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Serialized Form

Package org.geworkbench.algorithms

Class org.geworkbench.algorithms.AbstractTraining extends AbstractAnalysis implements Serializable

Serialized Fields

panel

AbstractTrainingPanel panel

Class org.geworkbench.algorithms.AbstractTrainingPanel extends AbstractSaveableParameterPanel implements Serializable

Serialized Fields

numberFolds

javax.swing.JFormattedTextField numberFolds

progressGraph

ProgressGraph progressGraph

trainingMessage

javax.swing.JLabel trainingMessage

falsePositives

javax.swing.JLabel falsePositives

falseNegatives

javax.swing.JLabel falseNegatives

truePositives

javax.swing.JLabel truePositives

trueNegatives

javax.swing.JLabel trueNegatives

maSet

DSMicroarraySet<T extends DSMicroarray> maSet

selectionPanel

DSPanel<T extends DSNamed> selectionPanel

crossTest

javax.swing.JButton crossTest

cancelTest

javax.swing.JButton cancelTest

worker

SwingWorker<T,V> worker

trainingTask

TrainingTask trainingTask

Package org.geworkbench.analysis

Class org.geworkbench.analysis.AbstractAnalysis extends java.lang.Object implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

aspp

AbstractSaveableParameterPanel aspp

The parameters panel to be use from within the AnalysisPane in order to collect the analysis parameters from the user.

parameterHash

java.util.Map<K,V> parameterHash

Contains indices that are used in order to recover the set of named parameter settings that have been saved for a particular analysis. The indices are (key, value) tuples, where 'key', 'value' are defined as:

key = (this.getIndex(), parameterSetName),
value = parameterSet

AbstractAnaysis

tmpDir

java.lang.String tmpDir

descriptions

CSDescribable descriptions

Used in the implementation of the Describable interface.

analysisId

DefaultIdentifiable analysisId

Used in the implementation of the Identifiable interface.

stopAlgorithm

boolean stopAlgorithm

Set stopAlgorithm to true to stop the Algorithm, in the Algorithm, you'll need to check this variable periodically.

lastParameterSetName

java.lang.String lastParameterSetName

className

java.lang.String className

Class org.geworkbench.analysis.AbstractGridAnalysis extends AbstractAnalysis implements Serializable

Serialized Fields

log

org.apache.commons.logging.Log log

Class org.geworkbench.analysis.AbstractSaveableParameterPanel extends ParameterPanel implements Serializable

serialVersionUID: 4513020172986430772L

Serialized Fields

log

org.apache.commons.logging.Log log

name

java.lang.String name

firstTime

boolean firstTime

callbackThread

java.lang.Thread callbackThread

stopNotifyTemporaryFlag

boolean stopNotifyTemporaryFlag

Class org.geworkbench.analysis.ParameterKey extends java.lang.Object implements Serializable

serialVersionUID: -8967255706305280349L

Serialized Fields

className

java.lang.String className

parameterName

java.lang.String parameterName

Package org.geworkbench.bison

Class org.geworkbench.bison.ReferenceImplMap extends java.util.HashMap<java.lang.Class,java.lang.Class> implements Serializable

Package org.geworkbench.bison.algorithm

Class org.geworkbench.bison.algorithm.AlgorithmEvent extends java.util.EventObject implements Serializable

serialVersionUID: -2005206404971429403L

Serialized Fields

algorithmState

int algorithmState

String describing the changed state of the analysis

success

boolean success

If the transition was made successfully

utilityObject

java.lang.Object utilityObject

Object that can be used to store any other useful information relating to the analysis

Package org.geworkbench.bison.algorithm.classification

Class org.geworkbench.bison.algorithm.classification.CSClassifier extends CSAncillaryDataSet implements Serializable

Serialized Fields

classifications

java.lang.String[] classifications

Class org.geworkbench.bison.algorithm.classification.CSVisualClassifier extends CSClassifier implements Serializable

serialVersionUID: 3965446427592157302L

Serialized Fields

modelFileContent

byte[] modelFileContent

featureNames

java.util.List<E> featureNames

casePanel

DSPanel<T extends DSNamed> casePanel

controlPanel

DSPanel<T extends DSNamed> controlPanel

Package org.geworkbench.bison.annotation

Class org.geworkbench.bison.annotation.CSAnnotationContext extends java.lang.Object implements Serializable

serialVersionUID: 8064184768541031268L

Serialized Fields

name

java.lang.String name

annotations

org.apache.commons.collections15.map.ListOrderedMap<K,V> annotations

labels

org.apache.commons.collections15.map.ListOrderedMap<K,V> labels

classes

org.apache.commons.collections15.map.ListOrderedMap<K,V> classes

defaultClass

java.lang.String defaultClass

Class org.geworkbench.bison.annotation.CSAnnotationContextManager.SerializableContexts extends java.lang.Object implements Serializable

serialVersionUID: -8930177139134699811L

Serialized Fields

contexts

org.apache.commons.collections15.set.ListOrderedSet<E> contexts

current

java.lang.String current

Class org.geworkbench.bison.annotation.CSCriteria extends java.util.HashMap<DSAnnotLabel,DSPanel<T extends DSNamed>> implements Serializable

Serialized Fields

selectedCriterion

DSPanel<T extends DSNamed> selectedCriterion

Package org.geworkbench.bison.datastructure.biocollections

Class org.geworkbench.bison.datastructure.biocollections.Collection extends java.util.ArrayList<T> implements Serializable

Class org.geworkbench.bison.datastructure.biocollections.CSAncillaryDataSet extends CSDataSet<T extends DSBioObject> implements Serializable

Serialized Fields

parent

DSDataSet<T extends DSBioObject> parent

Class org.geworkbench.bison.datastructure.biocollections.CSDataSet extends CSSequentialItemList<T extends DSBioObject> implements Serializable

serialVersionUID: 229744827492977524L

Serialized Fields

dirty

boolean dirty

file

java.io.File file

label

java.lang.String label

absPath

java.lang.String absPath

compatibilityLabel

java.lang.String compatibilityLabel

maResource

Resource maResource

arraySetId

DefaultIdentifiable arraySetId

Used for the implementation of Identifiable.

descriptions

CSDescribable descriptions

Used in the implementation of the Describable interface.

extend

CSExtendable extend

Used in the implementation of the Extendable interface.

experimentInfo

java.lang.String experimentInfo

Stores the experiment information (if any) associated with the microarray set.

dataSetProperties

java.util.HashMap<K,V> dataSetProperties

Class org.geworkbench.bison.datastructure.biocollections.CSMarkerVector extends CSSequentialItemList<DSGeneMarker> implements Serializable

serialVersionUID: -7674561735987333555L

Serialized Fields

geneIdMap

HashVector<K,V> geneIdMap

geneNameMap

HashVector<K,V> geneNameMap

mapGeneNames

boolean mapGeneNames

Class org.geworkbench.bison.datastructure.biocollections.GoAnalysisResult extends CSAncillaryDataSet<CSMicroarray> implements Serializable

serialVersionUID: -337000604982427702L

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Throws:: java.io.IOException; java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Throws:: java.io.IOException

Serialized Fields

changedGenes

java.util.Set<E> changedGenes

referenceGenes

java.util.Set<E> referenceGenes

result

java.util.Map<K,V> result

annotationFileName

java.lang.String annotationFileName

Package org.geworkbench.bison.datastructure.biocollections.gsea

Class org.geworkbench.bison.datastructure.biocollections.gsea.CSGSEAResultDataSet extends CSAncillaryDataSet implements Serializable

serialVersionUID: 1L

Serialized Fields

reportFile

java.lang.String reportFile

Package org.geworkbench.bison.datastructure.biocollections.medusa

Class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaCommand extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

featuresFile

java.lang.String featuresFile

minKer

int minKer

maxKer

int maxKer

base

double base

bound

double bound

minGap

int minGap

maxGap

int maxGap

usingDimers

boolean usingDimers

iter

int iter

pssmLength

int pssmLength

agg

int agg

reverseComplement

boolean reverseComplement

Class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaData extends java.lang.Object implements Serializable

serialVersionUID: 1L

Serialized Fields

arraySet

DSMicroarraySet<T extends DSMicroarray> arraySet

regulators

java.util.ArrayList<E> regulators

targets

java.util.ArrayList<E> targets

medusaCommand

MedusaCommand medusaCommand

Class org.geworkbench.bison.datastructure.biocollections.medusa.MedusaDataSet extends CSAncillaryDataSet<DSMicroarray> implements Serializable

serialVersionUID: 1L

Serialized Fields

data

MedusaData data

filename

java.lang.String filename

Package org.geworkbench.bison.datastructure.biocollections.microarrays

Class org.geworkbench.bison.datastructure.biocollections.microarrays.CSChipchipSet extends CSDataSet<CSPSAMMatch<CSPositionSpecificAffinityMatrix,CSPSAMRegistration>> implements Serializable

Serialized Fields

currentLocusId

int currentLocusId

loadingCancelled

boolean loadingCancelled

Class org.geworkbench.bison.datastructure.biocollections.microarrays.CSExprMicroarraySet extends CSMicroarraySet<DSMicroarray> implements Serializable

serialVersionUID: 6763897988197502601L

Serialized Fields

descriptions

java.util.ArrayList<E> descriptions

dataContext

DataParseContext dataContext

loadingCancelled

boolean loadingCancelled

initialized

boolean initialized

currGeneId

int currGeneId

Class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet extends CSDataSet<T extends DSMicroarray> implements Serializable

serialVersionUID: -8604116507886706853L

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream ois)
                 throws java.lang.ClassNotFoundException,
                        java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException

Throws:: java.io.IOException

Serialized Fields

markerVector

CSMarkerVector markerVector

timeStamp

java.util.Date timeStamp

mArrayProperties

java.util.HashMap<K,V> mArrayProperties

markerProperties

java.util.HashMap<K,V> markerProperties

maskedSpots

int maskedSpots

type

int type

annotationFileName

java.lang.String annotationFileName

Package org.geworkbench.bison.datastructure.biocollections.pca

Class org.geworkbench.bison.datastructure.biocollections.pca.CSPCADataSet extends CSAncillaryDataSet implements Serializable

serialVersionUID: 1L

Serialized Fields

u_Matrix

float[][] u_Matrix

numPCs

int numPCs

eigenValues

java.util.HashMap<K,V> eigenValues

percentVariations

java.util.HashMap<K,V> percentVariations

eigenVectors

java.util.HashMap<K,V> eigenVectors

variables

java.lang.String variables

Package org.geworkbench.bison.datastructure.biocollections.sequences

Class org.geworkbench.bison.datastructure.biocollections.sequences.CSSequenceSet extends CSDataSet<T extends DSSequence> implements Serializable

Serialized Fields

dirty

boolean dirty

isDNA

boolean isDNA

maxLength

int maxLength

label

java.lang.String label

sequenceNo

int sequenceNo

file

java.io.File file

markerList

DSItemList<T extends DSNamed> markerList

matchIndex

int[] matchIndex

reverseIndex

int[] reverseIndex

Package org.geworkbench.bison.datastructure.biocollections.views

Class org.geworkbench.bison.datastructure.biocollections.views.CSDataSetView extends java.lang.Object implements Serializable

serialVersionUID: -4914776743321648850L

Serialized Fields

dataSet

DSDataSet<T extends DSBioObject> dataSet

itemPanel

DSPanel<T extends DSNamed> itemPanel

Contains the active microarrays, organized as a DSPanel.

useItemPanel

boolean useItemPanel

Designates if the microarray subselection imposed by the activated phenotypic categories is imposed on the this microarray set view.

Class org.geworkbench.bison.datastructure.biocollections.views.CSMicroarraySetView extends CSDataSetView<Q extends DSMicroarray> implements Serializable

serialVersionUID: 1452815738190971373L

Serialized Fields

markerPanel

DSPanel<T extends DSNamed> markerPanel

Contains the active markers, organized as a DSPanel.

useMarkerPanel

boolean useMarkerPanel

Designates if the marker subselection imposed by the activated panels is imposed on the this microarray set view.

Package org.geworkbench.bison.datastructure.bioobjects

Package org.geworkbench.bison.datastructure.bioobjects.markers

Class org.geworkbench.bison.datastructure.bioobjects.markers.CSExpressionMarker extends CSGeneMarker implements Serializable

Serialization Methods

readObject

protected void readObject(java.io.ObjectInputStream ois)
                   throws java.lang.ClassNotFoundException,
                          java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

Serialized Fields

range

Range range

Class org.geworkbench.bison.datastructure.bioobjects.markers.CSGeneMarker extends java.lang.Object implements Serializable

serialVersionUID: -8778666154593978009L

Serialization Methods

readObject

protected void readObject(java.io.ObjectInputStream ois)
                   throws java.lang.ClassNotFoundException,
                          java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

protected void writeObject(java.io.ObjectOutputStream oos)
                    throws java.io.IOException

Throws:: java.io.IOException

Serialized Fields

label

java.lang.String label

description

java.lang.String description

abrev

java.lang.String abrev

markerId

int markerId

geneId

int geneId

unigene

DSUnigene unigene

geneName

java.lang.String geneName

disPlayType

int disPlayType

Class org.geworkbench.bison.datastructure.bioobjects.markers.SequenceMarker extends CSGeneMarker implements Serializable

Package org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser

Class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.AnnotationParser extends java.lang.Object implements Serializable

serialVersionUID: -117234619759135916L

Class org.geworkbench.bison.datastructure.bioobjects.markers.annotationparser.APSerializable extends java.lang.Object implements Serializable

serialVersionUID: 6455427625940524515L

Serialized Fields

currentDataSet

DSDataSet<T extends DSBioObject> currentDataSet

datasetToChipTypes

java.util.Map<K,V> datasetToChipTypes

chipTypeToAnnotation

java.util.Map<K,V> chipTypeToAnnotation

Package org.geworkbench.bison.datastructure.bioobjects.markers.genotype

Class org.geworkbench.bison.datastructure.bioobjects.markers.genotype.CSGenotypeMarker extends CSGeneMarker implements Serializable

serialVersionUID: 1232922167498738546L

Serialization Methods

readObject

protected void readObject(java.io.ObjectInputStream ois)
                   throws java.lang.ClassNotFoundException,
                          java.io.IOException

Throws:: java.lang.ClassNotFoundException; java.io.IOException

writeObject

protected void writeObject(java.io.ObjectOutputStream oos)
                    throws java.io.IOException

Throws:: java.io.IOException

Serialized Fields

Class org.geworkbench.bison.datastructure.bioobjects.markers.genotype.GenotypeColorContext extends java.lang.Object implements Serializable

Package org.geworkbench.bison.datastructure.bioobjects.microarray

Class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAffyMarkerValue extends CSExpressionMarkerValue implements Serializable

Serialization Overview

Serializable fields.

Serialized Fields

Class org.geworkbench.bison.datastructure.bioobjects.microarray.CSAnovaResultSet extends CSSignificanceResultSet implements Serializable

Serialized Fields

microarraySetView

DSMicroarraySetView<T extends DSGeneMarker,Q extends DSMicroarray> microarraySetView

alpha

double alpha

result2DArray

double[][] result2DArray

groupNames

java.lang.String[] groupNames

significantMarkerNames

java.lang.String[] significantMarkerNames

panel

DSPanel<T extends DSNamed> panel

map

java.util.Map<K,V> map

Class org.geworkbench.bison.datastructure.bioobjects.microarray.CSExpressionMarkerValue extends CSMarkerValue implements Serializable

serialVersionUID: 2927802879210446294L

Class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenepixMarkerValue extends CSMarkerValue implements Serializable

serialVersionUID: -6311145011982195192L

Serialization Overview

Serializable fields.

Serialized Fields

Class org.geworkbench.bison.datastructure.bioobjects.microarray.CSGenotypicMarkerValue extends CSMarkerValue implements Serializable

serialVersionUID: -2543764301206664390L

Serialized Fields

isGT

boolean isGT

Bit to specify if this marker contains two alleles

allele0

short allele0

allele1

short allele1

Class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMarkerValue extends java.lang.Object implements Serializable

Serialized Fields

value

float value

confidence

float confidence

Positive values are normal, negative values are masked. MISSING indicates missing value.

Class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorResultSet extends CSAncillaryDataSet implements Serializable

serialVersionUID: 1L

Serialized Fields

TF2GenesInRegulon

java.util.HashMap<K,V> TF2GenesInRegulon

TF2GenesInTargetList

java.util.HashMap<K,V> TF2GenesInTargetList

TF2PValue

java.util.HashMap<K,V> TF2PValue

TFGeneAndTargetGene2PValue

java.util.HashMap<K,V> TFGeneAndTargetGene2PValue

TFGeneAndTargetGene2TTestValue

java.util.HashMap<K,V> TFGeneAndTargetGene2TTestValue

sigSet

DSSignificanceResultSet<T extends DSGeneMarker> sigSet

maSet

DSMicroarraySet<T extends DSMicroarray> maSet

markerCount

int markerCount

Class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMicroarray extends java.lang.Object implements Serializable

serialVersionUID: -1624438489587615570L

Serialized Fields

type

int type

Microarray type, defined in DSMicroarraySet

serial

int serial

The relateive position (index) of the microarray within its host MicroarraySet.

descriptions

CSDescribable descriptions

Used in the implementation of the Describable interface.

arrayId

DefaultIdentifiable arrayId

Used in the implementation of the Identifiable interface.

extend

CSExtendable extend

Used in the implementation of the Extendable interface.

label

java.lang.String label

Label of the Microarray

markerArray

CSMarkerValue[] markerArray

Array of JMarkers containing the actual Microarray data

enabled

boolean enabled

A microarray that is not Enabled will be ignored

Class org.geworkbench.bison.datastructure.bioobjects.microarray.CSProbeIntensityArray extends CSAncillaryDataSet implements Serializable

Serialized Fields

dataFile

java.io.File dataFile

chipType

java.lang.String chipType

probeIntensities

float[][] probeIntensities

minMax

float[] minMax

Class org.geworkbench.bison.datastructure.bioobjects.microarray.CSSignificanceResultSet extends CSAncillaryDataSet implements Serializable

serialVersionUID: 1L

Serialized Fields

significance

java.util.HashMap<K,V> significance

foldChanges

java.util.HashMap<K,V> foldChanges

tValue

java.util.HashMap<K,V> tValue

alpha

double alpha

labels

java.lang.String[][] labels

panel

DSPanel<T extends DSNamed> panel

Class org.geworkbench.bison.datastructure.bioobjects.microarray.CSTTestResultSet extends CSSignificanceResultSet<T extends DSGeneMarker> implements Serializable

serialVersionUID: 1L

Package org.geworkbench.bison.datastructure.bioobjects.sequence

Class org.geworkbench.bison.datastructure.bioobjects.sequence.CSAlignmentResultSet extends CSAncillaryDataSet implements Serializable

Serialized Fields

fastaFile

java.io.File fastaFile

resultFile

java.io.File resultFile

blastedParentDataSet

DSDataSet<T extends DSBioObject> blastedParentDataSet

Class org.geworkbench.bison.datastructure.bioobjects.sequence.CSSequence extends java.lang.Object implements Serializable

serialVersionUID: 7157849532235539033L

Serialized Fields

id

java.lang.String id

serial

int serial

isEnabled

boolean isEnabled

sequence

java.lang.String sequence

label

java.lang.String label

extend

CSExtendable extend

Used in the implementation of the Extendable interface.

descriptions

CSDescribable descriptions

Used in the implementation of the Describable interface.

Package org.geworkbench.bison.datastructure.bioobjects.structure

Class org.geworkbench.bison.datastructure.bioobjects.structure.CSProteinStructure extends CSAncillaryDataSet implements Serializable

serialVersionUID: 7279040007729050440L

Serialized Fields

dataFile

java.io.File dataFile

chainoffset

int chainoffset

content

java.lang.String content

Class org.geworkbench.bison.datastructure.bioobjects.structure.CSPrtAnnotResultSet extends CSAncillaryDataSet implements Serializable

Serialized Fields

dataFile

java.io.File dataFile

Class org.geworkbench.bison.datastructure.bioobjects.structure.CSPrtDBResultSet extends CSAncillaryDataSet implements Serializable

Serialized Fields

dataFile

java.io.File dataFile

Class org.geworkbench.bison.datastructure.bioobjects.structure.MarkUsResultDataSet extends CSAncillaryDataSet<DSBioObject> implements Serializable

serialVersionUID: -5868552586583422711L

Serialized Fields

result

java.lang.String result

dataSetFile

java.io.File dataSetFile

Class org.geworkbench.bison.datastructure.bioobjects.structure.PudgeResultSet extends CSAncillaryDataSet implements Serializable

serialVersionUID: 1L

Serialized Fields

dataFile

java.io.File dataFile

result

java.lang.String result

Class org.geworkbench.bison.datastructure.bioobjects.structure.SkyLineResultDataSet extends CSAncillaryDataSet<DSBioObject> implements Serializable

serialVersionUID: -630087506848526523L

Serialized Fields

result

java.lang.String result

dataSetFile

java.io.File dataSetFile

Package org.geworkbench.bison.datastructure.complex.panels

Class org.geworkbench.bison.datastructure.complex.panels.CSAnnotPanel extends CSPanel<T extends DSNamed> implements Serializable

Serialized Fields

objects

java.util.HashMap<K,V> objects

needsSorting

boolean needsSorting

Class org.geworkbench.bison.datastructure.complex.panels.CSItemList extends java.util.ArrayList<T extends DSNamed> implements Serializable

serialVersionUID: -8885836819661037974L

Serialized Fields

id

java.lang.String id

objectMap

java.util.Hashtable<K,V> objectMap

Class org.geworkbench.bison.datastructure.complex.panels.CSPanel extends CSItemList<T extends DSNamed> implements Serializable

Serialized Fields

label

java.lang.String label

subLabel

java.lang.String subLabel

active

boolean active

serial

int serial

panelId

DefaultIdentifiable panelId

Used in the implementation of the Identifiable interface.

descriptions

CSDescribable descriptions

Used in the implementation of the Describable interface.

subPanels

DSItemList<T extends DSNamed> subPanels

The subPanels

selection

DSPanel<T extends DSNamed> selection

The manually selected items

Class org.geworkbench.bison.datastructure.complex.panels.CSSequentialItemList extends CSItemList<T extends DSSequential> implements Serializable

serialVersionUID: -8308605657087399359L

Package org.geworkbench.bison.datastructure.complex.pattern

Class org.geworkbench.bison.datastructure.complex.pattern.Parameters extends java.lang.Object implements Serializable

Serialized Fields

minSupport

int minSupport

minTokens

int minTokens

window

int window

minWTokens

int minWTokens

exactTokens

int exactTokens

countSeq

int countSeq

exact

int exact

printDetails

int printDetails

groupingType

int groupingType

groupingN

int groupingN

sortMode

int sortMode

outputMode

int outputMode

minPer100Support

double minPer100Support

computePValue

int computePValue

minPValue

double minPValue

threadNo

int threadNo

threadId

int threadId

minPatternNo

int minPatternNo

maxPatternNo

int maxPatternNo

maxRunTime

int maxRunTime

similarityMatrix

java.lang.String similarityMatrix

similarityThreshold

double similarityThreshold

inputName

java.lang.String inputName

outputName

java.lang.String outputName

__equalsCalc

java.lang.Object __equalsCalc

__hashCodeCalc

boolean __hashCodeCalc

minSupportType

java.lang.String minSupportType

Class org.geworkbench.bison.datastructure.complex.pattern.SoapParmsDataSet extends CSAncillaryDataSet implements Serializable

Serialized Fields

patternDB

PatternDB patternDB

parms

Parameters parms

dirty

boolean dirty

dataSetFile

java.io.File dataSetFile

label

java.lang.String label

resultFile

java.io.File resultFile

Package org.geworkbench.bison.datastructure.complex.pattern.matrix

Class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceExperiment extends java.lang.Object implements Serializable

Serialized Fields

pvalue

double pvalue

tvalue

double tvalue

coeff

double coeff

psamId

java.lang.String psamId

name

java.lang.String name

experimentId

java.lang.String experimentId

Class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSMatrixReduceSet extends CSAncillaryDataSet<DSPositionSpecificAffintyMatrix> implements Serializable

Serialized Fields

sequences

org.apache.commons.collections15.map.ListOrderedMap<K,V> sequences

experiments

org.apache.commons.collections15.map.ListOrderedMap<K,V> experiments

runlog

java.lang.String runlog

Class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPositionSpecificAffinityMatrix extends java.lang.Object implements Serializable

Serialized Fields

psamImage

javax.swing.ImageIcon psamImage

psamId

java.lang.String psamId

experimentName

java.lang.String experimentName

experimentId

java.lang.String experimentId

seedSequence

java.lang.String seedSequence

consensusSequence

java.lang.String consensusSequence

pValue

double pValue

tValue

double tValue

coeff

double coeff

scores

double[][] scores

trailingStrand

boolean trailingStrand

Class org.geworkbench.bison.datastructure.complex.pattern.matrix.CSPSAMMatch extends CSPatternMatch<T,R> implements Serializable

Serialized Fields

label

java.lang.String label

Package org.geworkbench.bison.datastructure.properties

Class org.geworkbench.bison.datastructure.properties.CSDescribable extends java.lang.Object implements Serializable

serialVersionUID: 6319385247916227865L

Serialization Overview

Serializable fields.

Serialized Fields

Class org.geworkbench.bison.datastructure.properties.CSExtendable extends java.lang.Object implements Serializable

Serialized Fields

nameValuePairs

java.util.Vector<E> nameValuePairs

Every entry in this vector is an object of type

Name and
 contains all values associated with a given name.








Class org.geworkbench.bison.datastructure.properties.CSUnigene extends java.lang.Object implements Serializable




serialVersionUID: 1738760385691617771L






Serialized Fields




unigeneId
int unigeneId






organism
int organism









Package org.geworkbench.bison.model.analysis








Class org.geworkbench.bison.model.analysis.FilteringAnalysis extends AbstractAnalysis implements Serializable




serialVersionUID: -7232110290771712959L






Serialized Fields




maSet
DSMicroarraySet<T extends DSMicroarray> maSet






criterionOption
FilteringAnalysis.CriterionOption criterionOption






percentThreshold
double percentThreshold






numberThreshold
int numberThreshold






expectedTypeName
java.lang.String expectedTypeName










Class org.geworkbench.bison.model.analysis.ParameterPanel extends javax.swing.JPanel implements Serializable








Serialized Fields




d
boolean d

Bit to retain dirty state, if this parameter set has been changed






name
java.lang.String name

The name of this parameter set









Package org.geworkbench.bison.model.clusters








Class org.geworkbench.bison.model.clusters.AbstractCluster extends java.lang.Object implements Serializable








Serialized Fields




children
java.util.ArrayList<E> children

Holds all children of this Cluster






parent
Cluster parent

Reference to Cluster which contains this Cluster
 as a child






iterator
java.util.Iterator<E> iterator

Iterator to walk through all the children of this
 Cluster






clusterID
DefaultIdentifiable clusterID

Unique ID acting as a key for this Cluster










Class org.geworkbench.bison.model.clusters.CSHierClusterDataSet extends CSAncillaryDataSet implements Serializable








Serialized Fields




clusters
HierCluster[] clusters






parentSet
DSDataSetView<Q extends DSBioObject> parentSet






selectedClusters
HierCluster[] selectedClusters






selectionEnabled
boolean selectionEnabled










Class org.geworkbench.bison.model.clusters.CSSOMClusterDataSet extends CSAncillaryDataSet implements Serializable








Serialized Fields




rows
int rows






columns
int columns






clusters
SOMCluster[][] clusters






parentSet
DSDataSetView<Q extends DSBioObject> parentSet










Class org.geworkbench.bison.model.clusters.DefaultHierCluster extends AbstractCluster implements Serializable




serialVersionUID: 756372128582359072L






Serialized Fields




height
double height






depth
int depth






maxHeight
double maxHeight










Class org.geworkbench.bison.model.clusters.DefaultSOMCluster extends AbstractCluster implements Serializable








Serialized Fields




representative
java.util.Vector<E> representative

Contains the Grid Representative cof the Grid this SOMCluster
 represents






x
int x

The X Grid coordinate of the Grid this SOMCluster represents






y
int y

The Y Grid coordinate of the Grid this SOMCluster represents










Class org.geworkbench.bison.model.clusters.LeafSOMCluster extends DefaultSOMCluster implements Serializable








Serialized Fields




mInfo
DSGeneMarker mInfo

DSMarker that contains a reference to a
 Genetic Marker defined by org.geworkbench.bison.model.microarray.MarkerValue and
 referred to by this LeafSOMCluster










Class org.geworkbench.bison.model.clusters.MarkerHierCluster extends DefaultHierCluster implements Serializable




serialVersionUID: 8296278482310224904L






Serialized Fields




mInfo
DSGeneMarker mInfo

Stores the marker associated with this cluster. For hierarchical clusters, only leaf nodes have a non-null value
 in this field.










Class org.geworkbench.bison.model.clusters.MicroarrayHierCluster extends DefaultHierCluster implements Serializable








Serialized Fields




microarray
DSMicroarray microarray

Stores the microarray associated with this cluster. For hierarchical
 clusters, only leaf nodes have a non-null value in this field.










Class org.geworkbench.bison.model.clusters.SimpleHierCluster extends DefaultHierCluster implements Serializable








Serialized Fields




item
java.lang.String item









Package org.geworkbench.bison.parsers








Class org.geworkbench.bison.parsers.AffyParseContext extends java.lang.Object implements Serializable




serialVersionUID: -7299827979956398558L






Serialization Overview




Serializable fields.








Serialized Fields









Class org.geworkbench.bison.parsers.DataParseContext extends java.lang.Object implements Serializable




serialVersionUID: -3486797732138045524L






Serialized Fields




type
int type

The marker type (e.g., genotype, gene expression, etc)






gtBase
int gtBase

The value used to encode genotypes as allele1 + allele2 * gtBase






isGenotype
boolean isGenotype

Is a genotype or two alleles with phase?






isLog
boolean isLog

used to replace the value v with Log(Math.max(v + addValue) , minValue)






addValue
double addValue






minValue
double minValue






sigma0
double sigma0

Various parameters used in the computationa of the statistical distributions of
 gene expression data. Used only by pattern discovery.






maxSigma
double maxSigma






deltaSigma
double deltaSigma






pdfMode
java.lang.String pdfMode






minSupport
int minSupport

Place holders for default values for some of the analytical tools. E.g., the minSupport
 and minMarkers for pattern discovery, whether patterns should be sorted






minMarkers
int minMarkers






sortKey
java.lang.String sortKey










Class org.geworkbench.bison.parsers.GenepixParseContext extends java.lang.Object implements Serializable




serialVersionUID: 8430221091524748106L






Serialization Overview




Serializable fields.








Serialized Fields









Class org.geworkbench.bison.parsers.NCIParseContext extends java.lang.Object implements Serializable








Serialization Overview




Serializable fields.








Serialized Fields








Package org.geworkbench.bison.util








Class org.geworkbench.bison.util.CSAnnotLabel extends java.lang.Object implements Serializable




serialVersionUID: -7099255143060473513L






Serialized Fields




object
java.lang.Object object










Class org.geworkbench.bison.util.CSAnnotValue extends java.lang.Object implements Serializable








Serialized Fields




key
int key






object
java.lang.Object object










Class org.geworkbench.bison.util.DefaultIdentifiable extends java.lang.Object implements Serializable








Serialization Overview




Serializable fields.








Serialized Fields









Class org.geworkbench.bison.util.HashVector extends java.util.HashMap<K,java.util.Vector<V>> implements Serializable








Serialized Fields




uniqueItems
boolean uniqueItems

AM -

 This will enforce that we don't put in duplicate items for a key. Would be more elegant
 to use the HashHashSet but I think creating so many HashSets is too heavy weight since we
 create so many of them. We lose a little bit of speed here but I don't think it's too bad
 because the Vectors here contain very few objects.

 watkin -

 Why is a Vector "lightweight" and a HashSet "heavyweight"?
 I find this implementation to be prohibitively slow. Linear search is unacceptable for an 'add' operation.
 Adding 50,000 markers to a CSMarkerVector takes many minutes.
 I think there are two potentital solutions for this:
 1) Do a full, proper map implementation backed by a Set rather than by a Vector.
 2) Don't enforce uniqueness at this low level.










Class org.geworkbench.bison.util.Normal extends java.lang.Object implements Serializable








Serialized Fields




mean
double mean






sigma
double sigma






variance
double variance






n
double n






sumX
double sumX






sumXX
double sumXX






status
boolean status










Class org.geworkbench.bison.util.Range extends java.lang.Object implements Serializable




serialVersionUID: 6422699987423693588L






Serialized Fields




min
double min






max
double max






norm
Normal norm









Package org.geworkbench.bison.util.colorcontext








Class org.geworkbench.bison.util.colorcontext.DefaultColorContext extends java.lang.Object implements Serializable








Serialized Fields




MISSING_VALUE_COLOR
java.awt.Color MISSING_VALUE_COLOR






magnitude
double magnitude










Class org.geworkbench.bison.util.colorcontext.ExpressionColorContext extends java.lang.Object implements Serializable










Class org.geworkbench.bison.util.colorcontext.ExpressionPValueColorContext extends java.lang.Object implements Serializable









Package org.geworkbench.builtin








Class org.geworkbench.builtin.ClassificationRunnerPlugin extends javax.swing.JPanel implements Serializable








Serialized Fields




microarraySet
DSMicroarraySet<T extends DSMicroarray> microarraySet






infoLabel
javax.swing.JLabel infoLabel






classifyButton
javax.swing.JButton classifyButton






classifier
CSClassifier classifier









Package org.geworkbench.builtin.projects








Class org.geworkbench.builtin.projects.DataSetNode extends ProjectTreeNode implements Serializable




serialVersionUID: 1423608759523479212L






Serialization Methods





readObject
private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException



Throws:
java.io.IOException
java.lang.ClassNotFoundException




writeObject
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException



Throws:
java.io.IOException






Serialized Fields




dataFile
DSDataSet<T extends DSBioObject> dataFile










Class org.geworkbench.builtin.projects.DataSetSaveNode extends java.lang.Object implements Serializable




serialVersionUID: 2094279433020194290L






Serialization Methods





readObject
private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException



Throws:
java.io.IOException
java.lang.ClassNotFoundException




writeObject
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException



Throws:
java.io.IOException






Serialized Fields




name
java.lang.String name






description
java.lang.String description






dataSet
DSDataSet<T extends DSBioObject> dataSet






visualSelected
java.lang.String visualSelected






commandSelected
java.lang.String commandSelected






selectionSelected
java.lang.String selectionSelected






children
java.util.ArrayList<E> children










Class org.geworkbench.builtin.projects.DataSetSubNode extends ProjectTreeNode implements Serializable








Serialized Fields




_aDataSet
DSAncillaryDataSet<T extends DSBioObject> _aDataSet










Class org.geworkbench.builtin.projects.ImageData extends CSAncillaryDataSet implements Serializable




serialVersionUID: 3899156889448935110L






Serialized Fields




imageFile
java.io.File imageFile






image
javax.swing.ImageIcon image






id
java.lang.String id






isDirty
boolean isDirty










Class org.geworkbench.builtin.projects.ImageNode extends DataSetSubNode implements Serializable




serialVersionUID: 1741751707465515060L






Serialized Fields




image
javax.swing.ImageIcon image

ImageIcon that this ImageNode refers to










Class org.geworkbench.builtin.projects.LoadData extends javax.swing.JDialog implements Serializable




serialVersionUID: -1983039293757013174L






Serialized Fields




log
org.apache.commons.logging.Log log






borderLayout1
java.awt.BorderLayout borderLayout1






jPanel1
javax.swing.JPanel jPanel1






gridLayout1
java.awt.GridLayout gridLayout1






jPanel2
javax.swing.JPanel jPanel2






jPanel3
javax.swing.JPanel jPanel3






flowLayout1
java.awt.FlowLayout flowLayout1






flowLayout2
java.awt.FlowLayout flowLayout2






localFileRadioButton
javax.swing.JRadioButton localFileRadioButton






jRadioButton2
javax.swing.JRadioButton jRadioButton2






jPanel4
javax.swing.JPanel jPanel4






borderLayout2
java.awt.BorderLayout borderLayout2






jFileChooser1
javax.swing.JFileChooser jFileChooser1






jPanel5
javax.swing.JPanel jPanel5






buttonGroup1
javax.swing.ButtonGroup buttonGroup1






buttonGroup2
javax.swing.ButtonGroup buttonGroup2






buttonGroup3
javax.swing.ButtonGroup buttonGroup3






jLabel3
javax.swing.JLabel jLabel3






jPanel9
javax.swing.JPanel jPanel9






jPanel11
javax.swing.JPanel jPanel11






jPanel12
javax.swing.JPanel jPanel12






jRadioButton6
javax.swing.JRadioButton jRadioButton6






jLabel2
javax.swing.JLabel jLabel2






jRadioButton5
javax.swing.JRadioButton jRadioButton5






gridLayout3
java.awt.GridLayout gridLayout3






jRadioButton4
javax.swing.JRadioButton jRadioButton4






jRadioButton3
javax.swing.JRadioButton jRadioButton3






jLabel1
javax.swing.JLabel jLabel1






gridLayout4
java.awt.GridLayout gridLayout4






gridBagLayout1
java.awt.GridBagLayout gridBagLayout1






jLabel4
javax.swing.JLabel jLabel4






experimentInfoArea
javax.swing.JTextArea experimentInfoArea






gridLayout2
java.awt.GridLayout gridLayout2






grid4
java.awt.GridLayout grid4






format
java.lang.String format






caArrayDisplayPanel
CaARRAYPanel caArrayDisplayPanel






mergeCheckBox
javax.swing.JCheckBox mergeCheckBox






lowerPanel
javax.swing.JPanel lowerPanel






mergePanel
javax.swing.JPanel mergePanel






remoteResourceDialog
RemoteResourceDialog remoteResourceDialog






currentRemoteResourceName
java.lang.String currentRemoteResourceName






currentDetailedResourceName
java.lang.String currentDetailedResourceName






caARRAYQueryPanel
CaARRAYQueryPanel caARRAYQueryPanel






parentProjectPanel
ProjectPanel parentProjectPanel

The project panel that manages the dialog box.






supportedInputFormats
FileFormat[] supportedInputFormats

Stores the FileFormat objects for the supported input
 formats.






borderLayout7
java.awt.BorderLayout borderLayout7






jPanel7
javax.swing.JPanel jPanel7






remoteRadioButton
javax.swing.JRadioButton remoteRadioButton






jPanel10
javax.swing.JPanel jPanel10






DEFAULTRESOUCES
java.lang.String[] DEFAULTRESOUCES






resourceModel
javax.swing.DefaultComboBoxModel resourceModel






jComboBox1
javax.swing.JComboBox jComboBox1






addButton
javax.swing.JButton addButton






queryButton
javax.swing.JButton queryButton






editButton
javax.swing.JButton editButton






deleteButton
javax.swing.JButton deleteButton






boxLayout21
javax.swing.BoxLayout boxLayout21






openRemoteResourceButton
javax.swing.JButton openRemoteResourceButton






isSynchronized
boolean isSynchronized






merge
boolean merge










Class org.geworkbench.builtin.projects.MicroarraySetNode extends ProjectTreeNode implements Serializable








Serialization Methods





readObject
private void readObject(java.io.ObjectInputStream oos)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException



Throws:
java.io.IOException
java.lang.ClassNotFoundException




writeObject
private void writeObject(java.io.ObjectOutputStream oos)
                  throws java.io.IOException



Throws:
java.io.IOException






Serialized Fields




microarraySet
DSMicroarraySet<T extends DSMicroarray> microarraySet

The MicroarraySet object associated with this project
 node.






maSetPersistFile
java.io.File maSetPersistFile

Stores the name of the file where the microarraySet gets
 persisted when the current node becomes unselected.










Class org.geworkbench.builtin.projects.PendingTreeNode extends ProjectTreeNode implements Serializable




serialVersionUID: 6783438582542203187L






Serialized Fields




gridEpr
org.ginkgo.labs.ws.GridEndpointReferenceType gridEpr










Class org.geworkbench.builtin.projects.ProjectNode extends ProjectTreeNode implements Serializable








Serialized Fields




dataSetNodeSelection
DataSetNode dataSetNodeSelection






dataSetSubNodeSelection
DataSetSubNode dataSetSubNodeSelection






microarraySetNodeSelection
MicroarraySetNode microarraySetNodeSelection

current MicroarraySetNode selection










Class org.geworkbench.builtin.projects.ProjectNode.JMAProject extends java.lang.Object implements Serializable








Serialized Fields




microarraySetSelection
MicroarraySetNode microarraySetSelection










Class org.geworkbench.builtin.projects.ProjectTreeNode extends javax.swing.tree.DefaultMutableTreeNode implements Serializable




serialVersionUID: 6368086703128743579L






Serialized Fields




description
java.lang.String description










Class org.geworkbench.builtin.projects.SaveTree extends java.lang.Object implements Serializable




serialVersionUID: 2534917305724421302L






Serialized Fields




nodes
java.util.List<E> nodes






selected
DSDataSet<T extends DSBioObject> selected










Class org.geworkbench.builtin.projects.TreeNodeRenderer extends javax.swing.tree.DefaultTreeCellRenderer implements Serializable




serialVersionUID: -1879887785935786137L






Serialized Fields




microarraySetNodeSelection
MicroarraySetNode microarraySetNodeSelection

Current MicroarraySetNode selection






projectNodeSelection
ProjectNode projectNodeSelection

Current ProjectNodeOld selection






imageNodeSelection
ImageNode imageNodeSelection

Current ImageNode selection






selection
ProjectSelection selection

Default Constructor









Package org.geworkbench.builtin.projects.remoteresources








Class org.geworkbench.builtin.projects.remoteresources.RemoteResourceDialog extends javax.swing.JDialog implements Serializable




serialVersionUID: -4311812466234532113L






Serialized Fields




isSourceDirty
boolean isSourceDirty






currentURL
java.lang.String currentURL






currentPortnumber
int currentPortnumber






currentUser
java.lang.String currentUser






currentPassword
java.lang.String currentPassword






jLabel1
javax.swing.JLabel jLabel1






jPanel1
javax.swing.JPanel jPanel1






jPanel2
javax.swing.JPanel jPanel2






borderLayout1
java.awt.BorderLayout borderLayout1






jLabel2
javax.swing.JLabel jLabel2






jLabel3
javax.swing.JLabel jLabel3






jPanel3
javax.swing.JPanel jPanel3






jPanel4
javax.swing.JPanel jPanel4






boxLayout21
javax.swing.BoxLayout boxLayout21






jTextField1
javax.swing.JTextField jTextField1






jLabel4
javax.swing.JLabel jLabel4






jPasswordField1
javax.swing.JPasswordField jPasswordField1






xYLayout1
java.awt.BorderLayout xYLayout1






jPanel6
javax.swing.JPanel jPanel6






jLabel5
javax.swing.JLabel jLabel5






jTextField2
javax.swing.JTextField jTextField2






jTextField3
javax.swing.JTextField jTextField3






jButton1
javax.swing.JButton jButton1






jButton6
javax.swing.JButton jButton6






border1
javax.swing.border.Border border1






jLabel6
javax.swing.JLabel jLabel6






jComboBox1
javax.swing.JComboBox jComboBox1






jPanel7
javax.swing.JPanel jPanel7






shortnameLabel
javax.swing.JLabel shortnameLabel






shortnameTextField
javax.swing.JTextField shortnameTextField






jPanel5
javax.swing.JPanel jPanel5






jPanel8
javax.swing.JPanel jPanel8






jPanel9
javax.swing.JPanel jPanel9






boxLayout22
javax.swing.BoxLayout boxLayout22









Package org.geworkbench.builtin.projects.remoteresources.carraydata








Class org.geworkbench.builtin.projects.remoteresources.carraydata.CaArray2Experiment extends java.lang.Object implements Serializable




serialVersionUID: 6474502004023481576L






Serialized Fields




name
java.lang.String name






hybridizations
java.util.Map<K,V> hybridizations






description
java.lang.String description






QuantitationTypes
java.lang.String[] QuantitationTypes






experimentReferenceId
java.lang.String experimentReferenceId









Package org.geworkbench.builtin.projects.remoteresources.query








Class org.geworkbench.builtin.projects.remoteresources.query.CaARRAYQueryPanel extends javax.swing.JDialog implements Serializable




serialVersionUID: -5214948658970068347L






Serialized Fields




username
java.lang.String username






password
java.lang.String password






portnumber
int portnumber






url
java.lang.String url






currentSelectedContent
java.lang.String currentSelectedContent






currentSelectedContentIndex
int currentSelectedContentIndex






jList
javax.swing.JList jList






jSplitPane1
javax.swing.JSplitPane jSplitPane1






jPanel1
javax.swing.JPanel jPanel1






jSplitPane2
javax.swing.JSplitPane jSplitPane2






jScrollPane1
javax.swing.JScrollPane jScrollPane1






jScrollPane2
javax.swing.JScrollPane jScrollPane2






jPanel2
javax.swing.JPanel jPanel2






progressBar
javax.swing.JProgressBar progressBar






jComboBox1
javax.swing.JComboBox jComboBox1






jToolBar1
javax.swing.JToolBar jToolBar1






searchButton
javax.swing.JButton searchButton






cancelButton
javax.swing.JButton cancelButton






refreshButton
javax.swing.JButton refreshButton






jCheckBox1
javax.swing.JCheckBox jCheckBox1






borderLayout1
java.awt.BorderLayout borderLayout1






jcatagoryComboBox
javax.swing.JComboBox jcatagoryComboBox






titledBorder1
javax.swing.border.TitledBorder titledBorder1






border1
javax.swing.border.Border border1






border2
javax.swing.border.Border border2






border3
javax.swing.border.Border border3






border4
javax.swing.border.Border border4






titledBorder2
javax.swing.border.TitledBorder titledBorder2






border5
javax.swing.border.Border border5






border6
javax.swing.border.Border border6






tableModel
org.geworkbench.builtin.projects.remoteresources.query.CaARRAYQueryPanel.ValueTableModel tableModel






loadData
LoadData loadData






loaded
boolean loaded






valueHits
java.util.Vector<E> valueHits






tissueHits
java.util.Vector<E> tissueHits






chipPlatformBox
javax.swing.JComboBox chipPlatformBox






piComboxBox
javax.swing.JComboBox piComboxBox






orginsmBox
javax.swing.JComboBox orginsmBox






tissueTypeBox
javax.swing.JComboBox tissueTypeBox









Package org.geworkbench.builtin.projects.util








Class org.geworkbench.builtin.projects.util.CaARRAYPanel extends javax.swing.JPanel implements Serializable




serialVersionUID: -4876378958265466224L






Serialized Fields




experimentsLoaded
boolean experimentsLoaded

Used to avoid querying the server for all experiments all the time.






currentResourceName
java.lang.String currentResourceName






previousResourceName
java.lang.String previousResourceName






displayLabel
javax.swing.JLabel displayLabel






jPanel6
javax.swing.JPanel jPanel6






grid4
java.awt.GridLayout grid4






caArrayDetailPanel
javax.swing.JPanel caArrayDetailPanel






caArrayTreePanel
javax.swing.JPanel caArrayTreePanel






borderLayout4
java.awt.BorderLayout borderLayout4






borderLayout7
java.awt.BorderLayout borderLayout7






border1
javax.swing.border.Border border1






border2
javax.swing.border.Border border2






jScrollPane1
javax.swing.JScrollPane jScrollPane1






jPanel10
javax.swing.JPanel jPanel10






jLabel4
javax.swing.JLabel jLabel4






experimentInfoArea
javax.swing.JTextArea experimentInfoArea






jScrollPane2
javax.swing.JScrollPane jScrollPane2






jPanel14
javax.swing.JPanel jPanel14






jPanel16
javax.swing.JPanel jPanel16






derivedLabel
javax.swing.JLabel derivedLabel






measuredField
javax.swing.JTextField measuredField






derivedField
javax.swing.JTextField derivedField






jPanel13
javax.swing.JPanel jPanel13






extendButton
javax.swing.JButton extendButton






openButton
javax.swing.JButton openButton






cancelButton
javax.swing.JButton cancelButton






parent
LoadData parent






root
javax.swing.tree.DefaultMutableTreeNode root






remoteTreeModel
javax.swing.tree.DefaultTreeModel remoteTreeModel






remoteFileTree
javax.swing.JTree remoteFileTree






jRemoteDataPopup
javax.swing.JPopupMenu jRemoteDataPopup






jGetRemoteDataMenu
javax.swing.JMenuItem jGetRemoteDataMenu






connectionSuccess
boolean connectionSuccess






user
java.lang.String user






passwd
java.lang.String passwd






url
java.lang.String url






portnumber
int portnumber






progressBar
ProgressBar progressBar






parentPanel
LoadData parentPanel






merge
boolean merge






stillWaitForConnecting
boolean stillWaitForConnecting






treeMap
java.util.TreeMap<K,V> treeMap






currentSelectedExperimentName
java.lang.String currentSelectedExperimentName






currentSelectedBioAssay
java.util.Map<K,V> currentSelectedBioAssay






currentLoadedExps
CaArray2Experiment[] currentLoadedExps






currentQuantitationType
java.lang.String currentQuantitationType






internalTimeoutLimit
int internalTimeoutLimit






numTotalArrays
int numTotalArrays






numCurrentArray
int numCurrentArray










Class org.geworkbench.builtin.projects.util.MAGEPanel extends javax.swing.JPanel implements Serializable










Class org.geworkbench.builtin.projects.util.NCIPanel extends javax.swing.JPanel implements Serializable









Package org.geworkbench.components.parsers








Class org.geworkbench.components.parsers.InputFileFormatException extends BaseException implements Serializable









Package org.geworkbench.engine.builder








Class org.geworkbench.engine.builder.VisualBuilder extends javax.swing.JDialog implements Serializable








Serialized Fields




availableList
javax.swing.JList availableList






selectedList
javax.swing.JList selectedList






availablePane
javax.swing.JScrollPane availablePane






selectedPane
javax.swing.JScrollPane selectedPane






availableComponents
java.util.ArrayList<E> availableComponents






selectedComponents
java.util.ArrayList<E> selectedComponents






availableModel
AutoListModel<T> availableModel






selectedModel
AutoListModel<T> selectedModel






areaChooser
javax.swing.JComboBox areaChooser









Package org.geworkbench.engine.cascript








Class org.geworkbench.engine.cascript.CasDataTypeImport extends java.util.HashMap implements Serializable










Class org.geworkbench.engine.cascript.CasException extends java.lang.RuntimeException implements Serializable








Serialized Fields




msg
java.lang.String msg









Package org.geworkbench.engine.config








Class org.geworkbench.engine.config.ConfigChooser extends javax.swing.JDialog implements Serializable








Serialized Fields




configList
javax.swing.JList configList






descriptionField
javax.swing.JTextArea descriptionField






defaultCheckBox
javax.swing.JCheckBox defaultCheckBox










Class org.geworkbench.engine.config.GUIFramework extends javax.swing.JFrame implements Serializable









Package org.geworkbench.engine.config.events








Class org.geworkbench.engine.config.events.AppEventListenerException extends BaseException implements Serializable










Class org.geworkbench.engine.config.events.ListenerEventMismatchException extends BaseException implements Serializable









Package org.geworkbench.engine.config.rules








Class org.geworkbench.engine.config.rules.DynamicMenuItemException extends BaseException implements Serializable










Class org.geworkbench.engine.config.rules.MalformedMenuItemException extends BaseException implements Serializable










Class org.geworkbench.engine.config.rules.NotEventSourceException extends BaseException implements Serializable










Class org.geworkbench.engine.config.rules.NotMenuListenerException extends BaseException implements Serializable










Class org.geworkbench.engine.config.rules.NotVisualPluginException extends BaseException implements Serializable









Package org.geworkbench.engine.management








Class org.geworkbench.engine.management.EventException extends java.lang.RuntimeException implements Serializable










Class org.geworkbench.engine.management.TypeMap extends java.util.HashMap<java.lang.Class,T> implements Serializable









Package org.geworkbench.engine.preferences








Class org.geworkbench.engine.preferences.ChoiceField extends Field implements Serializable




serialVersionUID: -2954745796506584166L






Serialized Fields




allowedValues
java.lang.String[] allowedValues






selection
int selection










Class org.geworkbench.engine.preferences.DoubleField extends Field implements Serializable








Serialized Fields




value
double value










Class org.geworkbench.engine.preferences.Field extends java.lang.Object implements Serializable








Serialized Fields




name
java.lang.String name










Class org.geworkbench.engine.preferences.FileField extends Field implements Serializable








Serialized Fields




value
java.io.File value






filter
javax.swing.filechooser.FileFilter filter










Class org.geworkbench.engine.preferences.Preferences extends java.lang.Object implements Serializable








Serialized Fields




fields
java.util.List<E> fields










Class org.geworkbench.engine.preferences.TextField extends Field implements Serializable








Serialized Fields




value
java.lang.String value










Class org.geworkbench.engine.preferences.ValidationException extends java.lang.Exception implements Serializable









Package org.geworkbench.engine.skin








Class org.geworkbench.engine.skin.Skin extends GUIFramework implements Serializable




serialVersionUID: 3617137568252369693L






Serialized Fields




contentPane
javax.swing.JPanel contentPane






statusBar
javax.swing.JLabel statusBar






borderLayout1
java.awt.BorderLayout borderLayout1






jSplitPane1
javax.swing.JSplitPane jSplitPane1






visualPanel
net.eleritec.docking.defaults.DefaultDockingPort visualPanel






commandPanel
net.eleritec.docking.defaults.DefaultDockingPort commandPanel






jSplitPane2
javax.swing.JSplitPane jSplitPane2






jSplitPane3
javax.swing.JSplitPane jSplitPane3






selectionPanel
net.eleritec.docking.defaults.DefaultDockingPort selectionPanel






jToolBar
javax.swing.JToolBar jToolBar






projectPanel
net.eleritec.docking.defaults.DefaultDockingPort projectPanel






areas
java.util.Map<K,V> areas






eventSink
org.geworkbench.engine.skin.Skin.DockingNotifier eventSink






acceptors
java.util.Set<E> acceptors






mainComponentClass
java.util.HashMap<K,V> mainComponentClass






visualLastSelected
org.apache.commons.collections15.map.ReferenceMap<K,V> visualLastSelected






commandLastSelected
org.apache.commons.collections15.map.ReferenceMap<K,V> commandLastSelected






selectionLastSelected
org.apache.commons.collections15.map.ReferenceMap<K,V> selectionLastSelected






visualDockables
java.util.ArrayList<E> visualDockables






commandDockables
java.util.ArrayList<E> commandDockables






selectorDockables
java.util.ArrayList<E> selectorDockables






currentDataSet
DSDataSet<T extends DSBioObject> currentDataSet






tabSwappingMode
boolean tabSwappingMode









Package org.geworkbench.events








Class org.geworkbench.events.HierClusterModelEvent extends java.util.EventObject implements Serializable








Serialized Fields




mASet
DSMicroarraySetView<T extends DSGeneMarker,Q extends DSMicroarray> mASet

The underlying micorarray set used in the hierarchical clustering
 analysis.






markerCluster
MarkerHierCluster markerCluster

The top-level marker cluster produced by the hierarchical clustering
 analysis.






arrayCluster
MicroarrayHierCluster arrayCluster

The top-level microarray cluster produced by the hierarchical clustering
 analysis.






selectedMarkerCluster
MarkerHierCluster selectedMarkerCluster






selectedArrayCluster
MicroarrayHierCluster selectedArrayCluster






selectionEnabled
boolean selectionEnabled






hierclusterSet
DSHierClusterDataSet hierclusterSet










Class org.geworkbench.events.LoginPanelModelEvent extends java.util.EventObject implements Serializable










Class org.geworkbench.events.MicroarraySetViewEvent extends java.util.EventObject implements Serializable








Serialized Fields




microarraySetModel
DSMicroarraySetView<T extends DSGeneMarker,Q extends DSMicroarray> microarraySetModel

The underlying MicorarraySet containing Panel and
 Phenotype groupings










Class org.geworkbench.events.SOMClusterModelEvent extends java.util.EventObject implements Serializable








Serialized Fields




mASet
DSMicroarraySetView<T extends DSGeneMarker,Q extends DSMicroarray> mASet

The underlying micorarray set used in the SOM clustering analysis.






somClusters
SOMCluster[][] somClusters

2-dimensional array representing the SOM clusters and their grid positions.
 The SOMCluster object at somClusters[x][y] should
 have (x, y) as its SOM grid coordinates.









Package org.geworkbench.util








Class org.geworkbench.util.AlgorithmSelectionPanel extends javax.swing.JPanel implements Serializable




serialVersionUID: -1469488867599091231L






Serialized Fields




algorithmGroup
javax.swing.ButtonGroup algorithmGroup






discovery
javax.swing.JRadioButton discovery






exhaustive
javax.swing.JRadioButton exhaustive










Class org.geworkbench.util.AutoListModel extends javax.swing.AbstractListModel implements Serializable








Serialized Fields




items
java.util.ArrayList<E> items










Class org.geworkbench.util.BaseException extends java.lang.Exception implements Serializable










Class org.geworkbench.util.BaseRuntimeException extends java.lang.RuntimeException implements Serializable










Class org.geworkbench.util.ClassifierException extends java.lang.Exception implements Serializable










Class org.geworkbench.util.ColorScale extends javax.swing.JPanel implements Serializable




serialVersionUID: 2426481070361078667L






Serialized Fields




minColor
java.awt.Color minColor






maxColor
java.awt.Color maxColor






centerColor
java.awt.Color centerColor










Class org.geworkbench.util.JAutoList extends javax.swing.JPanel implements Serializable








Serialized Fields




list
javax.swing.JList list






nextButton
javax.swing.JButton nextButton






searchField
javax.swing.JTextField searchField






model
javax.swing.ListModel model






scrollPane
javax.swing.JScrollPane scrollPane






topPanel
javax.swing.JPanel topPanel






lastSearchFailed
boolean lastSearchFailed






lastSearchWasAscending
boolean lastSearchWasAscending






prefixMode
boolean prefixMode










Class org.geworkbench.util.LED extends javax.swing.JComponent implements Serializable








Serialized Fields




dim
java.awt.Dimension dim






c
java.awt.Color c






c1
java.awt.Color c1






c2
java.awt.Color c2






insets
java.awt.Insets insets






interv
int interv






curWidth
int curWidth






curHeight
int curHeight






calculatePaintArea
boolean calculatePaintArea

If LED is resized, set calculatePaintArea to true in order to update






show
boolean show






goOn
boolean goOn






enabled
boolean enabled






blink
boolean blink






t
java.lang.Thread t






deeperGreen
java.awt.Color deeperGreen










Class org.geworkbench.util.OWFileChooser extends javax.swing.JFileChooser implements Serializable




serialVersionUID: -8841673089062156967L








Class org.geworkbench.util.ProgressBar extends javax.swing.JDialog implements Serializable








Serialized Fields




type
int type

Instance type






jProgressBar
javax.swing.JProgressBar jProgressBar

Visual widget






cancelButton
javax.swing.JButton cancelButton

Visual widget






winDisposed
org.geworkbench.util.ProgressBar.BarObservable winDisposed






jLabel1
javax.swing.JLabel jLabel1










Class org.geworkbench.util.ProgressBar.IncrementModel extends javax.swing.DefaultBoundedRangeModel implements Serializable








Serialized Fields




increment
int increment










Class org.geworkbench.util.ProgressBarT extends javax.swing.JDialog implements Serializable




serialVersionUID: 1L






Serialized Fields




type
int type

Instance type






borderLayout1
java.awt.BorderLayout borderLayout1

Visual widget






gridbagLayout
java.awt.GridBagLayout gridbagLayout

Visual widget






jProgressBar
javax.swing.JProgressBar jProgressBar

Visual widget






contentPane
javax.swing.JPanel contentPane

Visual widget






jPanel1
javax.swing.JPanel jPanel1

Visual widget






jPanel2
javax.swing.JPanel jPanel2

Visual widget






jPanel3
javax.swing.JPanel jPanel3

Visual widget






jPanel4
javax.swing.JPanel jPanel4

Visual widget






winDisposed
org.geworkbench.util.ProgressBarT.BarObservable winDisposed






jLabel1
javax.swing.JLabel jLabel1






gridLayout1
java.awt.GridLayout gridLayout1










Class org.geworkbench.util.ProgressBarT.IncrementModel extends javax.swing.DefaultBoundedRangeModel implements Serializable




serialVersionUID: 1L






Serialized Fields




increment
int increment










Class org.geworkbench.util.ProgressGraph extends javax.swing.JComponent implements Serializable








Serialized Fields




description
java.lang.String description






ymax
int ymax






ymin
int ymin






numPoints
int numPoints






points
java.util.List<E> points






bandMin
int bandMin






bandMax
int bandMax










Class org.geworkbench.util.SplashBitmap extends javax.swing.JWindow implements Serializable








Serialized Fields




bitmapURL
java.net.URL bitmapURL






bitmapLabel
javax.swing.JLabel bitmapLabel






timeoutTimer
javax.swing.Timer timeoutTimer






progressTimer
javax.swing.Timer progressTimer






timeout
int timeout






bar
javax.swing.JProgressBar bar






progressBarSmoothness
int progressBarSmoothness









Package org.geworkbench.util.network








Class org.geworkbench.util.network.CellularNetWorkElementInformation extends java.lang.Object implements Serializable




serialVersionUID: -4163326138016520667L






Serialized Fields




interactionNumMap
java.util.HashMap<K,V> interactionNumMap






dSGeneMarker
DSGeneMarker dSGeneMarker






goInfoStr
java.lang.String goInfoStr






geneType
java.lang.String geneType






interactionDetails
InteractionDetail[] interactionDetails






threshold
double threshold






isDirty
boolean isDirty










Class org.geworkbench.util.network.GeneNetworkEdgeImpl extends java.lang.Object implements Serializable








Serialized Fields




id1
int id1






m2
DSGeneMarker m2






a
double a






b
double b






c
double c






pValue
double pValue






active
boolean active










Class org.geworkbench.util.network.InteractionDetail extends java.lang.Object implements Serializable




serialVersionUID: -4163326138016520667L






Serialized Fields




dSGeneMarker1
java.lang.String dSGeneMarker1






dSGeneMarker2
java.lang.String dSGeneMarker2






dSGeneName1
java.lang.String dSGeneName1






dSGeneName2
java.lang.String dSGeneName2






isGene1EntrezId
boolean isGene1EntrezId






isGene2EntrezId
boolean isGene2EntrezId






confidence
double confidence






interactionType
java.lang.String interactionType









Package org.geworkbench.util.pathwaydecoder.mutualinformation








Class org.geworkbench.util.pathwaydecoder.mutualinformation.AdjacencyMatrix extends java.lang.Object implements Serializable




serialVersionUID: -4163326138016520666L






Serialized Fields




geneRows
java.util.HashMap<K,V> geneRows






geneInteractionRows
java.util.HashMap<K,V> geneInteractionRows






geneRowsNotInMicroarray
java.util.HashMap<K,V> geneRowsNotInMicroarray






geneInteractionRowsNotInMicroarray
java.util.HashMap<K,V> geneInteractionRowsNotInMicroarray






idToGeneMapper
java.util.Map<K,V> idToGeneMapper






snToGeneMapper
java.util.Map<K,V> snToGeneMapper






histogram
int[] histogram






maSet
DSMicroarraySet<T extends DSMicroarray> maSet






adjName
java.lang.String adjName










Class org.geworkbench.util.pathwaydecoder.mutualinformation.AdjacencyMatrixDataSet extends CSAncillaryDataSet implements Serializable




serialVersionUID: -6835973287728524201L






Serialized Fields




matrix
AdjacencyMatrix matrix






geneId
int geneId






threshold
double threshold






depth
int depth






networkName
java.lang.String networkName










Class org.geworkbench.util.pathwaydecoder.mutualinformation.Edge extends java.lang.Object implements Serializable








Serialized Fields




startNode
java.lang.String startNode






endNode
java.lang.String endNode










Class org.geworkbench.util.pathwaydecoder.mutualinformation.EdgeList extends java.lang.Object implements Serializable








Serialized Fields




edgeList
java.util.ArrayList<E> edgeList










Class org.geworkbench.util.pathwaydecoder.mutualinformation.EdgeListDataSet extends CSAncillaryDataSet implements Serializable




serialVersionUID: -6835973287728524201L






Serialized Fields




data
EdgeList data






filename
java.lang.String filename










Class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyData extends java.lang.Object implements Serializable








Serialized Fields




arraySet
CSMicroarraySet<T extends DSMicroarray> arraySet






arrayForMindyRun
java.util.ArrayList<E> arrayForMindyRun






transcriptionFactor
DSGeneMarker transcriptionFactor






targetInfoMap
java.util.HashMap<K,V> targetInfoMap






geneSortkeyMap
java.util.HashMap<K,V> geneSortkeyMap






modulatorInfoMap
java.util.HashMap<K,V> modulatorInfoMap






filteredModulatorInfoMap
java.util.HashMap<K,V> filteredModulatorInfoMap






setFraction
float setFraction






annotated
boolean annotated










Class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyDataSet extends CSAncillaryDataSet implements Serializable




serialVersionUID: -6835973287728524201L






Serialized Fields




data
MindyData data






filename
java.lang.String filename










Class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyGeneMarker extends java.lang.Object implements Serializable








Serialized Fields




marker
DSGeneMarker marker










Class org.geworkbench.util.pathwaydecoder.mutualinformation.MindyResultRow extends java.lang.Object implements Serializable




serialVersionUID: 504249177167902775L






Serialized Fields




modulator
DSGeneMarker modulator






target
DSGeneMarker target






score
float score










Class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorInfo extends java.lang.Object implements Serializable




serialVersionUID: 5637267668779649984L






Serialized Fields




modulator
DSGeneMarker modulator






modStat
ModulatorStatistics modStat






data
java.util.List<E> data






targetResultMap
java.util.HashMap<K,V> targetResultMap










Class org.geworkbench.util.pathwaydecoder.mutualinformation.ModulatorStatistics extends java.lang.Object implements Serializable




serialVersionUID: -8211657782772431551L






Serialized Fields




count
int count






mover
int mover






munder
int munder










Class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostAnalysisData extends java.lang.Object implements Serializable








Serialized Fields




edgelist
java.lang.String edgelist






selectedModels
java.lang.String selectedModels






subgraphCounting
java.lang.String subgraphCounting






trainingEx
int trainingEx






boostingIter
int boostingIter






crossValidFolds
int crossValidFolds










Class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostData extends java.lang.Object implements Serializable








Serialized Fields




scores
double[] scores






variances
double[] variances






confusions
double[][] confusions






trainloss
double[][] trainloss






testloss
double[][] testloss






models
java.lang.String[] models






s
java.lang.String s










Class org.geworkbench.util.pathwaydecoder.mutualinformation.NetBoostDataSet extends CSAncillaryDataSet implements Serializable




serialVersionUID: -6835973287728524201L






Serialized Fields




data
NetBoostData data






filename
java.lang.String filename










Class org.geworkbench.util.pathwaydecoder.mutualinformation.Parameter extends java.lang.Object implements Serializable








Serialized Fields




dataMatrixName
java.lang.String dataMatrixName






adjMatrixName
java.lang.String adjMatrixName






miThreshold
double miThreshold






mArrayNo
int mArrayNo






mArrayId
int[] mArrayId






reduce
boolean reduce






controlId
int controlId






percent
double percent






miErrorPercent
double miErrorPercent






type
int type






mean
double mean






variance
double variance






method
java.lang.String method










Class org.geworkbench.util.pathwaydecoder.mutualinformation.TargetInfo extends java.lang.Object implements Serializable




serialVersionUID: -2814826276781866410L






Serialized Fields




target
DSGeneMarker target






correlation
double correlation









Package org.geworkbench.util.patterns








Class org.geworkbench.util.patterns.FlexiblePattern extends java.util.ArrayList<DSPatternMatch<DSSequence,CSSeqRegistration>> implements Serializable








Serialized Fields




seqDB
DSSequenceSet<T extends DSSequence> seqDB

This class implements flexible patterns having more than one
 set of offsets. This is implemented by having an array of N offsets
 and N loci






seqNo
int seqNo






patterns
java.util.ArrayList<E> patterns






mLocus
java.util.ArrayList<E> mLocus






pValue
double pValue






ascii
java.lang.String ascii






length
int length






maxLen
int maxLen










Class org.geworkbench.util.patterns.PatternDB extends CSAncillaryDataSet implements Serializable








Serialization Methods





readObject
private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

TODO - unused



Throws:
java.io.IOException
java.lang.ClassNotFoundException




writeObject
private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

TODO - unused



Throws:
java.io.IOException






Serialized Fields









Class org.geworkbench.util.patterns.PatternFetchException extends java.lang.RuntimeException implements Serializable










Class org.geworkbench.util.patterns.PatternTableModel extends javax.swing.table.AbstractTableModel implements Serializable








Serialized Fields




pattern
java.util.ArrayList<E> pattern

Pattern array - contains the patterns.






maxLen
int maxLen

Maximum extension of all the patterns in the model.






patternSource
SequentialPatternSource patternSource

The patterns for this model will come from this source.






rowCount
int rowCount

Number of rows in the model.
 Note: the actual number of patterns may be smaller than rowCount.
 This is done so we do no need to get all patterns if they are not "used",
 i.e. requested from the model.






worker
org.geworkbench.util.patterns.PatternTableModelWorker worker

Will retrieve patterns from a Patterns Source.









Package org.geworkbench.util.promoter








Class org.geworkbench.util.promoter.SequencePatternDisplayPanel extends SequenceViewWidget implements Serializable




serialVersionUID: -1554529235054789483L






Serialized Fields




displayTF
boolean displayTF






displaySeqPattern
boolean displaySeqPattern






sequenceDB
DSSequenceSet<T extends DSSequence> sequenceDB






patternDisplay
java.util.HashMap<K,V> patternDisplay






patternMatches
java.util.Hashtable<K,V> patternMatches






patternTFMatches
java.util.HashMap<K,V> patternTFMatches






patternSeqMatches
java.util.HashMap<K,V> patternSeqMatches









Package org.geworkbench.util.sequences








Class org.geworkbench.util.sequences.SequenceViewWidget extends javax.swing.JPanel implements Serializable




serialVersionUID: -6141589995966150788L






Serialized Fields




patternLocationsMatches
java.util.HashMap<K,V> patternLocationsMatches






selectedPatterns
DSCollection<T> selectedPatterns






jToolBar1
javax.swing.JToolBar jToolBar1






seqViewWPanel
SequenceViewWidgetPanel seqViewWPanel






activeSequenceDB
CSSequenceSet<T extends DSSequence> activeSequenceDB






subsetMarkerOn
boolean subsetMarkerOn






activatedMarkers
DSPanel<T extends DSNamed> activatedMarkers






prevSeqId
int prevSeqId






prevSeqDx
int prevSeqDx






sequenceDB
DSSequenceSet<T extends DSSequence> sequenceDB






orgSequenceDB
DSSequenceSet<T extends DSSequence> orgSequenceDB






displaySequenceDB
DSSequenceSet<T extends DSSequence> displaySequenceDB






borderLayout2
java.awt.BorderLayout borderLayout2






sequencedetailPanel
org.geworkbench.util.sequences.SequenceViewWidget.JDetailPanel sequencedetailPanel






bottomPanel
javax.swing.JPanel bottomPanel






leftShiftButton
javax.swing.JButton leftShiftButton






rightShiftButton
javax.swing.JButton rightShiftButton






seqScrollPane
javax.swing.JScrollPane seqScrollPane






showAllBtn
javax.swing.JCheckBox showAllBtn






jAllSequenceCheckBox
javax.swing.JCheckBox jAllSequenceCheckBox






jViewLabel
javax.swing.JLabel jViewLabel






jViewComboBox
javax.swing.JComboBox jViewComboBox






jSequenceSummaryTextField
javax.swing.JTextField jSequenceSummaryTextField






isLineView
boolean isLineView






onlyShowPattern
boolean onlyShowPattern






goLeft
boolean goLeft






xStartPoint
int xStartPoint










Class org.geworkbench.util.sequences.SequenceViewWidgetPanel extends javax.swing.JPanel implements Serializable




serialVersionUID: 7202257250696337753L






Serialized Fields




xOff
int xOff






yOff
int yOff






xStep
int xStep






yStep
int yStep






scale
double scale






selected
int selected






maxSeqLen
int maxSeqLen






displayInfo
java.lang.String displayInfo






selectedPatterns
DSCollection<T> selectedPatterns






sequenceDB
DSSequenceSet<T extends DSSequence> sequenceDB






sequencePatternmatches
java.util.HashMap<K,V> sequencePatternmatches






showAll
boolean showAll






lineView
boolean lineView






singleSequenceView
boolean singleSequenceView






yBasescale
double yBasescale






xBaseCols
int xBaseCols






eachSeqStartRowNum
int[] eachSeqStartRowNum






xBasescale
double xBasescale






seqXclickPoint
int seqXclickPoint






selectedSequence
DSSequence selectedSequence






itemListPopup
javax.swing.JPopupMenu itemListPopup






imageSnapshotItem
javax.swing.JMenuItem imageSnapshotItem









Package org.geworkbench.util.threading








Class org.geworkbench.util.threading.SwingPropertyChangeSupport extends java.beans.PropertyChangeSupport implements Serializable




serialVersionUID: 7162625831330845068L






Serialized Fields




notifyOnEDT
boolean notifyOnEDT

whether to notify listeners on EDT

 
Since:
  1.6







Package org.geworkbench.util.visualproperties








Class org.geworkbench.util.visualproperties.JShapeButton extends javax.swing.JComponent implements Serializable








Serialized Fields




shape
java.awt.Shape shape






paint
java.awt.Paint paint






listener
java.awt.event.ActionListener listener






percentSize
int percentSize






drawBorder
boolean drawBorder






preferredSize
java.awt.Dimension preferredSize










Class org.geworkbench.util.visualproperties.JShapeDialog extends javax.swing.JDialog implements Serializable








Serialized Fields




result
int result










Class org.geworkbench.util.visualproperties.VisualPropertiesDialog extends javax.swing.JDialog implements Serializable








Serialized Fields




propertiesChanged
boolean propertiesChanged






display
JShapeButton display






properties
PanelVisualProperties properties






defaultProperties
PanelVisualProperties defaultProperties






defaults
boolean defaults






transientColor
java.awt.Color transientColor






transientShapeIndex
int transientShapeIndex

















  
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