java.lang.String MAIN_DELIMITER
           
static java.lang.String REFSEQ
           
static java.lang.String SWISSPROT
           
static java.lang.String UNIGENE
           
 
Constructor Summary
AnnotationParser()
           
 
Method Summary
static void cleanUpAnnotatioAfterUnload(DSDataSet<? extends DSBioObject> dataset)
           
static java.lang.String getChipType(DSMicroarraySet dataset)
           
static java.lang.String[] getInfo(DSMicroarraySet dataset, java.lang.String affyID, java.lang.String fieldID)
           
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 getLastAnnotationFileName()
           
static APSerializable getSerializable()
           
static void loadAnnotationFile(DSMicroarraySet dataset, java.io.File annotationData, AffyAnnotationParser parser)
           
static void setChipType(DSDataSet<? extends DSBioObject> dataset, java.lang.String chiptype)
           
static void setCurrentDataSet(DSDataSet<?> currentDataSet)
           
static void setFromSerializable(APSerializable aps)
           
 
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
See Also:
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
See Also:
Constant Field Values

GENE_SYMBOL

public static final java.lang.String GENE_SYMBOL
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

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

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
Constructor Detail

AnnotationParser

public AnnotationParser()
Method Detail

getSerializable

public static APSerializable getSerializable()

setFromSerializable

public static void setFromSerializable(APSerializable aps)

setCurrentDataSet

public static void setCurrentDataSet(DSDataSet<?> currentDataSet)

getChipType

public static java.lang.String getChipType(DSMicroarraySet dataset)

setChipType

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

getLastAnnotationFileName

public static java.lang.String getLastAnnotationFileName()

loadAnnotationFile

public static void loadAnnotationFile(DSMicroarraySet dataset,
                                      java.io.File annotationData,
                                      AffyAnnotationParser parser)
                               throws InputFileFormatException
Throws:
InputFileFormatException

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 -

getInfo

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

cleanUpAnnotatioAfterUnload

public static void cleanUpAnnotatioAfterUnload(DSDataSet<? extends DSBioObject> dataset)