Serialized Form


Package org.geworkbench.analysis

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

serialVersionUID: 7028809841554763107L

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:


tmpDir

java.lang.String tmpDir

description

java.lang.String description
Used in the implementation of the Describable 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

label

java.lang.String label

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

serialVersionUID: -7310721066701534971L

Serialized Fields

log

org.apache.commons.logging.Log log

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

serialVersionUID: 4513020172986430772L

Serialized Fields

name

java.lang.String name

selectorPanel

DSPanel<T extends DSNamed> selectorPanel

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.algorithm.classification

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

serialVersionUID: -735452597517969294L

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

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

Package org.geworkbench.bison.datastructure.biocollections

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

serialVersionUID: 2986018836859246187L

Serialized Fields

geneRows

java.util.HashMap<K,V> geneRows

name

java.lang.String name

interactionTypeSifMap

java.util.Map<K,V> interactionTypeSifMap

interactionEvidenceMap

java.util.Map<K,V> interactionEvidenceMap

geneRankingMap

java.util.Map<K,V> geneRankingMap

nodeSet

java.util.Set<E> nodeSet

Class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.EdgeInfo extends java.lang.Object implements Serializable

serialVersionUID: 8884626375173162244L

Serialized Fields

value

float value

type

java.lang.String type

evidenceId

java.lang.Short evidenceId

Class org.geworkbench.bison.datastructure.biocollections.AdjacencyMatrix.Node extends java.lang.Object implements Serializable

serialVersionUID: -6472302414584701593L

Serialized Fields

type

AdjacencyMatrix.NodeType type

marker

DSGeneMarker marker

stringId

java.lang.String stringId

intId

int intId

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

serialVersionUID: 2222442531807486171L

Serialized Fields

matrix

AdjacencyMatrix matrix

threshold

double threshold

networkName

java.lang.String networkName

Class org.geworkbench.bison.datastructure.biocollections.AracneResult extends AdjacencyMatrixDataSet implements Serializable

serialVersionUID: -1321892354613689799L

Serialized Fields

hubList

java.util.List<E> hubList

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

serialVersionUID: -2828423786652899938L

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

file

java.io.File file

label

java.lang.String label

compatibilityLabel

java.lang.String compatibilityLabel

arraySetId

java.lang.String arraySetId
Used for the implementation of Identifiable.


description

java.lang.String description
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

columnOrder

java.util.ArrayList<E> columnOrder

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

serialVersionUID: -7674561735987333555L

Serialized Fields

geneIdMap

java.util.Hashtable<K,V> geneIdMap

geneNameMap

java.util.Hashtable<K,V> geneNameMap

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

serialVersionUID: -337000604982427702L

Serialized Fields

changedGenes

java.util.Set<E> changedGenes

referenceGenes

java.util.Set<E> referenceGenes

result

java.util.Map<K,V> result

term2Gene

java.util.HashMap<K,V> term2Gene

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

serialVersionUID: 739774613405629498L

Serialized Fields

model

byte[] model

modelFile

java.io.File modelFile

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

serialVersionUID: -6487530369595384222L

Serialized Fields

classifications

java.lang.String[] classifications

predModel

PredictionModel predModel

trainPredResultModel

PredictionModel trainPredResultModel

testPredResultModel

PredictionModel testPredResultModel

casePanel

DSPanel<T extends DSNamed> casePanel

controlPanel

DSPanel<T extends DSNamed> controlPanel

data

java.util.List<E> data

rowNames

java.lang.String[] rowNames

columnNames

java.lang.String[] columnNames

password

java.lang.String password

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

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

serialVersionUID: 1L

Serialized Fields

reportFile

java.lang.String reportFile

Package org.geworkbench.bison.datastructure.biocollections.lincs

Class org.geworkbench.bison.datastructure.biocollections.lincs.LincsDataSet extends CSAncillaryDataSet<DSMicroarray> implements Serializable

serialVersionUID: 2691812481782483733L

Serialized Fields

tissue

java.lang.String tissue

cellLine

java.lang.String cellLine

drug1

java.lang.String drug1

drug2

java.lang.String drug2

assayType

java.lang.String assayType

measurement

java.lang.String measurement

pValues

double[][] pValues

levelTwoIds

long[][] levelTwoIds

freeVariableNames

java.lang.String[] freeVariableNames

isExperimental

boolean isExperimental

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 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: -4273265470689892987L

Serialized Fields

data

MedusaData data

filename

java.lang.String filename

outputPath

java.lang.String outputPath

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

Class org.geworkbench.bison.datastructure.biocollections.microarrays.CSMicroarraySet extends CSDataSet<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

annotationFileName

java.lang.String annotationFileName

newid

int[] newid

markerOrder

java.lang.String markerOrder

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

Class org.geworkbench.bison.datastructure.biocollections.pca.CSPCADataSet extends CSAncillaryDataSet<DSBioObject> 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

serialVersionUID: -2426885649247874087L

Serialized Fields

dirty

boolean dirty

isDNA

boolean isDNA

maxLength

int maxLength

label

java.lang.String label

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.CSMicroarraySetView extends java.lang.Object implements Serializable

serialVersionUID: 1452815738190971373L

Serialized Fields

dataSet

DSMicroarraySet dataSet

itemPanel

DSPanel<T extends DSNamed> itemPanel
Contains the active microarrays, organized as a DSPanel.


markerPanel

DSPanel<T extends DSNamed> markerPanel
Contains the active markers, organized as a DSPanel.


Package org.geworkbench.bison.datastructure.bioobjects

Class org.geworkbench.bison.datastructure.bioobjects.FoldChangeResult extends CSAncillaryDataSet<DSMicroarray> implements Serializable

serialVersionUID: -4049899027384245969L

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

serialVersionUID: 7415476418084003832L

Serialized Fields

probe1

java.lang.String probe1

geneSymbol1

java.lang.String geneSymbol1

probe2

java.lang.String probe2

geneSymbol2

java.lang.String geneSymbol2

mi

double mi

deltaMi

double deltaMi

zScore

double zScore

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

serialVersionUID: 6652015492936201564L

Serialized Fields

probe1

java.lang.String probe1

probe2

java.lang.String probe2

connType

java.lang.String connType

gLoc

java.lang.String gLoc

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

serialVersionUID: 1610758764072258387L

Serialized Fields

probe

java.lang.String probe

geneSymbol

java.lang.String geneSymbol

chrBand

java.lang.String chrBand

conn

int conn

nes

double nes

loc

int loc

loCHits

int loCHits

loCEs

double loCEs

loCNes

double loCNes

goc

int goc

goCHits

int goCHits

goCEs

double goCEs

goCNes

double goCNes

Class org.geworkbench.bison.datastructure.bioobjects.IdeaResultDataSet extends CSAncillaryDataSet<DSMicroarray> implements Serializable

serialVersionUID: 1728642489420856774L

Serialized Fields

locList

java.util.List<E> locList

gocList

java.util.List<E> gocList

nodeList

java.util.List<E> nodeList

moduleList

java.util.List<E> moduleList

pvalue

double pvalue

Class org.geworkbench.bison.datastructure.bioobjects.KMeansResult extends CSAncillaryDataSet implements Serializable

serialVersionUID: -5747912398049332993L

Serialized Fields

clusterBy

int clusterBy

resultList

java.util.ArrayList<E> resultList

maSet

DSMicroarraySet maSet

Class org.geworkbench.bison.datastructure.bioobjects.KMeansResultMarkers extends KMeansResult implements Serializable

serialVersionUID: 4763004042149705168L

Serialized Fields

rows

int rows

columns

int columns

clusters

SOMCluster[][] clusters

parentSet

DSMicroarraySetView<T extends DSGeneMarker,Q extends DSMicroarray> parentSet

Class org.geworkbench.bison.datastructure.bioobjects.SamResultData extends CSAncillaryDataSet<DSMicroarray> implements Serializable

serialVersionUID: -4551408651966188747L

Serialized Fields

deltaInc

float deltaInc

deltaMax

float deltaMax

dd

float[] dd

dbar

float[] dbar

pvalue

float[] pvalue

fold

float[] fold

fdr

float[] fdr

maSet

DSMicroarraySet maSet

data

DSMicroarraySetView<T extends DSGeneMarker,Q extends DSMicroarray> data

Class org.geworkbench.bison.datastructure.bioobjects.SelectorResult extends CSAncillaryDataSet<DSMicroarray> implements Serializable

serialVersionUID: -4049899027384245969L

Serialized Fields

message

java.lang.String message

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

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

serialVersionUID: 1573294343188088869L

Serialized Fields

range

Range range

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

serialVersionUID: -8778666154593978009L

Serialized Fields

label

java.lang.String label

description

java.lang.String description

abrev

java.lang.String abrev

markerId

int markerId

geneId

int geneId

geneIds

int[] geneIds

unigene

DSUnigene unigene

geneName

java.lang.String geneName

annotation

java.lang.String annotation

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

serialVersionUID: -575408154089692683L


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

DSMicroarraySet currentDataSet

datasetToChipTypes

java.util.Map<K,V> datasetToChipTypes

datasetToAnnotation

java.util.Map<K,V> datasetToAnnotation

annotationFileToType

java.util.Map<K,V> annotationFileToType

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

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

serialVersionUID: -6938649275579408900L

Serialization Overview
Serializable fields.

Serialized Fields

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

serialVersionUID: -1727538221152553424L

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

fStat

boolean fStat

pVal

boolean pVal

mean

boolean mean

std

boolean std

header

java.lang.String[] header

A

java.lang.Object[][] A

Class org.geworkbench.bison.datastructure.bioobjects.microarray.CSDemandResultSet extends CSAncillaryDataSet<DSMicroarray> implements Serializable

serialVersionUID: 3402703191461767022L

Serialized Fields

result

java.lang.Object[][] result

edge

java.lang.Object[][] edge

module

java.lang.Object[][] module

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.CSMarkerValue extends java.lang.Object implements Serializable

serialVersionUID: -8400920535680410429L

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<DSMicroarray> implements Serializable

serialVersionUID: -416598071322541982L

Serialized Fields

TF2GenesInRegulon

java.util.HashMap<K,V> TF2GenesInRegulon

TF2GenesInTargetList

java.util.HashMap<K,V> TF2GenesInTargetList

TF2PValue

java.util.HashMap<K,V> TF2PValue

TF2Mode

java.util.HashMap<K,V> TF2Mode

TF2OddRatio

java.util.HashMap<K,V> TF2OddRatio

TF2Nes

java.util.HashMap<K,V> TF2Nes

maSet

DSMicroarraySet maSet

markerCount

int markerCount

values

java.util.Map<K,V> values

ranks

java.util.Map<K,V> ranks

minVal

double minVal

maxVal

double maxVal

Class org.geworkbench.bison.datastructure.bioobjects.microarray.CSMasterRegulatorTableResultSet extends CSAncillaryDataSet<DSMicroarray> implements Serializable

serialVersionUID: 4079428629682719155L

Serialized Fields

data

java.lang.Object[][] data

leadingEdge

java.util.Map<K,V> leadingEdge

regulon

java.util.Map<K,V> regulon

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

serialVersionUID: -1624438489587615570L

Serialized Fields

serial

int serial
The relative position (index) of the microarray within its host MicroarraySet.


arrayId

java.lang.String 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

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

serialVersionUID: 1471476047956028360L

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<DSMicroarray> implements Serializable

serialVersionUID: -5558984697240843050L

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: -6724936547706753609L

Serialized Fields

isLogNormalized

boolean isLogNormalized

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

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

serialVersionUID: -7617429744234644109L

Serialized Fields

databaseID

java.lang.String databaseID
The Database ID of the protein sequence hit in this BlastObj.


name

java.lang.String name
The accession number of the protein sequence hit in this BlastObj.


description

java.lang.String description
The description of the protein sequence hit in this BlastObj.


percentAligned

int percentAligned
The percentage of the query that's aligned with protein sequence hit in this BlastObj.


evalue

java.lang.String evalue
The score of the alignment of query and hit in this BlastObj.


subject

java.lang.String subject
The String of hit sequence in this BlastObj in alignment with query sequence.


include

boolean include
whether this BlastObj is included in the MSA analysis


seqURL

java.net.URL seqURL
URL of seq.


detailedAlignment

java.lang.String detailedAlignment

identity

java.lang.String identity

startPoint

int startPoint

alignmentLength

int alignmentLength

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

serialVersionUID: 3284079552620104447L

Serialized Fields

fastaFile

java.io.File fastaFile

resultFile

java.io.File resultFile

blastDataSet

java.util.List<E> blastDataSet

summary

java.lang.String summary

totalHitCount

int totalHitCount

blastedParentDataSet

DSSequenceSet<T extends DSSequence> 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

sequence

java.lang.String sequence

label

java.lang.String label

extend

CSExtendable extend
Used in the implementation of the Extendable interface.


description

java.lang.String description
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<DSBioObject> 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.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<DSSequence> implements Serializable

serialVersionUID: 1L

Serialized Fields

dataFile

java.io.File dataFile

result

java.lang.String result

Class org.geworkbench.bison.datastructure.bioobjects.structure.SkybaseResultSet extends CSAncillaryDataSet<DSSequence> implements Serializable

serialVersionUID: 7101429038894550594L

Serialized Fields

dataFile

java.io.File dataFile

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

serialVersionUID: -574208562647926731L

Serialized Fields

comparator

java.util.Comparator<T> comparator

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

serialVersionUID: 8634609117930075231L

Serialized Fields

label

java.lang.String label

subLabel

java.lang.String subLabel

active

boolean active

serial

int serial

panelId

java.lang.String panelId
Used in the implementation of the Identifiable interface.


description

java.lang.String description
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.PatternDiscoveryParameters extends java.lang.Object implements Serializable

serialVersionUID: -1314270495289691759L

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

Class org.geworkbench.bison.datastructure.complex.pattern.PatternResult extends CSAncillaryDataSet<DSSequence> implements Serializable

serialVersionUID: -66278700941966192L

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

patterns

java.util.List<E> patterns

dataSetFile

java.io.File dataSetFile

sequenceDB

DSSequenceSet<T extends DSSequence> sequenceDB

minSupport

int minSupport

minTokens

int minTokens

minWTokens

int minWTokens

window

int window

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

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

serialVersionUID: 3971178468487179811L

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

serialVersionUID: -2001831766990425659L

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

serialVersionUID: 6336253934311295851L

Serialized Fields

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

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

Class org.geworkbench.bison.datastructure.complex.pattern.sequence.CSSeqPatternMatch extends CSPatternMatch<DSSequence,CSSeqRegistration> implements Serializable

serialVersionUID: 6705539541328990492L


Package org.geworkbench.bison.datastructure.properties

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

serialVersionUID: -2136995152001635498L

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 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

serialVersionUID: 510957897262336390L

Serialized Fields

hasParametersToSave

boolean hasParametersToSave

Package org.geworkbench.bison.model.clusters

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

serialVersionUID: 2957512324725164458L

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

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

serialVersionUID: 8176955646021386560L

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
Customized serialization to avoid recursive call that may cause stack overflow.

Throws:
java.io.IOException
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

serialVersionUID: -1517435442151993543L

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

serialVersionUID: 2894691282983664326L

Serialized Fields

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

serialVersionUID: -1100675244807369959L

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

serialVersionUID: 3866574425702788704L

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.NonRecursiveClusterSet extends java.lang.Object implements Serializable

serialVersionUID: 5767070276541277929L

Serialized Fields

list

java.util.List<E> list

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.GenepixParseContext extends java.lang.Object implements Serializable

serialVersionUID: 8430221091524748106L

Serialization Overview
Serializable fields.

Serialized Fields

Package org.geworkbench.bison.util

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

serialVersionUID: 815454764380381809L

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

serialVersionUID: -8105939139046926331L

Serialized Fields

MISSING_VALUE_COLOR

java.awt.Color MISSING_VALUE_COLOR

magnitude

double magnitude

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

serialVersionUID: 7733639267835219074L


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

description

java.lang.String description

dataSet

DSDataSet<T extends DSBioObject> dataSet

visualSelected

java.lang.String visualSelected

selectionSelected

java.lang.String selectionSelected

children

java.util.ArrayList<E> children

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

serialVersionUID: 790047443850868022L

Serialized Fields

_aDataSet

DSAncillaryDataSet<T extends DSBioObject> _aDataSet

Class org.geworkbench.builtin.projects.ImageData extends CSAncillaryDataSet<DSBioObject> implements Serializable

serialVersionUID: 3899156889448935110L

Serialized Fields

imageFile

java.io.File imageFile

image

javax.swing.ImageIcon image

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.InformationPanel extends javax.swing.JPanel implements Serializable

serialVersionUID: -4544518025307954674L

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

serialVersionUID: -1983039293757013174L

Serialized Fields

log

org.apache.commons.logging.Log log

jPanel1

javax.swing.JPanel jPanel1

jPanel2

javax.swing.JPanel jPanel2

localFileRadioButton

javax.swing.JRadioButton localFileRadioButton

jPanel4

javax.swing.JPanel jPanel4

jFileChooser1

javax.swing.JFileChooser jFileChooser1

experimentInfoArea

javax.swing.JTextArea experimentInfoArea

format

java.lang.String format

caArrayDisplayPanel

CaARRAYPanel caArrayDisplayPanel

lowerPanel

javax.swing.JPanel lowerPanel

remoteResourceDialog

RemoteResourceDialog remoteResourceDialog

currentRemoteResourceName

java.lang.String currentRemoteResourceName

currentDetailedResourceName

java.lang.String currentDetailedResourceName

caarrayFilterQueryDialog

CaArrayFilteringDialog caarrayFilterQueryDialog

supportedInputFormats

FileFormat[] supportedInputFormats
Stores the FileFormat objects for the supported input formats.


remoteRadioButton

javax.swing.JRadioButton remoteRadioButton

jPanel10

javax.swing.JPanel jPanel10

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

openRemoteResourceButton

javax.swing.JButton openRemoteResourceButton

isSynchronized

boolean isSynchronized

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

serialVersionUID: 3418980725205404590L

Serialized Fields

remote

javax.swing.JRadioButton remote

local

javax.swing.JRadioButton local

sourceLocation

javax.swing.JTextField sourceLocation

ok

javax.swing.JButton ok

cancel

javax.swing.JButton cancel

oboSourcePreference

OboSourcePreference oboSourcePreference

chooseFileButton

javax.swing.JButton chooseFileButton

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

serialVersionUID: 6783438582542203187L

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

serialVersionUID: 6368086703128743579L

Serialized Fields

description

java.lang.String description

dirPropertyKey

java.lang.String dirPropertyKey

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

serialVersionUID: -197070883150097095L

Serialized Fields

fname

java.lang.String fname

lname

java.lang.String lname

username

java.lang.String username

password

java.lang.String password

confirmPasswd

java.lang.String confirmPasswd

oldPasswd

java.lang.String oldPasswd

email

java.lang.String email

workTitle

java.lang.String workTitle

phoneNumber

java.lang.String phoneNumber

labAffiliation

java.lang.String labAffiliation

addr1

java.lang.String addr1

addr2

java.lang.String addr2

city

java.lang.String city

state

java.lang.String state

zipcode

java.lang.String zipcode

createdat

java.lang.String createdat

logdata

int logdata

datavisibility

int datavisibility

message

java.lang.String message

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

serialVersionUID: 7446637434069686093L

Serialized Fields

pdnonmodal

ProgressDialog pdnonmodal

jframe

javax.swing.JFrame jframe

userId

javax.swing.JTextField userId

password

javax.swing.JPasswordField password

passwordDup

javax.swing.JPasswordField passwordDup

fname

javax.swing.JTextField fname

lname

javax.swing.JTextField lname

labaff

javax.swing.JTextField labaff

email

javax.swing.JTextField email

phone

javax.swing.JTextField phone

addr1

javax.swing.JTextField addr1

addr2

javax.swing.JTextField addr2

city

javax.swing.JTextField city

state

javax.swing.JTextField state

zipcode

javax.swing.JTextField zipcode

save

javax.swing.JButton save

reset

javax.swing.JButton reset

b_login

javax.swing.JButton b_login

jp

javax.swing.JLabel jp

jpc

javax.swing.JLabel jpc

jpo

javax.swing.JLabel jpo

passwordo

javax.swing.JPasswordField passwordo

Class org.geworkbench.builtin.projects.RWspHelper.ColorRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable

serialVersionUID: -8091519198660967004L

Class org.geworkbench.builtin.projects.RWspHelper.DetailTableModel extends javax.swing.table.AbstractTableModel implements Serializable

serialVersionUID: 2482447217249689117L

Serialized Fields

data

java.lang.String[][] data

header

java.lang.String[] header

Class org.geworkbench.builtin.projects.RWspHelper.WspTableModel extends RWspHelper.DetailTableModel implements Serializable

serialVersionUID: -5175211782386134949L

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

serialVersionUID: 2534917305724421302L

Serialized Fields

selected

DSDataSet<T extends DSBioObject> selected

wspId

int wspId

dirty

boolean dirty

checkout

java.lang.String checkout

lastchange

java.lang.String lastchange

rootNode

DataSetSaveNode rootNode

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

serialVersionUID: -1879887785935786137L


Package org.geworkbench.builtin.projects.remoteresources

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

serialVersionUID: -5214948658970068347L

Serialized Fields

log

org.apache.commons.logging.Log log

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

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

borderLayout1

java.awt.BorderLayout borderLayout1

jcatagoryComboBox

javax.swing.JComboBox jcatagoryComboBox

loadData

LoadDataDialog loadData

loaded

boolean loaded

chipPlatformBox

javax.swing.JComboBox chipPlatformBox

piComboxBox

javax.swing.JComboBox piComboxBox

orginsmBox

javax.swing.JComboBox orginsmBox

tissueTypeBox

javax.swing.JComboBox tissueTypeBox

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

publicIdentifier

java.lang.String publicIdentifier

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

LoadDataDialog 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

LoadDataDialog parentPanel

stillWaitForConnecting

boolean stillWaitForConnecting

numTotalArrays

int numTotalArrays

numCurrentArray

int numCurrentArray

experimentIdLabel

javax.swing.JLabel experimentIdLabel

Package org.geworkbench.engine

Class org.geworkbench.engine.WelcomeScreen extends javax.swing.JPanel implements Serializable

serialVersionUID: -4675518732204562565L

Serialized Fields

textFieldPanel

javax.swing.JPanel textFieldPanel

textField

javax.swing.JEditorPane textField

button

javax.swing.JButton button

buttonPanel

javax.swing.JPanel buttonPanel

Package org.geworkbench.engine.config

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

serialVersionUID: 1498878343817031247L


Package org.geworkbench.engine.config.rules

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

serialVersionUID: -1785392318270874137L

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

serialVersionUID: -4892433534916486892L

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

serialVersionUID: 1294386556835006669L

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

serialVersionUID: -879145735495136862L


Package org.geworkbench.engine.management

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

serialVersionUID: -8737440962644347200L

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

serialVersionUID: -2937673130196166730L


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

serialVersionUID: 3399952170903150872L

Serialized Fields

value

double value

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

serialVersionUID: 4966790497816410607L

Serialized Fields

name

java.lang.String name

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

serialVersionUID: -2701969431540105989L

Serialized Fields

value

java.io.File value

filter

javax.swing.filechooser.FileFilter filter

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

serialVersionUID: -8862041536368416988L

Serialized Fields

value

int value

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

serialVersionUID: -3239003390502930623L

Serialized Fields

fields

java.util.List<E> fields

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

serialVersionUID: -5984019099671463020L

Serialized Fields

value

java.lang.String value

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

serialVersionUID: -811286462820397093L


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

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

acceptors

java.util.Set<E> acceptors

mainComponentClass

java.util.HashMap<K,V> mainComponentClass

visualLastSelected

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

selectionLastSelected

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

visualDockables

java.util.ArrayList<E> visualDockables

selectorDockables

java.util.ArrayList<E> selectorDockables

currentDataSet

DSDataSet<T extends DSBioObject> currentDataSet

tabSwappingMode

boolean tabSwappingMode

appTitle

java.lang.String appTitle

showMemoryUsage

boolean showMemoryUsage

Package org.geworkbench.events

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

serialVersionUID: -3433240912097398524L

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

Package org.geworkbench.parsers

Class org.geworkbench.parsers.EfficientMicroarraySet extends java.lang.Object implements Serializable

serialVersionUID: 982267023582096902L

Serialized Fields

arrayNumber

int arrayNumber

markerNumber

int markerNumber

arrayLabels

java.lang.String[] arrayLabels

markerLabels

java.lang.String[] markerLabels

values

float[][] values

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

serialVersionUID: -6720821904782135107L


Package org.geworkbench.util

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

serialVersionUID: -7980428838765239847L

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

serialVersionUID: 2439482773256837713L

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

serialVersionUID: 7217613511326291355L

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

serialVersionUID: 5278164284154657596L

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.OWFileChooser extends javax.swing.JFileChooser implements Serializable

serialVersionUID: -8841673089062156967L

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

serialVersionUID: 8319899130441466097L

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

serialVersionUID: 6028593195582948256L

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.ProgressDialog extends javax.swing.JDialog implements Serializable

serialVersionUID: 1L

Serialized Fields

tasks

java.util.Vector<E> tasks

jp

javax.swing.JPanel jp

gl

java.awt.GridLayout gl

jsp

javax.swing.JScrollPane jsp

maxWidth

int maxWidth

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

serialVersionUID: -5412121631161441914L

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.ProgressItem extends javax.swing.JPanel implements Serializable

serialVersionUID: -4287056285516981445L

Serialized Fields

type

int type
Instance type


jProgressBar

javax.swing.JProgressBar jProgressBar
Visual widget


cancelButton

javax.swing.JButton cancelButton
Visual widget


jLabel1

javax.swing.JLabel jLabel1

jp1

javax.swing.JPanel jp1

jp2

javax.swing.JPanel jp2

task

ProgressTask<T,V> task

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

serialVersionUID: 1L

Serialized Fields

increment

int increment

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

serialVersionUID: -398655317017316525L

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

Class org.geworkbench.util.UnAuthenticatedException extends BaseException implements Serializable

serialVersionUID: 6379819293142168996L


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.CellularNetworkPreference extends java.lang.Object implements Serializable

serialVersionUID: -3049737574513104023L

Serialized Fields

title

java.lang.String title

context

java.lang.String context

version

java.lang.String version

displaySelectedInteractionTypes

java.util.List<E> displaySelectedInteractionTypes

selectedConfidenceType

java.lang.Short selectedConfidenceType

confidenceTypeList

java.util.List<E> confidenceTypeList

maxConfidenceValueMap

java.util.Map<K,V> maxConfidenceValueMap

smallestIncrement

double smallestIncrement

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

serialVersionUID: -4163326138016520667L

Serialized Fields

dSGeneId

java.lang.String dSGeneId

dSGeneName

java.lang.String dSGeneName

dbSource

java.lang.String dbSource

interactionType

java.lang.String interactionType

evidenceId

java.lang.Short evidenceId

confidenceList

java.util.List<E> confidenceList

Package org.geworkbench.util.pathwaydecoder.mutualinformation

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

serialVersionUID: 742062775524951624L

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

serialVersionUID: -1146449113733368462L

Serialized Fields

edgeList

java.util.ArrayList<E> edgeList

Class org.geworkbench.util.pathwaydecoder.mutualinformation.EdgeListDataSet extends CSAncillaryDataSet<DSBioObject> 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

serialVersionUID: 6291084231320914541L

Serialized Fields

arraySet

CSMicroarraySet 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<DSMicroarray> 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

serialVersionUID: 3982199635486005070L

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

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.NetBoostData extends java.lang.Object implements Serializable

serialVersionUID: -4449531098587826175L

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<DSBioObject> implements Serializable

serialVersionUID: -6835973287728524201L

Serialized Fields

data

NetBoostData data

filename

java.lang.String filename

Package org.geworkbench.util.patterns

Class org.geworkbench.util.patterns.CSMatchedSeqPattern extends CSMatchedPattern<DSSequence,CSSeqRegistration> implements Serializable

serialVersionUID: -8809856414947634034L

Serialized Fields

idNo

int idNo

seqNo

int seqNo

seqDB

DSSequenceSet<T extends DSSequence> seqDB

locus

byte[] locus

offset

java.util.ArrayList<E> offset

ascii

java.lang.String ascii

matches

java.util.ArrayList<E> matches

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

serialVersionUID: -6269930506232901690L

Class org.geworkbench.util.patterns.PatternOfflet extends java.lang.Object implements Serializable

serialVersionUID: -6441126412656981789L

Serialized Fields

position

int position

token

java.lang.String token

Package org.geworkbench.util.sequences

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

serialVersionUID: 9144326847214513997L

Serialized Fields

pattern

java.util.List<E> pattern

rowCount

int rowCount

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

serialVersionUID: 1451645981046343519L

Serialized Fields

model

PatternTableModel model

borderLayout1

java.awt.BorderLayout borderLayout1

jScrollPane

javax.swing.JScrollPane jScrollPane

patternMenu

javax.swing.JPopupMenu patternMenu

maskPatternItem

javax.swing.JMenuItem maskPatternItem

unmaskAllPatternItem

javax.swing.JMenuItem unmaskAllPatternItem

jSavePatternsItem

javax.swing.JMenuItem jSavePatternsItem

jSavePatternsWInfoItem

javax.swing.JMenuItem jSavePatternsWInfoItem

jSaveSelectedPatternsWInfoItem

javax.swing.JMenuItem jSaveSelectedPatternsWInfoItem

saveAllPatterns

boolean saveAllPatterns

patternTable

org.geworkbench.util.sequences.PatternTableView.JPTable patternTable

sequenceSet

DSSequenceSet<T extends DSSequence> sequenceSet

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

serialVersionUID: -6141589995966150788L

Serialized Fields

patternLocationsMatches

java.util.HashMap<K,V> patternLocationsMatches

selectedPatterns

java.util.List<E> 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

sequencedetailPanel

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

isLineView

boolean isLineView

onlyShowPattern

boolean onlyShowPattern

goLeft

boolean goLeft

xStartPoint

int xStartPoint

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

serialVersionUID: -1720620118289765818L

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

serialVersionUID: 7202257250696337753L

Serialized Fields

xOff

int xOff

yOff

int yOff

yStep

int yStep

scale

double scale

selected

int selected

maxSeqLen

int maxSeqLen

sequenceDB

DSSequenceSet<T extends DSSequence> sequenceDB

sequencePatternmatches

java.util.HashMap<K,V> sequencePatternmatches

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

Package org.geworkbench.util.visualproperties

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

serialVersionUID: -35780996506593330L

Serialized Fields

shape

java.awt.Shape shape

paint

java.awt.Paint paint

listener

java.awt.event.ActionListener listener

percentSize

int percentSize

drawBorder

boolean drawBorder

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

serialVersionUID: -7320339264841448126L

Serialized Fields

result

int result

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

serialVersionUID: -1324174157721236396L

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