Serialized Form

  • Package bacnet.datamodel.annotation

  • Package bacnet.datamodel.dataset

  • Package bacnet.datamodel.expdesign

    • Class bacnet.datamodel.expdesign.BioCondition

      class BioCondition extends Object implements Serializable
      serialVersionUID:
      -8545052328831545661L

      • Serialized Fields

        • antiComparisons
          ArrayList<String> antiComparisons
          List of Data for which the BioCondition is the reference bioCodntion for the comparison: BioCondComparison vs This Biocondition
        • arrayExpressId
          String arrayExpressId
          ArrayExpressId if this data is public
        • arrayExpressTechnoId
          String arrayExpressTechnoId
          ArrayExpressId of the technology used
        • comment
          String comment
          Different comment
        • comparisons
          ArrayList<String> comparisons
          List of Data for which we have comparison data: This Biocondition vs BioCondComparison
        • date
          String date
          Date of creation or data of publication
        • experienceNb
          int experienceNb
          For experiment from Cossart lab, ID of the experiment
        • geneExprs
          ArrayList<GeneExpression> geneExprs
          All Listeria GeneExpression arrays associated to this BioCondition
        • genomeName
          String genomeName
          Reference genome ID to used for this BioCondition
        • genomeUsed
          String genomeUsed
          Actual strain used to create this BioCondition, might be different from genomeName
        • growth
          ArrayList<String> growth
          Growth conditions are specified here
        • linkedBioCondition
          ArrayList<String> linkedBioCondition
          Data associated to this BioCondition to use in the case of timepoint experiment, or same mutant in different condition
        • localization
          ArrayList<String> localization
          If it is a proteome, this parameters tells you where in the bacteria cell the proteins have been extracted
        • matrices
          ArrayList<ExpressionMatrix> matrices
          All data in ExpressioMatrix associated to this BioCondition
        • media
          ArrayList<String> media
          Growth media is specified here
        • mediaGrowthProperties
          ArrayList<String> mediaGrowthProperties
          Quantity/properties of drugs added to the media if specified: quantity of glucose, type of Broth
        • mutant
          ArrayList<String> mutant
          If it is a mutant, the locus is indicated (example: prfA, lmo0200 or rliA), leave empty otherwise
        • name
          String name
          Name of the BioCondition
        • ngss
          ArrayList<NGS> ngss
          All RNASeq data associated to this BioCondition
        • noData
          boolean noData
          True if no data are associated to this BioCondition
          It is used principaly to indicate that the BioCondition is a reference condition for another BioCondition, and thus no data are available for it, as the data are in the other BioCondition
        • nTerms
          ArrayList<NTermData> nTerms
          All NTermData data associated to this BioCondition
        • proteomes
          ArrayList<ProteomicsData> proteomes
          All ProteomicsData data associated to this BioCondition
        • reference
          String reference
          Article in which data is published
        • studyName
          String studyName
          Name of the study from which the data is extracted
        • temperature
          String temperature
          Temperature is specified here
        • tilings
          ArrayList<Tiling> tilings
          All Listeria Tiling arrays associated to this BioCondition
        • time
          String time
          time point if necessary
        • typeDataContained
          TreeSet<OmicsData.TypeData> typeDataContained
          Type of bioCondition : TSS only, TIS only, RNASeq + Tiling + GeneExpr, RNASeq only ...
        • wildType
          boolean wildType
          True if this BioCondition is a wild-type strain, to be used as a reference condition

    • Class bacnet.datamodel.expdesign.Experiment

      class Experiment extends Object implements Serializable
      serialVersionUID:
      993350014891502366L

  • Package bacnet.datamodel.proteomics

    • Class bacnet.datamodel.proteomics.NTerm

      class NTerm extends Sequence implements Serializable
      serialVersionUID:
      -7191352336233310587L

      • Serialized Fields

        • antiSDBindingFreeEnergy
          double antiSDBindingFreeEnergy
          Value of the binding between anti-SD sequence and the region -20bp upstream to the peptide
        • codonUsage
          double codonUsage
          CodonUsage of the peptideSequence
        • duplicates
          ArrayList<String> duplicates
          Number of duplicates having same sequencePeptide (e.g. peptide mapped on different regions)
        • insoluble
          boolean insoluble
          Indicate if it was found in soluble part
        • mappingFrame
          NTerm.MappingFrame mappingFrame
          Frame where the peptide has been mapped
        • maxQuant
          String maxQuant
          If the peptide has also been found with MaxQuant analysis software, we write something in this attribute, otherwise its blank
        • maxQuantum
          String[] maxQuantum
          If the peptide has also been found with MaxQuant analysis software, we write something in this attribute, otherwise its blank, each column is for one type of experiments.
        • modifSequence
          String modifSequence
          Modify sequence provided by Francis
        • nextCodon
          String nextCodon
          Codon downstream to first codon of mapped sequence
        • overlap
          String overlap
          Name of the genome element which NTerm overlaps
        • overlapInFrame
          boolean overlapInFrame
          Check if the peptide is in frame with genome element which it overlaps
        • previousCodon
          String previousCodon
          Codon upstream to mapped sequence
        • score
          int score
        • sequenceMap
          String sequenceMap
          Translated sequence of the mapped peptide
        • sequencePeptide
          String sequencePeptide
          Peptide sequence extracted from modified Sequence
        • soluble
          boolean soluble
          Indicate if it was found in soluble part
        • spectra
          int spectra
          Total number of spectra found
        • spectrum
          int[] spectrum
          Each column of this vector give the number of spectra for each condition
        • startCode
          String startCode
          Indicates if the first codon or previousCodon is a Start codon
        • startCodon
          String startCodon
          First codon of the mapped sequence
        • threshold
          int threshold
        • TISName
          String TISName
          TIS Name : A TIS is a group of NTerm have same position but a slightly different position
        • tssDownCoverage
          int tssDownCoverage
          Coverage of the closest TSS downstream to this NTerm
        • tssDownDistance
          int tssDownDistance
          Distance where can be found a TSS downstream to this NTerm
        • tssDowntype
          String tssDowntype
          Type of TSS downstream to this NTerm : i.e. internal, intergenic, ...
        • tssUpCoverage
          int tssUpCoverage
          Coverage of the closest TSS upstream to this NTerm
        • tssUpDistance
          int tssUpDistance
          Distance where can be found a TSS upstream to this NTerm
        • tssUptype
          String tssUptype
          Type of TSS upstream to this NTerm : i.e. internal, intergenic, ...
        • typeModif
          NTerm.TypeModif typeModif
          Type of modification
        • typeOverlap
          String typeOverlap
          Potential type of TIS of this NTerm

    • Class bacnet.datamodel.proteomics.TIS

      class TIS extends Sequence implements Serializable
      serialVersionUID:
      3452878896031108870L

  • Package bacnet.datamodel.sequence

  • Package bacnet.e4.rap

    • Class bacnet.e4.rap.BannerView

      class BannerView extends Object implements Serializable
      serialVersionUID:
      8818752955596747659L

      • Serialized Fields

        • canvas
          org.eclipse.swt.widgets.Canvas canvas
          In this Canvas we will draw the Banner of the website/software
        • modelService
          org.eclipse.e4.ui.workbench.modeling.EModelService modelService
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tltmAbout
          org.eclipse.swt.widgets.ToolItem tltmAbout
        • tltmGenomics
          org.eclipse.swt.widgets.ToolItem tltmGenomics
        • tltmGitlab
          org.eclipse.swt.widgets.ToolItem tltmGitlab
        • tltmProteomics
          org.eclipse.swt.widgets.ToolItem tltmProteomics
        • tltmTranscriptomics
          org.eclipse.swt.widgets.ToolItem tltmTranscriptomics
        • toolBar
          org.eclipse.swt.widgets.ToolBar toolBar

    • Class bacnet.e4.rap.InitViewBacnet

      class InitViewBacnet extends Object implements Serializable
      serialVersionUID:
      -3252983689419871498L

      • Serialized Fields

        • btnCRISPR
          org.eclipse.swt.widgets.Button btnCRISPR
        • btnLeishmania
          org.eclipse.swt.widgets.Button btnLeishmania
        • btnLightlisteriomics
          org.eclipse.swt.widgets.Button btnLightlisteriomics
        • btnListeriomics
          org.eclipse.swt.widgets.Button btnListeriomics
        • btnYersiniomics
          org.eclipse.swt.widgets.Button btnYersiniomics
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • linkHUB
          org.eclipse.swt.widgets.Link linkHUB
        • linkLicenceField
          org.eclipse.swt.widgets.Link linkLicenceField
        • linkPubli
          org.eclipse.swt.widgets.Link linkPubli
        • modelService
          org.eclipse.e4.ui.workbench.modeling.EModelService modelService
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • shell
          org.eclipse.swt.widgets.Shell shell

    • Class bacnet.e4.rap.InitViewListeria

      class InitViewListeria extends Object implements Serializable
      serialVersionUID:
      -3252983689419871498L

      • Serialized Fields

        • btnAccessWiki
          org.eclipse.swt.widgets.Button btnAccessWiki
        • btnBHI37
          org.eclipse.swt.widgets.Button btnBHI37
        • btnCoExpression
          org.eclipse.swt.widgets.Button btnCoExpression
        • btnGeneView
          org.eclipse.swt.widgets.Button btnGeneView
        • btnGenomics
          org.eclipse.swt.widgets.Button btnGenomics
        • btnIntracellular
          org.eclipse.swt.widgets.Button btnIntracellular
        • btnLoadData
          org.eclipse.swt.widgets.Button btnLoadData
        • btnNTerm
          org.eclipse.swt.widgets.Button btnNTerm
        • btnNTermTable
          org.eclipse.swt.widgets.Button btnNTermTable
        • btnProteomics
          org.eclipse.swt.widgets.Button btnProteomics
        • btnSrnas
          org.eclipse.swt.widgets.Button btnSrnas
        • btnStat
          org.eclipse.swt.widgets.Button btnStat
        • btnTranscriptomics
          org.eclipse.swt.widgets.Button btnTranscriptomics
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • link_NTerm
          org.eclipse.swt.widgets.Link link_NTerm
        • linkHUB
          org.eclipse.swt.widgets.Link linkHUB
        • linkLicenceField
          org.eclipse.swt.widgets.Link linkLicenceField
        • linkPubli
          org.eclipse.swt.widgets.Link linkPubli
        • linkUIBC
          org.eclipse.swt.widgets.Link linkUIBC
        • modelService
          org.eclipse.e4.ui.workbench.modeling.EModelService modelService
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • shell
          org.eclipse.swt.widgets.Shell shell

    • Class bacnet.e4.rap.InitViewListeriaSample

      class InitViewListeriaSample extends Object implements Serializable
      serialVersionUID:
      -3252983689419871498L

      • Serialized Fields

        • btnBHI37
          org.eclipse.swt.widgets.Button btnBHI37
        • btnGeneView
          org.eclipse.swt.widgets.Button btnGeneView
        • btnGenomics
          org.eclipse.swt.widgets.Button btnGenomics
        • btnLoadData
          org.eclipse.swt.widgets.Button btnLoadData
        • btnNetwork
          org.eclipse.swt.widgets.Button btnNetwork
        • btnProteomics
          org.eclipse.swt.widgets.Button btnProteomics
        • btnTranscriptomics
          org.eclipse.swt.widgets.Button btnTranscriptomics
        • btnWiki
          org.eclipse.swt.widgets.Button btnWiki
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • linkHUB
          org.eclipse.swt.widgets.Link linkHUB
        • linkLicenceField
          org.eclipse.swt.widgets.Link linkLicenceField
        • linkPubli
          org.eclipse.swt.widgets.Link linkPubli
        • linkUIBC
          org.eclipse.swt.widgets.Link linkUIBC
        • modelService
          org.eclipse.e4.ui.workbench.modeling.EModelService modelService
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • shell
          org.eclipse.swt.widgets.Shell shell

    • Class bacnet.e4.rap.InitViewYersinia

      class InitViewYersinia extends Object implements Serializable
      serialVersionUID:
      -9052983689419871498L

      • Serialized Fields

        • btn8081
          org.eclipse.swt.widgets.Button btn8081
        • btn91001
          org.eclipse.swt.widgets.Button btn91001
        • btnAccessWiki
          org.eclipse.swt.widgets.Button btnAccessWiki
        • btnCO92
          org.eclipse.swt.widgets.Button btnCO92
        • btnCoExpression
          org.eclipse.swt.widgets.Button btnCoExpression
        • btnGeneView
          org.eclipse.swt.widgets.Button btnGeneView
        • btnGenomics
          org.eclipse.swt.widgets.Button btnGenomics
        • btnIP32953
          org.eclipse.swt.widgets.Button btnIP32953
        • btnKIM
          org.eclipse.swt.widgets.Button btnKIM
        • btnLoadData
          org.eclipse.swt.widgets.Button btnLoadData
        • btnPB1
          org.eclipse.swt.widgets.Button btnPB1
        • btnPestoides
          org.eclipse.swt.widgets.Button btnPestoides
        • btnProteomics
          org.eclipse.swt.widgets.Button btnProteomics
        • btnQMA0440
          org.eclipse.swt.widgets.Button btnQMA0440
        • btnTranscriptomics
          org.eclipse.swt.widgets.Button btnTranscriptomics
        • btnWA
          org.eclipse.swt.widgets.Button btnWA
        • btnY11
          org.eclipse.swt.widgets.Button btnY11
        • btnYPIII
          org.eclipse.swt.widgets.Button btnYPIII
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • linkHUB
          org.eclipse.swt.widgets.Link linkHUB
        • linkLicenceField
          org.eclipse.swt.widgets.Link linkLicenceField
        • linkPubli
          org.eclipse.swt.widgets.Link linkPubli
        • modelService
          org.eclipse.e4.ui.workbench.modeling.EModelService modelService
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • shell
          org.eclipse.swt.widgets.Shell shell

    • Class bacnet.e4.rap.SynTView

      class SynTView extends Object implements Serializable
      serialVersionUID:
      -4429010895850129342L

      • Serialized Fields

        • browserGraph
          org.eclipse.swt.browser.Browser browserGraph
        • btnHelp
          org.eclipse.swt.widgets.Button btnHelp
        • btnSelectGenomeElements
          org.eclipse.swt.widgets.Button btnSelectGenomeElements
        • compositeTitle
          org.eclipse.swt.widgets.Composite compositeTitle
        • filteredNetwork
          Network filteredNetwork
        • generalNetwork
          Network generalNetwork
        • genome
          Genome genome
        • genomeName
          String genomeName
        • lblSearch
          org.eclipse.swt.widgets.Label lblSearch
        • listGenomeElements
          ArrayList<String> listGenomeElements
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • shell
          org.eclipse.swt.widgets.Shell shell
        • svgName
          String svgName
        • tableGenes
          org.eclipse.swt.widgets.Table tableGenes
        • txtSearch
          org.eclipse.swt.widgets.Text txtSearch

  • Package bacnet.e4.rap.setup

    • Class bacnet.e4.rap.setup.SetupPart

      class SetupPart extends Object implements Serializable
      serialVersionUID:
      -3563942149356313184L

      • Serialized Fields

        • btnAddBiologicalConditions
          org.eclipse.swt.widgets.Button btnAddBiologicalConditions
        • btnAddComparisonsFrom
          org.eclipse.swt.widgets.Button btnAddComparisonsFrom
        • btnAddGenomes
          org.eclipse.swt.widgets.Button btnAddGenomes
        • btnAddHomologsInformation
          org.eclipse.swt.widgets.Button btnAddHomologsInformation
        • btnAddProteomesFrom
          org.eclipse.swt.widgets.Button btnAddProteomesFrom
        • btnCheckBlastResult
          org.eclipse.swt.widgets.Button btnCheckBlastResult
        • btnCreatBlastpScript
          org.eclipse.swt.widgets.Button btnCreatBlastpScript
        • btnCreateBlastDB
          org.eclipse.swt.widgets.Button btnCreateBlastDB
        • btnCreateCoExpressionDataList
          org.eclipse.swt.widgets.Button btnCreateCoExpressionDataList
        • btnCreateCoExpressionNetwork
          org.eclipse.swt.widgets.Button btnCreateCoExpressionNetwork
        • btnCreateExprPrteome
          org.eclipse.swt.widgets.Button btnCreateExprPrteome
        • btnCreateGenomeSummary
          org.eclipse.swt.widgets.Button btnCreateGenomeSummary
        • btnCreateHomologTables
          org.eclipse.swt.widgets.Button btnCreateHomologTables
        • btnCreateLogfcTranscriptome
          org.eclipse.swt.widgets.Button btnCreateLogfcTranscriptome
        • btnCreateProteomicsComparisons
          org.eclipse.swt.widgets.Button btnCreateProteomicsComparisons
        • btnCreateProteomicsTable
          org.eclipse.swt.widgets.Button btnCreateProteomicsTable
        • btnCreateTranscriptomicsComparisons
          org.eclipse.swt.widgets.Button btnCreateTranscriptomicsComparisons
        • btnCreateTranscriptomicsTable
          org.eclipse.swt.widgets.Button btnCreateTranscriptomicsTable
        • btnDownloadGenomesFrom
          org.eclipse.swt.widgets.Button btnDownloadGenomesFrom
        • btnOrganizeGenomeTable
          org.eclipse.swt.widgets.Button btnOrganizeGenomeTable
        • btnRunPhylogenomicTree
          org.eclipse.swt.widgets.Button btnRunPhylogenomicTree
        • btnValidateBioconditionsDatabase
          org.eclipse.swt.widgets.Button btnValidateBioconditionsDatabase
        • btnValidateCoExpr
          org.eclipse.swt.widgets.Button btnValidateCoExpr
        • btnValidateComparisonsDatabase
          org.eclipse.swt.widgets.Button btnValidateComparisonsDatabase
        • btnValidateGenomicsDatabase
          org.eclipse.swt.widgets.Button btnValidateGenomicsDatabase
        • btnValidateProteomics
          org.eclipse.swt.widgets.Button btnValidateProteomics
        • buttonAddTranscriptomics
          org.eclipse.swt.widgets.Button buttonAddTranscriptomics
        • buttonValidateTrancriptomics
          org.eclipse.swt.widgets.Button buttonValidateTrancriptomics
        • comboProject
          org.eclipse.swt.widgets.Combo comboProject
        • composite_8
          org.eclipse.swt.widgets.Composite composite_8
        • composite_9
          org.eclipse.swt.widgets.Composite composite_9
        • console
          org.eclipse.swt.widgets.Text console
        • dataValidation
          DataValidation dataValidation
        • label_Transcriptomics
          org.eclipse.swt.widgets.Label label_Transcriptomics
        • labelGenomes
          org.eclipse.swt.widgets.Label labelGenomes
        • labelNetwork
          org.eclipse.swt.widgets.Label labelNetwork
        • labelProteomics
          org.eclipse.swt.widgets.Label labelProteomics
        • lblBioconditions
          org.eclipse.swt.widgets.Label lblBioconditions
        • lblBioCondPath
          org.eclipse.swt.widgets.Label lblBioCondPath
        • lblComparisons
          org.eclipse.swt.widgets.Label lblComparisons
        • lblComparisonsPath
          org.eclipse.swt.widgets.Label lblComparisonsPath
        • lblHaveYouCreated
          org.eclipse.swt.widgets.Label lblHaveYouCreated
        • lblHomologpath
          org.eclipse.swt.widgets.Label lblHomologpath
        • lblHomopathfound
          org.eclipse.swt.widgets.Label lblHomopathfound
        • lblNetworkPath
          org.eclipse.swt.widgets.Label lblNetworkPath
        • lblNewLabel_1
          org.eclipse.swt.widgets.Label lblNewLabel_1
        • lblPathData
          org.eclipse.swt.widgets.Label lblPathData
        • lblPathGenomics
          org.eclipse.swt.widgets.Label lblPathGenomics
        • lblPhylofigfound
          org.eclipse.swt.widgets.Label lblPhylofigfound
        • lblPhylogenomicsfigure
          org.eclipse.swt.widgets.Label lblPhylogenomicsfigure
        • lblProteomePath
          org.eclipse.swt.widgets.Label lblProteomePath
        • lblTechno
          org.eclipse.swt.widgets.Label lblTechno
        • lblTranscriPath
          org.eclipse.swt.widgets.Label lblTranscriPath
        • logs
          String logs
        • modelService
          org.eclipse.e4.ui.workbench.modeling.EModelService modelService
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tableBioCondition
          org.eclipse.swt.widgets.Table tableBioCondition
        • tableComparisons
          org.eclipse.swt.widgets.Table tableComparisons
        • tableGenome
          org.eclipse.swt.widgets.Table tableGenome
        • tableNetwork
          org.eclipse.swt.widgets.Table tableNetwork
        • tableProteomics
          org.eclipse.swt.widgets.Table tableProteomics
        • tableTranscriptomes
          org.eclipse.swt.widgets.Table tableTranscriptomes
        • tbtmComparisons
          org.eclipse.swt.widgets.TabItem tbtmComparisons
        • tbtmPhylogeny
          org.eclipse.swt.widgets.TabItem tbtmPhylogeny

  • Package bacnet.expressionAtlas

    • Class bacnet.expressionAtlas.HeatMapMultiOmicsView

      class HeatMapMultiOmicsView extends Object implements Serializable
      serialVersionUID:
      -2640442866422682301L

      • Serialized Fields

        • allButtons
          ArrayList<org.eclipse.swt.widgets.Button> allButtons
        • browserGraph
          org.eclipse.swt.browser.Browser browserGraph
        • btnDnDNA
          org.eclipse.swt.widgets.Button btnDnDNA
        • btnDnProt
          org.eclipse.swt.widgets.Button btnDnProt
        • btnDnRNA
          org.eclipse.swt.widgets.Button btnDnRNA
        • btnListIntersection
          org.eclipse.swt.widgets.Button btnListIntersection
        • btnListUnion
          org.eclipse.swt.widgets.Button btnListUnion
        • btnNoDNA
          org.eclipse.swt.widgets.Button btnNoDNA
        • btnNoProt
          org.eclipse.swt.widgets.Button btnNoProt
        • btnNoRNA
          org.eclipse.swt.widgets.Button btnNoRNA
        • btnPrint
          org.eclipse.swt.widgets.Button btnPrint
        • btnSavePNG
          org.eclipse.swt.widgets.Button btnSavePNG
        • btnUpdateCutoff
          org.eclipse.swt.widgets.Button btnUpdateCutoff
        • btnUpDNA
          org.eclipse.swt.widgets.Button btnUpDNA
        • btnUpProt
          org.eclipse.swt.widgets.Button btnUpProt
        • btnUpRNA
          org.eclipse.swt.widgets.Button btnUpRNA
        • cmbXaxis
          org.eclipse.swt.widgets.Combo cmbXaxis
        • cmbYaxis
          org.eclipse.swt.widgets.Combo cmbYaxis
        • compFilter
          org.eclipse.swt.widgets.Composite compFilter
        • composite
          org.eclipse.swt.widgets.Composite composite
        • compositeSummary
          org.eclipse.swt.widgets.Composite compositeSummary
        • downDNAList
          ArrayList<String> downDNAList
          List of genes down for DNA
        • downProtList
          ArrayList<String> downProtList
          List of genes down for Prot
        • downRNAList
          ArrayList<String> downRNAList
          List of genes down for RNA
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • genomeName
          String genomeName
        • intersect
          boolean intersect
          Describe comportment of list overlap
        • logfcOmicsMatrix
          ExpressionMatrix logfcOmicsMatrix
          LogFC Matrix = Multiomics with only the logFC values
        • noDNAList
          ArrayList<String> noDNAList
          List of genes no change for DNA
        • noProtList
          ArrayList<String> noProtList
          List of genes no change for Prot
        • noRNAList
          ArrayList<String> noRNAList
          List of genes no change for RNA
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • sequence
          String sequence
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tabFolder
          org.eclipse.swt.widgets.TabFolder tabFolder
        • tableComposite
          TableCompositeHeatMap tableComposite
        • tbtmHeatmap
          org.eclipse.swt.widgets.TabItem tbtmHeatmap
        • tbtmScatterPlot
          org.eclipse.swt.widgets.TabItem tbtmScatterPlot
        • txtCutoffLogFC
          org.eclipse.swt.widgets.Text txtCutoffLogFC
        • upDNAList
          ArrayList<String> upDNAList
          List of genes up for DNA
        • upProtList
          ArrayList<String> upProtList
          List of genes up for Prot
        • upRNAList
          ArrayList<String> upRNAList
          List of genes up for RNA
        • viewId
          String viewId
          Current viewId = ID + math.random()

    • Class bacnet.expressionAtlas.HeatMapProteomicsExpressionView

      class HeatMapProteomicsExpressionView extends Object implements Serializable
      serialVersionUID:
      7806377909856153015L

      • Serialized Fields

        • bioConditions
          ArrayList<String> bioConditions
        • compositeSummary
          org.eclipse.swt.widgets.Composite compositeSummary
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • genomeName
          String genomeName
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tableComposite
          TableCompositeHeatMap tableComposite
        • viewId
          String viewId

    • Class bacnet.expressionAtlas.HeatMapProteomicsView

      class HeatMapProteomicsView extends Object implements Serializable
      serialVersionUID:
      -2640442866422682301L

      • Serialized Fields

        • btnUpdateCutoff
          org.eclipse.swt.widgets.Button btnUpdateCutoff
        • cmbDataUsed
          org.eclipse.swt.widgets.Combo cmbDataUsed
        • compositeSummary
          org.eclipse.swt.widgets.Composite compositeSummary
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • genomeName
          String genomeName
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • sequence
          String sequence
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tableComposite
          TableCompositeHeatMap tableComposite
        • txtCutoffLogFC
          org.eclipse.swt.widgets.Text txtCutoffLogFC
        • viewId
          String viewId

    • Class bacnet.expressionAtlas.HeatMapTranscriptomicsView

      class HeatMapTranscriptomicsView extends Object implements Serializable
      serialVersionUID:
      -2640442866422682301L

      • Serialized Fields

        • btnUpdateCutoff
          org.eclipse.swt.widgets.Button btnUpdateCutoff
        • cmbDataUsed
          org.eclipse.swt.widgets.Combo cmbDataUsed
        • compositeSummary
          org.eclipse.swt.widgets.Composite compositeSummary
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • genomeName
          String genomeName
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • sequence
          String sequence
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tableComposite
          TableCompositeHeatMap tableComposite
        • txtCutoffLogFC
          org.eclipse.swt.widgets.Text txtCutoffLogFC
        • viewId
          String viewId

    • Class bacnet.expressionAtlas.ProteomicsDataFilterComposite

      class ProteomicsDataFilterComposite extends org.eclipse.swt.widgets.Composite implements Serializable
      serialVersionUID:
      -4827398812522159453L

      • Serialized Fields

        • allButtons
          ArrayList<org.eclipse.swt.widgets.Button> allButtons
        • btnAllMutant
          org.eclipse.swt.widgets.Button btnAllMutant
        • btnBCSBroth
          org.eclipse.swt.widgets.Button btnBCSBroth
        • btnCellWall
          org.eclipse.swt.widgets.Button btnCellWall
        • btnChooseOneMutant
          org.eclipse.swt.widgets.Button btnChooseOneMutant
        • btnCytoplasm
          org.eclipse.swt.widgets.Button btnCytoplasm
        • btnDMEM
          org.eclipse.swt.widgets.Button btnDMEM
        • btnExponential
          org.eclipse.swt.widgets.Button btnExponential
        • btnHumanPlasma
          org.eclipse.swt.widgets.Button btnHumanPlasma
        • btnLbBroth
          org.eclipse.swt.widgets.Button btnLbBroth
        • btnMembrane
          org.eclipse.swt.widgets.Button btnMembrane
        • btnMinimalMediaBroth
          org.eclipse.swt.widgets.Button btnMinimalMediaBroth
        • btnNoneMutant
          org.eclipse.swt.widgets.Button btnNoneMutant
        • btnSecretome
          org.eclipse.swt.widgets.Button btnSecretome
        • btnStationnary
          org.eclipse.swt.widgets.Button btnStationnary
        • comboGenome
          org.eclipse.swt.widgets.Combo comboGenome
        • comboMutant
          org.eclipse.swt.widgets.Combo comboMutant
        • textSearch
          org.eclipse.swt.widgets.Text textSearch
        • view
          ProteomicsView view

    • Class bacnet.expressionAtlas.ProteomicsExpressionView

      class ProteomicsExpressionView extends Object implements Serializable
      serialVersionUID:
      3273618417542386059L

      • Serialized Fields

        • bioConds
          ArrayList<String[]> bioConds
          List used to init data
        • bioCondsArray
          String[][] bioCondsArray
          Array used to init data
        • bioCondsToDisplay
          ArrayList<String[]> bioCondsToDisplay
          Array which will be displayed
        • btnGenomeViewer
          org.eclipse.swt.widgets.Button btnGenomeViewer
        • btnHeatmap
          org.eclipse.swt.widgets.Button btnHeatmap
        • btnHelp
          org.eclipse.swt.widgets.Button btnHelp
        • btnSaveTxt
          org.eclipse.swt.widgets.Button btnSaveTxt
        • btnSelectall
          org.eclipse.swt.widgets.Button btnSelectall
        • btnUnselectall
          org.eclipse.swt.widgets.Button btnUnselectall
        • columnNames
          ArrayList<String> columnNames
        • comparatorBioCondition
          BioConditionComparator comparatorBioCondition
        • compositeDataFilter
          ProteomicsDataFilterComposite compositeDataFilter
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • imageGeneExpr
          org.eclipse.swt.graphics.Image imageGeneExpr
        • imageTSS
          org.eclipse.swt.graphics.Image imageTSS
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • selectedProteomes
          ArrayList<String> selectedProteomes
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tableProteome
          org.eclipse.swt.widgets.Table tableProteome
        • tableProteomeViewer
          org.eclipse.jface.viewers.TableViewer tableProteomeViewer

    • Class bacnet.expressionAtlas.ProteomicsView

      class ProteomicsView extends Object implements Serializable
      serialVersionUID:
      3273618417542386059L

      • Serialized Fields

        • bioConds
          ArrayList<String[]> bioConds
          List used to init data
        • bioCondsArray
          String[][] bioCondsArray
          Array used to init data
        • bioCondsToDisplay
          ArrayList<String[]> bioCondsToDisplay
          Array which will be displayed
        • btnGenomeViewer
          org.eclipse.swt.widgets.Button btnGenomeViewer
        • btnHeatmap
          org.eclipse.swt.widgets.Button btnHeatmap
        • btnHelp
          org.eclipse.swt.widgets.Button btnHelp
        • btnSaveTxt
          org.eclipse.swt.widgets.Button btnSaveTxt
        • btnSelectall
          org.eclipse.swt.widgets.Button btnSelectall
        • btnUnselectall
          org.eclipse.swt.widgets.Button btnUnselectall
        • columnNames
          ArrayList<String> columnNames
        • comparatorBioCondition
          BioConditionComparator comparatorBioCondition
        • compositeDataFilter
          ProteomicsDataFilterComposite compositeDataFilter
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • imageGeneExpr
          org.eclipse.swt.graphics.Image imageGeneExpr
        • imageTSS
          org.eclipse.swt.graphics.Image imageTSS
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • selectedProteomes
          ArrayList<String> selectedProteomes
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tableProteome
          org.eclipse.swt.widgets.Table tableProteome
        • tableProteomeViewer
          org.eclipse.jface.viewers.TableViewer tableProteomeViewer

    • Class bacnet.expressionAtlas.TableCompositeHeatMap

      class TableCompositeHeatMap extends org.eclipse.swt.widgets.Composite implements Serializable
      serialVersionUID:
      -5898609236718602892L

      • Serialized Fields

        • btnColormapper
          org.eclipse.swt.widgets.Button btnColormapper
        • btnDisplayValues
          org.eclipse.swt.widgets.Button btnDisplayValues
        • btnHelp
          org.eclipse.swt.widgets.Button btnHelp
        • btnHide
          org.eclipse.swt.widgets.Button btnHide
        • btnSaveText
          org.eclipse.swt.widgets.Button btnSaveText
        • btnZoomIn
          org.eclipse.swt.widgets.Button btnZoomIn
        • btnZoomOut
          org.eclipse.swt.widgets.Button btnZoomOut
        • colorMapperList
          ColorMapperList colorMapperList
        • columnNames
          ArrayList<String> columnNames
        • comparator
          TableViewerComparator comparator
        • composite
          org.eclipse.swt.widgets.Composite composite
        • composite_4
          org.eclipse.swt.widgets.Composite composite_4
        • displayValues
          boolean displayValues
        • excludeColumn
          ArrayList<String> excludeColumn
        • excludeRow
          ArrayList<String> excludeRow
        • genomeName
          String genomeName
        • labelColumn
          org.eclipse.swt.widgets.Label labelColumn
        • labelRow
          org.eclipse.swt.widgets.Label labelRow
        • lblX
          org.eclipse.swt.widgets.Label lblX
        • matrix
          ExpressionMatrix matrix
        • matrixDisplayed
          ExpressionMatrix matrixDisplayed
        • matrixSize
          MatrixSize matrixSize
        • packColumns
          boolean packColumns
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • searchFilter
          TableFilter searchFilter
        • shell
          org.eclipse.swt.widgets.Shell shell
        • table
          org.eclipse.swt.widgets.Table table
        • tableViewer
          org.eclipse.jface.viewers.TableViewer tableViewer
        • transcriptomics
          boolean transcriptomics
          Boolean describing if it is a transcriptomics or proteomic heatmap viewer

    • Class bacnet.expressionAtlas.TranscriptomicsDataFilterComposite

      class TranscriptomicsDataFilterComposite extends org.eclipse.swt.widgets.Composite implements Serializable
      serialVersionUID:
      7804472924985182424L

      • Serialized Fields

        • allButtons
          ArrayList<org.eclipse.swt.widgets.Button> allButtons
        • btnAllMutant
          org.eclipse.swt.widgets.Button btnAllMutant
        • btnChooseOneMutant
          org.eclipse.swt.widgets.Button btnChooseOneMutant
        • btnDeath
          org.eclipse.swt.widgets.Button btnDeath
        • btnExponential
          org.eclipse.swt.widgets.Button btnExponential
        • btnGeneExpression
          org.eclipse.swt.widgets.Button btnGeneExpression
        • btnLagPhase
          org.eclipse.swt.widgets.Button btnLagPhase
        • btnNoneMutant
          org.eclipse.swt.widgets.Button btnNoneMutant
        • btnRegrowth
          org.eclipse.swt.widgets.Button btnRegrowth
        • btnRiboSeq
          org.eclipse.swt.widgets.Button btnRiboSeq
        • btnRnaseq
          org.eclipse.swt.widgets.Button btnRnaseq
        • btnStationnary
          org.eclipse.swt.widgets.Button btnStationnary
        • btnSurvival
          org.eclipse.swt.widgets.Button btnSurvival
        • btnTermSeq
          org.eclipse.swt.widgets.Button btnTermSeq
        • btnTiling
          org.eclipse.swt.widgets.Button btnTiling
        • btnTss
          org.eclipse.swt.widgets.Button btnTss
        • btnUnpublished
          org.eclipse.swt.widgets.Button btnUnpublished
        • comboGenome
          org.eclipse.swt.widgets.Combo comboGenome
        • comboMutant
          org.eclipse.swt.widgets.Combo comboMutant
        • textSearch
          org.eclipse.swt.widgets.Text textSearch
        • view
          TranscriptomicsView view

    • Class bacnet.expressionAtlas.TranscriptomicsView

      class TranscriptomicsView extends Object implements Serializable
      serialVersionUID:
      -5118476676200457964L

      • Serialized Fields

        • bioConds
          ArrayList<String[]> bioConds
          List used to init data
        • bioCondsArray
          String[][] bioCondsArray
          Array used to init data
        • bioCondsToDisplay
          ArrayList<String[]> bioCondsToDisplay
          Array which will be displayed
        • btnExpressionAtlas
          org.eclipse.swt.widgets.Button btnExpressionAtlas
        • btnGenomeViewer
          org.eclipse.swt.widgets.Button btnGenomeViewer
        • btnHelp
          org.eclipse.swt.widgets.Button btnHelp
        • btnSaveTxt
          org.eclipse.swt.widgets.Button btnSaveTxt
        • btnSelectall
          org.eclipse.swt.widgets.Button btnSelectall
        • btnUnselectall
          org.eclipse.swt.widgets.Button btnUnselectall
        • columnNames
          ArrayList<String> columnNames
        • comparatorBioCondition
          BioConditionComparator comparatorBioCondition
        • compositeDataFilter
          TranscriptomicsDataFilterComposite compositeDataFilter
          Composite to filter list of data
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • imageGeneExpr
          org.eclipse.swt.graphics.Image imageGeneExpr
        • imageRNASeq
          org.eclipse.swt.graphics.Image imageRNASeq
        • imageTiling
          org.eclipse.swt.graphics.Image imageTiling
        • imageTilingGeneExpr
          org.eclipse.swt.graphics.Image imageTilingGeneExpr
        • imageTSS
          org.eclipse.swt.graphics.Image imageTSS
        • imageTSSTilingGeneExpr
          org.eclipse.swt.graphics.Image imageTSSTilingGeneExpr
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • selectedTranscriptomes
          ArrayList<String> selectedTranscriptomes
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tableBioCondition
          org.eclipse.swt.widgets.Table tableBioCondition
        • tableBioConditionViewer
          org.eclipse.jface.viewers.TableViewer tableBioConditionViewer

  • Package bacnet.expressionAtlas.core

    • Class bacnet.expressionAtlas.core.ComparisonAtlas

      class ComparisonAtlas extends Object implements Serializable
      serialVersionUID:
      3461420201661554414L

      • Serialized Fields

        • excludeRows
          ArrayList<String> excludeRows
        • name
          String name
        • notDiffExpressedASrnas
          String[] notDiffExpressedASrnas
        • notDiffExpressedCisRegs
          String[] notDiffExpressedCisRegs
        • notDiffExpressedGenes
          String[] notDiffExpressedGenes
        • notDiffExpressedSrnas
          String[] notDiffExpressedSrnas
        • overASrnas
          String[] overASrnas
        • overCisRegs
          String[] overCisRegs
        • overExpressed
          ArrayList<String> overExpressed
        • overGenes
          String[] overGenes
        • overSrnas
          String[] overSrnas
        • underASrnas
          String[] underASrnas
        • underCisRegs
          String[] underCisRegs
        • underExpressed
          ArrayList<String> underExpressed
        • underGenes
          String[] underGenes
        • underSrnas
          String[] underSrnas

    • Class bacnet.expressionAtlas.core.GenomeElementAtlas

      class GenomeElementAtlas extends Object implements Serializable
      serialVersionUID:
      6277013816841128158L

    • Class bacnet.expressionAtlas.core.SelectGenomeElementDialog

      class SelectGenomeElementDialog extends org.eclipse.jface.dialogs.TitleAreaDialog implements Serializable
      serialVersionUID:
      3481072975746172059L

      • Serialized Fields

        • btnDeselAS
          org.eclipse.swt.widgets.Button btnDeselAS
        • btnDeselGene
          org.eclipse.swt.widgets.Button btnDeselGene
        • btnDeselRNA
          org.eclipse.swt.widgets.Button btnDeselRNA
        • btnLoad
          org.eclipse.swt.widgets.Button btnLoad
        • btnSave
          org.eclipse.swt.widgets.Button btnSave
        • btnSelectAS
          org.eclipse.swt.widgets.Button btnSelectAS
        • btnSelectGene
          org.eclipse.swt.widgets.Button btnSelectGene
        • btnSelectRNA
          org.eclipse.swt.widgets.Button btnSelectRNA
        • btnSelectSpecificList
          org.eclipse.swt.widgets.Button btnSelectSpecificList
        • composite
          org.eclipse.swt.widgets.Composite composite
        • compositeButton
          org.eclipse.swt.widgets.Composite compositeButton
        • excludedElements
          TreeSet<String> excludedElements
        • includeElements
          TreeSet<String> includeElements
        • listasRNAs
          ArrayList<String> listasRNAs
        • listcisRegs
          ArrayList<String> listcisRegs
        • listGenes
          ArrayList<String> listGenes
        • listsRNAs
          ArrayList<String> listsRNAs
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • rFamAnnot
          boolean rFamAnnot
        • scrolledComposite
          org.eclipse.swt.custom.ScrolledComposite scrolledComposite
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tableASRNAs
          org.eclipse.swt.widgets.Table tableASRNAs
        • tableGenes
          org.eclipse.swt.widgets.Table tableGenes
        • tableSRNAs
          org.eclipse.swt.widgets.Table tableSRNAs

    • Class bacnet.expressionAtlas.core.SignatureSelectionDialog

      class SignatureSelectionDialog extends org.eclipse.jface.dialogs.TitleAreaDialog implements Serializable
      serialVersionUID:
      1941320621284175887L

      • Serialized Fields

        • composite_1
          org.eclipse.swt.widgets.Composite composite_1
        • lblDescription
          org.eclipse.swt.widgets.Label lblDescription
        • lblGenesInclude
          org.eclipse.swt.widgets.Label lblGenesInclude
        • lblGenome
          org.eclipse.swt.widgets.Label lblGenome
        • lblID
          org.eclipse.swt.widgets.Label lblID
        • lblName
          org.eclipse.swt.widgets.Label lblName
        • lblRef
          org.eclipse.swt.widgets.Label lblRef
        • lblSelectYourList
          org.eclipse.swt.widgets.Label lblSelectYourList
        • lblSize
          org.eclipse.swt.widgets.Label lblSize
        • listGenes
          org.eclipse.swt.widgets.List listGenes
        • signature
          Signature signature
        • signatures
          ArrayList<String> signatures
        • tableSignature
          org.eclipse.swt.widgets.Table tableSignature
        • txtDescription
          org.eclipse.swt.widgets.Text txtDescription

  • Package bacnet.genomeBrowser

    • Class bacnet.genomeBrowser.CompositeNTermInfo

      class CompositeNTermInfo extends org.eclipse.swt.widgets.Composite implements Serializable
      serialVersionUID:
      -9089207362586510739L

      • Serialized Fields

        • lblMaxquant
          org.eclipse.swt.widgets.Label lblMaxquant
        • lblModifv
          org.eclipse.swt.widgets.Label lblModifv
        • lblOverlap
          org.eclipse.swt.widgets.Label lblOverlap
        • lblPosition
          org.eclipse.swt.widgets.Label lblPosition
        • lblSize
          org.eclipse.swt.widgets.Label lblSize
        • lblSpectrav
          org.eclipse.swt.widgets.Label lblSpectrav
        • lblType
          org.eclipse.swt.widgets.Label lblType
        • txtSequence
          org.eclipse.swt.widgets.Text txtSequence

    • Class bacnet.genomeBrowser.NTerminomicsView

      class NTerminomicsView extends Object implements Serializable
      serialVersionUID:
      -4058433027371889806L

      • Serialized Fields

        • bioConds
          ArrayList<String[]> bioConds
        • bioCondsArray
          String[][] bioCondsArray
          Array used to init data
        • bioCondsToDisplay
          ArrayList<String[]> bioCondsToDisplay
        • btnHide
          org.eclipse.swt.widgets.Button btnHide
        • btnSaveTxt
          org.eclipse.swt.widgets.Button btnSaveTxt
        • columnNames
          ArrayList<String> columnNames
        • comparatorBioCondition
          BioConditionComparator comparatorBioCondition
        • compositeSummary
          org.eclipse.swt.widgets.Composite compositeSummary
        • focused
          boolean focused
        • lblXxSrnas
          org.eclipse.swt.widgets.Label lblXxSrnas
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • selectedNTerms
          ArrayList<String> selectedNTerms
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tableBioCondition
          org.eclipse.jface.viewers.TableViewer tableBioCondition
        • txtSearch
          org.eclipse.swt.widgets.Text txtSearch

  • Package bacnet.genomeBrowser.core

    • Class bacnet.genomeBrowser.core.Region

      class Region extends Object implements Serializable
      serialVersionUID:
      -1103556086987455111L

      • Serialized Fields

        • height
          int height
        • middleH
          int middleH
        • middleV
          int middleV
        • regionChanged
          boolean regionChanged
        • width
          int width
        • x1
          int x1
        • x2
          int x2
        • y1
          int y1
        • y2
          int y2

    • Class bacnet.genomeBrowser.core.Track

      class Track extends Object implements Serializable
      serialVersionUID:
      4061565768191225185L

      • Serialized Fields

        • chromosomeID
          String chromosomeID
        • dataRegion
          Region dataRegion
        • datas
          DataTrack datas
        • displayRegion
          Region displayRegion
        • displaySequence
          boolean displaySequence
        • displayType
          Track.DisplayType displayType
        • genomeName
          String genomeName
        • trackChangedFlag
          boolean trackChangedFlag
        • zoom
          Zoom zoom

    • Class bacnet.genomeBrowser.core.Zoom

      class Zoom extends Object implements Serializable
      serialVersionUID:
      5926414787821636159L

      • Serialized Fields

        • totalBP
          int totalBP
        • zoomChangedFlag
          boolean zoomChangedFlag
        • zoomHeightMax
          int zoomHeightMax
          Maximal value for the zoom
        • zoomHeightPosition
          int zoomHeightPosition
          Position of the zoom for height
        • zoomNumber
          int zoomNumber
        • zoomPosition
          int zoomPosition
        • zoomRatio
          double zoomRatio

  • Package bacnet.genomeBrowser.dialog

    • Class bacnet.genomeBrowser.dialog.AddProteomicsDataDialog

      class AddProteomicsDataDialog extends org.eclipse.jface.dialogs.TitleAreaDialog implements Serializable
      serialVersionUID:
      -8202496409867913492L

      • Serialized Fields

        • bioConds
          ArrayList<String[]> bioConds
          List used to init data
        • bioCondsArray
          String[][] bioCondsArray
          Array used to init data
        • bioCondsToDisplay
          ArrayList<String[]> bioCondsToDisplay
          Array which will be displayed
        • btnBhiBroth
          org.eclipse.swt.widgets.Button btnBhiBroth
        • btnCellWall
          org.eclipse.swt.widgets.Button btnCellWall
        • btnCytoplasm
          org.eclipse.swt.widgets.Button btnCytoplasm
        • btnExponential
          org.eclipse.swt.widgets.Button btnExponential
        • btnHumanBloodCells
          org.eclipse.swt.widgets.Button btnHumanBloodCells
        • btnLbBroth
          org.eclipse.swt.widgets.Button btnLbBroth
        • btnMembrane
          org.eclipse.swt.widgets.Button btnMembrane
        • btnMinimalMediaBroth
          org.eclipse.swt.widgets.Button btnMinimalMediaBroth
        • btnMouseMacrophagesCells
          org.eclipse.swt.widgets.Button btnMouseMacrophagesCells
        • btnSecretome
          org.eclipse.swt.widgets.Button btnSecretome
        • btnStationnary
          org.eclipse.swt.widgets.Button btnStationnary
        • btnUnpublished
          org.eclipse.swt.widgets.Button btnUnpublished
        • columnNames
          ArrayList<String> columnNames
        • comboGenome
          org.eclipse.swt.widgets.Combo comboGenome
        • comparatorBioCondition
          BioConditionComparator comparatorBioCondition
        • imageGeneExpr
          org.eclipse.swt.graphics.Image imageGeneExpr
        • imageRNASeq
          org.eclipse.swt.graphics.Image imageRNASeq
        • imageTilingGeneExpr
          org.eclipse.swt.graphics.Image imageTilingGeneExpr
        • imageTSS
          org.eclipse.swt.graphics.Image imageTSS
        • imageTSSTilingGeneExpr
          org.eclipse.swt.graphics.Image imageTSSTilingGeneExpr
        • lblTssAvailable
          org.eclipse.swt.widgets.Label lblTssAvailable
        • lblTSSImage
          org.eclipse.swt.widgets.Label lblTSSImage
        • tableBioCondition
          org.eclipse.jface.viewers.TableViewer tableBioCondition
        • textSearch
          org.eclipse.swt.widgets.Text textSearch
        • track
          Track track

    • Class bacnet.genomeBrowser.dialog.AddTranscriptomicsDataDialog

      class AddTranscriptomicsDataDialog extends org.eclipse.jface.dialogs.TitleAreaDialog implements Serializable
      serialVersionUID:
      -2962428673771724278L

      • Serialized Fields

        • bioConds
          ArrayList<String[]> bioConds
          List used to init data
        • bioCondsArray
          String[][] bioCondsArray
          Array used to init data
        • bioCondsToDisplay
          ArrayList<String[]> bioCondsToDisplay
          Array which will be displayed
        • btnAllMutant
          org.eclipse.swt.widgets.Button btnAllMutant
        • btnBhiBroth
          org.eclipse.swt.widgets.Button btnBhiBroth
        • btnCacoCells
          org.eclipse.swt.widgets.Button btnCacoCells
        • btnChooseOneMutant
          org.eclipse.swt.widgets.Button btnChooseOneMutant
        • btnDeath
          org.eclipse.swt.widgets.Button btnDeath
        • btnExponential
          org.eclipse.swt.widgets.Button btnExponential
        • btnGeneExpression
          org.eclipse.swt.widgets.Button btnGeneExpression
        • btnHumanBloodCells
          org.eclipse.swt.widgets.Button btnHumanBloodCells
        • btnLagPhase
          org.eclipse.swt.widgets.Button btnLagPhase
        • btnLbBroth
          org.eclipse.swt.widgets.Button btnLbBroth
        • btnMinimalMediaBroth
          org.eclipse.swt.widgets.Button btnMinimalMediaBroth
        • btnMouseIntestineCells
          org.eclipse.swt.widgets.Button btnMouseIntestineCells
        • btnMouseMacrophagesCells
          org.eclipse.swt.widgets.Button btnMouseMacrophagesCells
        • btnMouseSpleenCells
          org.eclipse.swt.widgets.Button btnMouseSpleenCells
        • btnNoneMutant
          org.eclipse.swt.widgets.Button btnNoneMutant
        • btnPorcineBileCells
          org.eclipse.swt.widgets.Button btnPorcineBileCells
        • btnRegrowth
          org.eclipse.swt.widgets.Button btnRegrowth
        • btnRiboSeq
          org.eclipse.swt.widgets.Button btnRiboSeq
        • btnRnaseq
          org.eclipse.swt.widgets.Button btnRnaseq
        • btnStationnary
          org.eclipse.swt.widgets.Button btnStationnary
        • btnSurvival
          org.eclipse.swt.widgets.Button btnSurvival
        • btnTermSeq
          org.eclipse.swt.widgets.Button btnTermSeq
        • btnTiling
          org.eclipse.swt.widgets.Button btnTiling
        • btnTrypticSoyBroth
          org.eclipse.swt.widgets.Button btnTrypticSoyBroth
        • btnTss
          org.eclipse.swt.widgets.Button btnTss
        • btnTurkeyDeliMeat
          org.eclipse.swt.widgets.Button btnTurkeyDeliMeat
        • btnUnpublished
          org.eclipse.swt.widgets.Button btnUnpublished
        • columnNames
          ArrayList<String> columnNames
        • comboGenome
          org.eclipse.swt.widgets.Combo comboGenome
        • comboMutant
          org.eclipse.swt.widgets.Combo comboMutant
        • comparatorBioCondition
          BioConditionComparator comparatorBioCondition
        • imageGeneExpr
          org.eclipse.swt.graphics.Image imageGeneExpr
        • imageRNASeq
          org.eclipse.swt.graphics.Image imageRNASeq
        • imageTilingGeneExpr
          org.eclipse.swt.graphics.Image imageTilingGeneExpr
        • imageTSS
          org.eclipse.swt.graphics.Image imageTSS
        • imageTSSTilingGeneExpr
          org.eclipse.swt.graphics.Image imageTSSTilingGeneExpr
        • tableBioCondition
          org.eclipse.jface.viewers.TableViewer tableBioCondition
        • textSearch
          org.eclipse.swt.widgets.Text textSearch
        • track
          Track track

    • Class bacnet.genomeBrowser.dialog.LegendDialog

      class LegendDialog extends org.eclipse.jface.dialogs.TitleAreaDialog implements Serializable
      serialVersionUID:
      3331773901037609884L

      • Serialized Fields

        • btnRemoveSelectedBiological
          org.eclipse.swt.widgets.Button btnRemoveSelectedBiological
        • imageChecked
          org.eclipse.swt.graphics.Image imageChecked
        • imageGeneExpr
          org.eclipse.swt.graphics.Image imageGeneExpr
        • imageRNASeq
          org.eclipse.swt.graphics.Image imageRNASeq
        • imageTilingGeneExpr
          org.eclipse.swt.graphics.Image imageTilingGeneExpr
        • imageTSS
          org.eclipse.swt.graphics.Image imageTSS
        • imageTSSTilingGeneExpr
          org.eclipse.swt.graphics.Image imageTSSTilingGeneExpr
        • imageUnchecked
          org.eclipse.swt.graphics.Image imageUnchecked
        • scrolledComposite
          org.eclipse.swt.custom.ScrolledComposite scrolledComposite
        • tableBioCondition
          org.eclipse.swt.widgets.Table tableBioCondition
        • tableData
          org.eclipse.swt.widgets.Table tableData
        • track
          Track track

  • Package bacnet.genomeBrowser.tracksGUI

    • Class bacnet.genomeBrowser.tracksGUI.TrackCanvasData

      class TrackCanvasData extends org.eclipse.swt.widgets.Canvas implements Serializable
      serialVersionUID:
      1080025663659839957L

      • Serialized Fields

        • annotation
          Annotation annotation
          Annotation data for all Genome information
        • bpSizeH
          double bpSizeH
          Width in pixel of one base pair (fundamental unit for the rest of the display)
        • chromoID
          String chromoID
        • dataSizeReference
          int dataSizeReference
          Height of on data
        • dataWindowSize
          int dataWindowSize
          Height of all the data window = all data combine
        • decaySliderVBar
          int decaySliderVBar
          Vertical decay imposed by the vertical slider
        • displayMouseLine
          boolean displayMouseLine
          If true we display a vertical line at the pointer of the mouse
        • genomeName
          String genomeName
        • heightPix
          int heightPix
          Height in pixels of the drawing area
        • massSpecData
          NTermData massSpecData
          MassSpecData where the selected NTerm is
        • MINIMUM_DATA_SIZE
          int MINIMUM_DATA_SIZE
          Minimal height of a data track
        • mouseXPosition
          int mouseXPosition
          When mouse is clicked we displayed a line is displayed to show synteny: mouseYPosition gives the X position
        • mouseYPosition
          int mouseYPosition
          When mouse is clicked we displayed a line is displayed to show synteny: mouseYPosition gives the Y position
        • Name
          String Name
        • nTermHighlight
          NTerm nTermHighlight
          NTerm which will be highlighted
        • nTermTypeOverlap
          String nTermTypeOverlap
          Type of NTerm to display, if = All display all types
        • saveData
          TreeMap<String,String[][]> saveData
        • sequenceHeight
          int sequenceHeight
          Height of the sequence track
        • testData
          boolean testData
        • track
          Track track
          All information about the data to display
        • trackComposite
          org.eclipse.swt.widgets.Composite trackComposite
        • widthBP
          int widthBP
          Width in Base pairs of the drawing area
        • zoomVertical
          double zoomVertical
          Vertical zoom

    • Class bacnet.genomeBrowser.tracksGUI.TrackCanvasGenome

      class TrackCanvasGenome extends org.eclipse.swt.widgets.Canvas implements Serializable
      serialVersionUID:
      1080025663659839957L

      • Serialized Fields

        • annotation
          Annotation annotation
          Annotation data for all Genome information
        • annotElementHeight
          int annotElementHeight
          Height of one annnotation element
        • annotNumber
          float annotNumber
        • annotSeparationHeight
          int annotSeparationHeight
          Height of the separation between two annotation element
        • annotSeparationNumber
          int annotSeparationNumber
        • bpSizeH
          double bpSizeH
          Width in pixel of one base pair (fundamental unit for the rest of the display)
        • displayMouseLine
          boolean displayMouseLine
          If true we display a vertical line at the pointer of the mouse
        • heightPix
          int heightPix
        • mouseXPosition
          int mouseXPosition
          When mouse is clicked we displayed a line is displayed to show synteny: mouseYPosition gives the X position
        • mouseYPosition
          int mouseYPosition
          When mouse is clicked we displayed a line is displayed to show synteny: mouseYPosition gives the Y position
        • track
          Track track
          data to display
        • widthBP
          int widthBP

    • Class bacnet.genomeBrowser.tracksGUI.TracksComposite

      class TracksComposite extends org.eclipse.swt.widgets.Composite implements Serializable
      serialVersionUID:
      -1957427699848660677L

      • Serialized Fields

        • btnAddProteomicsData
          org.eclipse.swt.widgets.Button btnAddProteomicsData
        • btnAddTranscriptomicsData
          org.eclipse.swt.widgets.Button btnAddTranscriptomicsData
        • btnHelp
          org.eclipse.swt.widgets.Button btnHelp
        • btnHideNterminomicsPanel
          org.eclipse.swt.widgets.Button btnHideNterminomicsPanel
        • btnLegendManagement
          org.eclipse.swt.widgets.Button btnLegendManagement
        • btnLoadData
          org.eclipse.swt.widgets.Button btnLoadData
        • btnNextnterm
          org.eclipse.swt.widgets.Button btnNextnterm
        • btnPreviousnterm
          org.eclipse.swt.widgets.Button btnPreviousnterm
        • btnSaveDataSelection
          org.eclipse.swt.widgets.Button btnSaveDataSelection
        • btnSequence
          org.eclipse.swt.widgets.Button btnSequence
        • btnZoomIn
          org.eclipse.swt.widgets.Button btnZoomIn
        • btnZoomInVertical
          org.eclipse.swt.widgets.Button btnZoomInVertical
        • btnZoomOut
          org.eclipse.swt.widgets.Button btnZoomOut
        • btnZoomOutVertical
          org.eclipse.swt.widgets.Button btnZoomOutVertical
        • canvasData
          TrackCanvasData canvasData
        • canvasGenome
          TrackCanvasGenome canvasGenome
        • cmpNTermInfo
          org.eclipse.swt.widgets.Composite cmpNTermInfo
        • comboAbsoluteRelative
          org.eclipse.swt.widgets.Combo comboAbsoluteRelative
        • comboChromosome
          org.eclipse.swt.widgets.Combo comboChromosome
        • comboNTermData
          org.eclipse.swt.widgets.Combo comboNTermData
        • comboNTermFilter
          org.eclipse.swt.widgets.Combo comboNTermFilter
        • comboTypeDisplay
          org.eclipse.swt.widgets.Combo comboTypeDisplay
        • compositeAddData
          org.eclipse.swt.widgets.Composite compositeAddData
        • compositeChromosome
          org.eclipse.swt.widgets.Composite compositeChromosome
        • compositeGenome_1
          org.eclipse.swt.widgets.Composite compositeGenome_1
        • compositeNterm
          CompositeNTermInfo compositeNterm
        • compositeTypeDisplay
          org.eclipse.swt.widgets.Composite compositeTypeDisplay
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • gridDataCmpInfo
          org.eclipse.swt.layout.GridData gridDataCmpInfo
        • hideInfo
          org.eclipse.swt.layout.GridLayout hideInfo
        • lblTutorial
          org.eclipse.swt.widgets.Label lblTutorial
        • massSpecData
          NTermData massSpecData
          MassSpecData where the selected NTerm is
        • nTerm
          NTerm nTerm
          Selected NTerm
        • parentViewId
          String parentViewId
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • shell
          org.eclipse.swt.widgets.Shell shell
        • showInfo
          org.eclipse.swt.layout.GridLayout showInfo
        • sliderHbar
          org.eclipse.swt.widgets.Slider sliderHbar
        • sliderVBar
          org.eclipse.swt.widgets.Slider sliderVBar
        • tableNtermInfo
          org.eclipse.swt.widgets.Table tableNtermInfo
        • track
          Track track
        • transcriptome
          boolean transcriptome

  • Package bacnet.scripts.genome

  • Package bacnet.sequenceTools

    • Class bacnet.sequenceTools.AnnotationView

      class AnnotationView extends Object implements Serializable
      serialVersionUID:
      -4058433027371889806L

      • Serialized Fields

        • bioConds
          ArrayList<String[]> bioConds
        • bioCondsArray
          String[][] bioCondsArray
          Array used to init data
        • bioCondsToDisplay
          ArrayList<String[]> bioCondsToDisplay
        • btnHide
          org.eclipse.swt.widgets.Button btnHide
        • btnSaveTxt
          org.eclipse.swt.widgets.Button btnSaveTxt
        • btnSelectall
          org.eclipse.swt.widgets.Button btnSelectall
        • btnUnselectall
          org.eclipse.swt.widgets.Button btnUnselectall
        • columnNames
          ArrayList<String> columnNames
        • comparatorBioCondition
          BioConditionComparator comparatorBioCondition
        • compositeSummary
          org.eclipse.swt.widgets.Composite compositeSummary
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • genome
          Genome genome
        • lblXxSrnas
          org.eclipse.swt.widgets.Label lblXxSrnas
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • selectedGenes
          ArrayList<String> selectedGenes
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tableBioCondition
          org.eclipse.jface.viewers.TableViewer tableBioCondition
        • txtSearch
          org.eclipse.swt.widgets.Text txtSearch
        • viewID
          String viewID

    • Class bacnet.sequenceTools.GeneView

      class GeneView extends Object implements Serializable
      serialVersionUID:
      -5632436594051134260L

      • Serialized Fields

        • arrayDataList
          String[][] arrayDataList
        • arrayGeneToLocalization
          String[][] arrayGeneToLocalization
        • arrayProteinAtlasList
          String[][] arrayProteinAtlasList
        • arrayProteomeList
          String[][] arrayProteomeList
        • arrayTranscriptomesList
          String[][] arrayTranscriptomesList
        • bioConds
          ArrayList<String[]> bioConds
          List used to init data
        • bioCondsArray
          String[][] bioCondsArray
          Array used to init data
        • bioCondsToDisplay
          ArrayList<String[]> bioCondsToDisplay
          Array which will be displayed
        • browserHomolog
          org.eclipse.swt.browser.Browser browserHomolog
        • browserIsFocus
          boolean browserIsFocus
        • browserLocalization
          org.eclipse.swt.browser.Browser browserLocalization
        • browserSynteny
          org.eclipse.swt.browser.Browser browserSynteny
        • btnAminoAcidSequence
          org.eclipse.swt.widgets.Button btnAminoAcidSequence
        • btnDonwloadtxt
          org.eclipse.swt.widgets.Button btnDonwloadtxt
        • btnExportToFasta
          org.eclipse.swt.widgets.Button btnExportToFasta
        • btnGenomeViewer
          org.eclipse.swt.widgets.Button btnGenomeViewer
        • btnGenomeViewerProteome
          org.eclipse.swt.widgets.Button btnGenomeViewerProteome
        • btnGetAnnotationInformation
          org.eclipse.swt.widgets.Button btnGetAnnotationInformation
        • btnHeatmapview
          org.eclipse.swt.widgets.Button btnHeatmapview
        • btnHeatmapviewProteome
          org.eclipse.swt.widgets.Button btnHeatmapviewProteome
        • btnHelp
          org.eclipse.swt.widgets.Button btnHelp
        • btnLocalization
          org.eclipse.swt.widgets.Button btnLocalization
        • btnNcbiChromosome
          org.eclipse.swt.widgets.Button btnNcbiChromosome
        • btnNucleotideSequence
          org.eclipse.swt.widgets.Button btnNucleotideSequence
        • btnSaveAsPng
          org.eclipse.swt.widgets.Button btnSaveAsPng
        • btnSaveAsSvg
          org.eclipse.swt.widgets.Button btnSaveAsSvg
        • btnSelectall
          org.eclipse.swt.widgets.Button btnSelectall
        • btnUnselectall
          org.eclipse.swt.widgets.Button btnUnselectall
        • btnUpdateCutoff
          org.eclipse.swt.widgets.Button btnUpdateCutoff
        • btnUpdateCutoffProteome
          org.eclipse.swt.widgets.Button btnUpdateCutoffProteome
        • btnZoomminus
          org.eclipse.swt.widgets.Button btnZoomminus
        • btnZoomplus
          org.eclipse.swt.widgets.Button btnZoomplus
        • canvasGenome
          TrackCanvasGenome canvasGenome
        • chromoID
          String chromoID
        • columnNames
          ArrayList<String> columnNames
        • comboChromosome
          org.eclipse.swt.widgets.Combo comboChromosome
        • comboGenome
          org.eclipse.swt.widgets.Combo comboGenome
        • comparatorBioCondition
          BioConditionComparator comparatorBioCondition
        • composite_09
          org.eclipse.swt.widgets.Composite composite_09
        • composite_091
          org.eclipse.swt.widgets.Composite composite_091
        • composite_092
          org.eclipse.swt.widgets.Composite composite_092
        • composite_101
          org.eclipse.swt.widgets.Composite composite_101
        • composite_102
          org.eclipse.swt.widgets.Composite composite_102
        • composite_103
          org.eclipse.swt.widgets.Composite composite_103
        • composite_13
          org.eclipse.swt.widgets.Composite composite_13
        • composite_14
          org.eclipse.swt.widgets.Composite composite_14
        • composite_15
          org.eclipse.swt.widgets.Composite composite_15
        • composite_localization
          org.eclipse.swt.widgets.Composite composite_localization
        • compositeGenome
          org.eclipse.swt.widgets.Composite compositeGenome
        • compositeInteractome
          org.eclipse.swt.widgets.Composite compositeInteractome
        • compositeProteome
          org.eclipse.swt.widgets.Composite compositeProteome
        • compositeSynteny
          org.eclipse.swt.widgets.Composite compositeSynteny
        • compositeTranscriptome
          org.eclipse.swt.widgets.Composite compositeTranscriptome
        • compSuppInfo
          org.eclipse.swt.widgets.Composite compSuppInfo
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • genome
          Genome genome
          Egde Genome loaded
        • lblBegin
          org.eclipse.swt.widgets.Text lblBegin
        • lblCog
          org.eclipse.swt.widgets.Text lblCog
        • lblConservation
          org.eclipse.swt.widgets.Text lblConservation
        • lblConservation2
          org.eclipse.swt.widgets.Label lblConservation2
        • lblEnd
          org.eclipse.swt.widgets.Text lblEnd
        • lblExprProteomes
          org.eclipse.swt.widgets.Label lblExprProteomes
        • lblExprTranscriptomes
          org.eclipse.swt.widgets.Label lblExprTranscriptomes
        • lblGene
          org.eclipse.swt.widgets.Label lblGene
        • lblLocus
          org.eclipse.swt.widgets.Text lblLocus
        • lblName
          org.eclipse.swt.widgets.Text lblName
        • lblNodiff
          org.eclipse.swt.widgets.Label lblNodiff
        • lblNodiffProteome
          org.eclipse.swt.widgets.Label lblNodiffProteome
        • lblOperon
          org.eclipse.swt.widgets.Text lblOperon
        • lblOver
          org.eclipse.swt.widgets.Label lblOver
        • lblOverProteome
          org.eclipse.swt.widgets.Label lblOverProteome
        • lblPredictedSubcellularLocalization
          org.eclipse.swt.widgets.Label lblPredictedSubcellularLocalization
        • lblProduct
          org.eclipse.swt.widgets.Text lblProduct
        • lblProtID
          org.eclipse.swt.widgets.Label lblProtID
        • lblSizeaa
          org.eclipse.swt.widgets.Text lblSizeaa
        • lblSizeBP
          org.eclipse.swt.widgets.Text lblSizeBP
        • lblStrand
          org.eclipse.swt.widgets.Text lblStrand
        • lblTranscriptomesData
          org.eclipse.swt.widgets.Label lblTranscriptomesData
        • lblUnder
          org.eclipse.swt.widgets.Label lblUnder
        • lblUnderProteome
          org.eclipse.swt.widgets.Label lblUnderProteome
        • listGenes
          ArrayList<String> listGenes
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • selectedGenomes
          ArrayList<String> selectedGenomes
        • sequence
          Gene sequence
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tabFolder
          org.eclipse.swt.widgets.TabFolder tabFolder
        • tableGenes
          org.eclipse.swt.widgets.Table tableGenes
        • tableHomolog
          org.eclipse.swt.widgets.Table tableHomolog
        • tableHomologViewer
          org.eclipse.jface.viewers.TableViewer tableHomologViewer
        • tableNodiff
          org.eclipse.swt.widgets.Table tableNodiff
        • tableNodiffProteome
          org.eclipse.swt.widgets.Table tableNodiffProteome
        • tableOver
          org.eclipse.swt.widgets.Table tableOver
        • tableOverProteome
          org.eclipse.swt.widgets.Table tableOverProteome
        • tableProteomes
          org.eclipse.swt.widgets.Table tableProteomes
        • tableTranscriptomes
          org.eclipse.swt.widgets.Table tableTranscriptomes
        • tableUnder
          org.eclipse.swt.widgets.Table tableUnder
        • tableUnderProteome
          org.eclipse.swt.widgets.Table tableUnderProteome
        • tbtmExpressionData
          org.eclipse.swt.widgets.TabItem tbtmExpressionData
        • tbtmGeneralInformation
          org.eclipse.swt.widgets.TabItem tbtmGeneralInformation
        • tbtmHomologs
          org.eclipse.swt.widgets.TabItem tbtmHomologs
        • tbtmInteractome
          org.eclipse.swt.widgets.TabItem tbtmInteractome
        • tbtmProteomeData
          org.eclipse.swt.widgets.TabItem tbtmProteomeData
        • tbtmProteomes
          org.eclipse.swt.widgets.TabItem tbtmProteomes
        • tbtmSynteny
          org.eclipse.swt.widgets.TabItem tbtmSynteny
        • tbtmTranscriptomes
          org.eclipse.swt.widgets.TabItem tbtmTranscriptomes
        • textFeature
          org.eclipse.swt.widgets.Text textFeature
        • trackGenome
          Track trackGenome
        • txtCutoffLogFC
          org.eclipse.swt.widgets.Text txtCutoffLogFC
        • txtCutoffLogFCProteome
          org.eclipse.swt.widgets.Text txtCutoffLogFCProteome
        • txtCutoffPvalue
          org.eclipse.swt.widgets.Text txtCutoffPvalue
        • txtSearch
          org.eclipse.swt.widgets.Text txtSearch
        • txtSearchGenome
          org.eclipse.swt.widgets.Text txtSearchGenome
        • viewID
          String viewID
          Current viewId = ID + math.random()

    • Class bacnet.sequenceTools.GenomicsView

      class GenomicsView extends Object implements Serializable
      serialVersionUID:
      497572638968902304L

      • Serialized Fields

        • bioCondsArray
          String[][] bioCondsArray
          Array used to init data
        • bioCondsToDisplay
          ArrayList<String[]> bioCondsToDisplay
        • browserPhylo
          org.eclipse.swt.browser.Browser browserPhylo
        • btnHelp
          org.eclipse.swt.widgets.Button btnHelp
        • btnSavePng
          org.eclipse.swt.widgets.Button btnSavePng
        • btnSaveSVG
          org.eclipse.swt.widgets.Button btnSaveSVG
        • btnSaveTxt
          org.eclipse.swt.widgets.Button btnSaveTxt
        • btnSelectall
          org.eclipse.swt.widgets.Button btnSelectall
        • btnUnselectall
          org.eclipse.swt.widgets.Button btnUnselectall
        • columnNames
          ArrayList<String> columnNames
        • comparatorBioCondition
          BioConditionComparator comparatorBioCondition
        • compositeSummary
          org.eclipse.swt.widgets.Composite compositeSummary
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • lblXxSrnas
          org.eclipse.swt.widgets.Label lblXxSrnas
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • selectedGenomes
          ArrayList<String> selectedGenomes
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tableGenome
          org.eclipse.swt.widgets.Table tableGenome
        • tableGenomeViewer
          org.eclipse.jface.viewers.TableViewer tableGenomeViewer
        • txtSearch
          org.eclipse.swt.widgets.Text txtSearch
        • url
          String url

    • Class bacnet.sequenceTools.LocalizationDialog

      class LocalizationDialog extends org.eclipse.jface.dialogs.Dialog implements Serializable
      serialVersionUID:
      8150068655518237507L

      • Serialized Fields

        • arrayGeneToLocalization
          String[][] arrayGeneToLocalization
        • bioCondsArray
          String[][] bioCondsArray
        • genome
          Genome genome
        • sequence
          Sequence sequence

    • Class bacnet.sequenceTools.SecondStructureRNADialog

      class SecondStructureRNADialog extends org.eclipse.jface.dialogs.Dialog implements Serializable
      serialVersionUID:
      -8357071260167781918L

      • Serialized Fields

    • Class bacnet.sequenceTools.SequenceDisplayDialog

      class SequenceDisplayDialog extends org.eclipse.jface.dialogs.Dialog implements Serializable
      serialVersionUID:
      -3418095326728894710L

      • Serialized Fields

        • begin
          int begin
        • btnAminoAcidSequence
          org.eclipse.swt.widgets.Button btnAminoAcidSequence
        • btnNucleotideSequence
          org.eclipse.swt.widgets.Button btnNucleotideSequence
        • btnSaveToFasta
          org.eclipse.swt.widgets.Button btnSaveToFasta
        • btnStrandMinus
          org.eclipse.swt.widgets.Button btnStrandMinus
        • btnStrandplus
          org.eclipse.swt.widgets.Button btnStrandplus
        • chromoId
          String chromoId
        • cmbChromo
          org.eclipse.swt.widgets.Combo cmbChromo
        • comboGenome
          org.eclipse.swt.widgets.Combo comboGenome
        • end
          int end
        • genome
          Genome genome
        • lblInfo
          org.eclipse.swt.widgets.Label lblInfo
        • nucleotide
          boolean nucleotide
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • seqFasta
          String seqFasta
        • shell
          org.eclipse.swt.widgets.Shell shell
        • strand
          Strand strand
        • textBegin
          org.eclipse.swt.widgets.Text textBegin
        • textEnd
          org.eclipse.swt.widgets.Text textEnd
        • textSequence
          org.eclipse.swt.widgets.Text textSequence

    • Class bacnet.sequenceTools.SrnaSummaryView

      class SrnaSummaryView extends Object implements Serializable
      serialVersionUID:
      5574893108478572129L

      • Serialized Fields

        • array
          String[][] array
        • btnAsrnas
          org.eclipse.swt.widgets.Button btnAsrnas
        • btnCisRegs
          org.eclipse.swt.widgets.Button btnCisRegs
        • btnDownloadtext
          org.eclipse.swt.widgets.Button btnDownloadtext
        • btnSrnas
          org.eclipse.swt.widgets.Button btnSrnas
        • composite
          org.eclipse.swt.widgets.Composite composite
        • composite_1
          org.eclipse.swt.widgets.Composite composite_1
        • composite_2
          org.eclipse.swt.widgets.Composite composite_2
        • composite_3
          org.eclipse.swt.widgets.Composite composite_3
        • displayType
          Srna.TypeSrna displayType
        • label
          org.eclipse.swt.widgets.Label label
        • lblImage
          org.eclipse.swt.widgets.Label lblImage
        • lblSelectAType
          org.eclipse.swt.widgets.Label lblSelectAType
        • lblXxSrnas
          org.eclipse.swt.widgets.Label lblXxSrnas
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • scrolledComposite
          org.eclipse.swt.custom.ScrolledComposite scrolledComposite
        • shell
          org.eclipse.swt.widgets.Shell shell
        • table
          org.eclipse.swt.widgets.Table table
        • url
          String url

    • Class bacnet.sequenceTools.SrnaView

      class SrnaView extends Object implements Serializable
      serialVersionUID:
      -2943857063947928839L

      • Serialized Fields

        • arrayDataList
          String[][] arrayDataList
        • btnDisplayNucleotideSequence
          org.eclipse.swt.widgets.Button btnDisplayNucleotideSequence
        • btnGenomeViewer
          org.eclipse.swt.widgets.Button btnGenomeViewer
        • btnHeatmapview
          org.eclipse.swt.widgets.Button btnHeatmapview
        • btnHelp
          org.eclipse.swt.widgets.Button btnHelp
        • btnOpenStructure
          org.eclipse.swt.widgets.Button btnOpenStructure
        • btnUpdateCutoff
          org.eclipse.swt.widgets.Button btnUpdateCutoff
        • btnZoomminus
          org.eclipse.swt.widgets.Button btnZoomminus
        • btnZoomplus
          org.eclipse.swt.widgets.Button btnZoomplus
        • canvasGenome
          TrackCanvasGenome canvasGenome
        • composite
          org.eclipse.swt.widgets.Composite composite
        • composite_2
          org.eclipse.swt.widgets.Composite composite_2
        • composite_3
          org.eclipse.swt.widgets.Composite composite_3
        • composite_6
          org.eclipse.swt.widgets.Composite composite_6
        • composite_7
          org.eclipse.swt.widgets.Composite composite_7
        • composite_8_1
          org.eclipse.swt.widgets.Composite composite_8_1
        • composite_pvalue
          org.eclipse.swt.widgets.Composite composite_pvalue
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • genome
          Genome genome
          Egde Genome loaded
        • label_2
          org.eclipse.swt.widgets.Label label_2
        • label_3
          org.eclipse.swt.widgets.Label label_3
        • lblBegin
          org.eclipse.swt.widgets.Text lblBegin
        • lblDescribedIn
          org.eclipse.swt.widgets.Label lblDescribedIn
        • lblEnd
          org.eclipse.swt.widgets.Text lblEnd
        • lblGene
          org.eclipse.swt.widgets.Label lblGene
        • lblNewLabel
          org.eclipse.swt.widgets.Label lblNewLabel
        • lblNodiff
          org.eclipse.swt.widgets.Label lblNodiff
        • lblNote
          org.eclipse.swt.widgets.Text lblNote
        • lblOrAnyOther
          org.eclipse.swt.widgets.Label lblOrAnyOther
        • lblOver
          org.eclipse.swt.widgets.Label lblOver
        • lblPredictedSecondaryStructure
          org.eclipse.swt.widgets.Label lblPredictedSecondaryStructure
        • lblRef
          org.eclipse.swt.widgets.Label lblRef
        • lblSizeBP
          org.eclipse.swt.widgets.Text lblSizeBP
        • lblStrand
          org.eclipse.swt.widgets.Text lblStrand
        • lblStructure
          org.eclipse.swt.widgets.Label lblStructure
        • lblSynonims
          org.eclipse.swt.widgets.Text lblSynonims
        • lblUnder
          org.eclipse.swt.widgets.Label lblUnder
        • listSrnas
          ArrayList<String> listSrnas
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • scrolledComposite
          org.eclipse.swt.custom.ScrolledComposite scrolledComposite
        • seq
          Srna seq
        • shell
          org.eclipse.swt.widgets.Shell shell
        • sRNARefToLink
          HashMap<String,String> sRNARefToLink
        • tabFolder
          org.eclipse.swt.widgets.TabFolder tabFolder
        • tableNoDiff
          org.eclipse.swt.widgets.Table tableNoDiff
        • tableOtherInfo
          org.eclipse.swt.widgets.Table tableOtherInfo
        • tableOver
          org.eclipse.swt.widgets.Table tableOver
        • tableSrnas
          org.eclipse.swt.widgets.Table tableSrnas
        • tableUnder
          org.eclipse.swt.widgets.Table tableUnder
        • tbtmExpressionAtlas
          org.eclipse.swt.widgets.TabItem tbtmExpressionAtlas
        • tbtmGeneralInformation
          org.eclipse.swt.widgets.TabItem tbtmGeneralInformation
        • txtCutoffLogFC
          org.eclipse.swt.widgets.Text txtCutoffLogFC
        • txtCutoffPvalue
          org.eclipse.swt.widgets.Text txtCutoffPvalue
        • txtSearch
          org.eclipse.swt.widgets.Text txtSearch
        • txtSeqnucleotide
          org.eclipse.swt.widgets.Text txtSeqnucleotide
        • viewId
          String viewId
          Current viewId = ID + math.random()

  • Package bacnet.table

    • Class bacnet.table.TableSWTComposite

      class TableSWTComposite extends org.eclipse.swt.widgets.Composite implements Serializable
      serialVersionUID:
      -5019287630134430710L

      • Serialized Fields

        • btnColormapper
          org.eclipse.swt.widgets.Button btnColormapper
        • btnDisplayValues
          org.eclipse.swt.widgets.Button btnDisplayValues
        • btnFilter
          org.eclipse.swt.widgets.Button btnFilter
        • btnHide
          org.eclipse.swt.widgets.Button btnHide
        • btnSavepng
          org.eclipse.swt.widgets.Button btnSavepng
        • btnSaveText
          org.eclipse.swt.widgets.Button btnSaveText
        • btnZoomIn
          org.eclipse.swt.widgets.Button btnZoomIn
        • btnZoomOut
          org.eclipse.swt.widgets.Button btnZoomOut
        • colorMapperList
          ColorMapperList colorMapperList
        • columnNames
          ArrayList<String> columnNames
        • comparator
          TableViewerComparator comparator
        • composite
          org.eclipse.swt.widgets.Composite composite
        • composite_4
          org.eclipse.swt.widgets.Composite composite_4
        • displayValues
          boolean displayValues
        • excludeColumn
          ArrayList<String> excludeColumn
        • excludeRow
          ArrayList<String> excludeRow
        • filters
          FilterList filters
        • genome
          Genome genome
        • hideDialogExcludeColumn
          ArrayList<String> hideDialogExcludeColumn
        • hideDialogExcludeRow
          ArrayList<String> hideDialogExcludeRow
        • labelColumn
          org.eclipse.swt.widgets.Label labelColumn
        • labelRow
          org.eclipse.swt.widgets.Label labelRow
        • labelVoid
          org.eclipse.swt.widgets.Label labelVoid
        • lblSearch
          org.eclipse.swt.widgets.Label lblSearch
        • lblX
          org.eclipse.swt.widgets.Label lblX
        • matrix
          ExpressionMatrix matrix
        • matrixDisplayed
          ExpressionMatrix matrixDisplayed
        • matrixSize
          MatrixSize matrixSize
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • searchFilter
          TableFilter searchFilter
        • searchText
          org.eclipse.swt.widgets.Text searchText
        • shell
          org.eclipse.swt.widgets.Shell shell
        • table
          org.eclipse.swt.widgets.Table table
        • tableViewer
          org.eclipse.jface.viewers.TableViewer tableViewer

  • Package bacnet.table.core

    • Class bacnet.table.core.BioConditionComparator

      class BioConditionComparator extends org.eclipse.jface.viewers.ViewerComparator implements Serializable
      serialVersionUID:
      4101481773521242366L

      • Serialized Fields

        • columnNames
          ArrayList<String> columnNames
        • direction
          int direction
        • propertyIndex
          int propertyIndex

    • Class bacnet.table.core.ColorMapper

      class ColorMapper extends Object implements Serializable
      serialVersionUID:
      26986650775300526L

      • Serialized Fields

        • centerColorSWT
          ColorSWT centerColorSWT
        • centerPos
          double centerPos
        • columnNames
          TreeSet<String> columnNames
        • displayValues
          boolean displayValues
        • fontDouble
          org.eclipse.swt.graphics.Font fontDouble
        • fontRowName
          org.eclipse.swt.graphics.Font fontRowName
        • fontText
          org.eclipse.swt.graphics.Font fontText
        • headerColorSWT
          ColorSWT headerColorSWT
        • maxColorSWT
          ColorSWT maxColorSWT
        • maxPos
          double maxPos
        • midLeftColorSWT
          ColorSWT midLeftColorSWT
        • midLeftPos
          double midLeftPos
        • midRightColorSWT
          ColorSWT midRightColorSWT
        • midRightPos
          double midRightPos
        • minColorSWT
          ColorSWT minColorSWT
        • minPos
          double minPos
        • textColorSWT
          ColorSWT textColorSWT
        • textHeaderColorSWT
          ColorSWT textHeaderColorSWT

    • Class bacnet.table.core.ColorMapperRCP

      class ColorMapperRCP extends Object implements Serializable
      serialVersionUID:
      26986650775300526L

      • Serialized Fields

        • centerColorSWT
          ColorSWT centerColorSWT
        • centerPos
          double centerPos
        • deviation
          double deviation
        • displayValues
          boolean displayValues
        • fontDouble
          Font fontDouble
        • fontString
          Font fontString
        • headerColorSWT
          ColorSWT headerColorSWT
        • max
          double max
        • maxColorSWT
          ColorSWT maxColorSWT
        • maxPos
          double maxPos
        • mean
          double mean
        • median
          double median
        • midLeftColorSWT
          ColorSWT midLeftColorSWT
        • midLeftPos
          double midLeftPos
        • midRightColorSWT
          ColorSWT midRightColorSWT
        • midRightPos
          double midRightPos
        • min
          double min
        • minColorSWT
          ColorSWT minColorSWT
        • minPos
          double minPos
        • nbElements
          int nbElements
        • textColorSWT
          ColorSWT textColorSWT
        • textHeaderColorSWT
          ColorSWT textHeaderColorSWT
        • var
          double var

    • Class bacnet.table.core.ColorSWT

      class ColorSWT extends Object implements Serializable
      serialVersionUID:
      3693115797571798995L

      • Serialized Fields

        • blue
          int blue
        • green
          int green
        • red
          int red

    • Class bacnet.table.core.Filter

      class Filter extends Object implements Serializable
      serialVersionUID:
      6834197254054420424L

      • Serialized Fields

        • cutOff1
          double cutOff1
        • cutOff2
          double cutOff2
        • filterColumn
          boolean filterColumn
        • name
          String name
        • tableElementName
          String tableElementName
        • typeFilter
          Filter.TypeFilter typeFilter

    • Class bacnet.table.core.MatrixSize

      class MatrixSize extends Object implements Serializable
      serialVersionUID:
      3440001575014228874L

    • Class bacnet.table.core.TableViewerComparator

      class TableViewerComparator extends org.eclipse.jface.viewers.ViewerComparator implements Serializable
      serialVersionUID:
      -9021641281635843621L

      • Serialized Fields

        • direction
          int direction
        • propertyIndex
          int propertyIndex

  • Package bacnet.table.gui

    • Class bacnet.table.gui.ColorMapperWizardPage

      class ColorMapperWizardPage extends org.eclipse.jface.wizard.WizardPage implements Serializable
      serialVersionUID:
      -3829149015717789437L

      • Serialized Fields

        • btnFont
          org.eclipse.swt.widgets.Button btnFont
        • btnFontNumber
          org.eclipse.swt.widgets.Button btnFontNumber
        • btnLoadColorMapper
          org.eclipse.swt.widgets.Button btnLoadColorMapper
        • btnNumberTextColor
          org.eclipse.swt.widgets.Button btnNumberTextColor
        • btnSaveColorMapper
          org.eclipse.swt.widgets.Button btnSaveColorMapper
        • btnSelectCenterColor
          org.eclipse.swt.widgets.Button btnSelectCenterColor
        • btnSelectHeaderColor
          org.eclipse.swt.widgets.Button btnSelectHeaderColor
        • btnSelectMaxColor
          org.eclipse.swt.widgets.Button btnSelectMaxColor
        • btnSelectMidleftColor
          org.eclipse.swt.widgets.Button btnSelectMidleftColor
        • btnSelectMidRightColor
          org.eclipse.swt.widgets.Button btnSelectMidRightColor
        • btnSelectMinColor
          org.eclipse.swt.widgets.Button btnSelectMinColor
        • btnTextHeaderColor
          org.eclipse.swt.widgets.Button btnTextHeaderColor
        • canvas
          org.eclipse.swt.widgets.Canvas canvas
        • colorMapper
          ColorMapper colorMapper
        • composite
          org.eclipse.swt.widgets.Composite composite
        • composite_10
          org.eclipse.swt.widgets.Composite composite_10
        • composite_11
          org.eclipse.swt.widgets.Composite composite_11
        • composite_12
          org.eclipse.swt.widgets.Composite composite_12
        • composite_13
          org.eclipse.swt.widgets.Composite composite_13
        • composite_8
          org.eclipse.swt.widgets.Composite composite_8
        • composite_9
          org.eclipse.swt.widgets.Composite composite_9
        • label_10
          org.eclipse.swt.widgets.Label label_10
        • label_11
          org.eclipse.swt.widgets.Label label_11
        • label_4
          org.eclipse.swt.widgets.Label label_4
        • label_9
          org.eclipse.swt.widgets.Label label_9
        • lblBoundleft
          org.eclipse.swt.widgets.Label lblBoundleft
        • lblBoundRight
          org.eclipse.swt.widgets.Label lblBoundRight
        • lblCenter
          org.eclipse.swt.widgets.Label lblCenter
        • lblMax
          org.eclipse.swt.widgets.Label lblMax
        • lblMidleft
          org.eclipse.swt.widgets.Label lblMidleft
        • lblMidright
          org.eclipse.swt.widgets.Label lblMidright
        • lblMin_1
          org.eclipse.swt.widgets.Label lblMin_1
        • lblSetColor
          org.eclipse.swt.widgets.Label lblSetColor
        • lblsliderCenter
          org.eclipse.swt.widgets.Text lblsliderCenter
        • lblsliderMidLeft
          org.eclipse.swt.widgets.Text lblsliderMidLeft
        • lblsliderMidRight
          org.eclipse.swt.widgets.Text lblsliderMidRight
        • previousColorMapper
          ColorMapper previousColorMapper
        • shell
          org.eclipse.swt.widgets.Shell shell
        • text
          String text
        • textMax
          org.eclipse.swt.widgets.Text textMax
        • textMin
          org.eclipse.swt.widgets.Text textMin

    • Class bacnet.table.gui.FilterDialog

      class FilterDialog extends org.eclipse.jface.dialogs.Dialog implements Serializable
      serialVersionUID:
      112312911659116561L

      • Serialized Fields

        • btnColumn
          org.eclipse.swt.widgets.Button btnColumn
        • btnRow
          org.eclipse.swt.widgets.Button btnRow
        • cmbColumn
          org.eclipse.swt.widgets.Combo cmbColumn
        • cmbRow
          org.eclipse.swt.widgets.Combo cmbRow
        • cmbType
          org.eclipse.swt.widgets.Combo cmbType
        • composite
          org.eclipse.swt.widgets.Composite composite
        • composite_1
          org.eclipse.swt.widgets.Composite composite_1
        • composite_2
          org.eclipse.swt.widgets.Composite composite_2
        • composite_3
          org.eclipse.swt.widgets.Composite composite_3
        • composite_4
          org.eclipse.swt.widgets.Composite composite_4
        • composite_5
          org.eclipse.swt.widgets.Composite composite_5
        • composite_6
          org.eclipse.swt.widgets.Composite composite_6
        • filter
          Filter filter
        • lblCutoff
          org.eclipse.swt.widgets.Label lblCutoff
        • lblNewLabel_1
          org.eclipse.swt.widgets.Label lblNewLabel_1
        • lblSetTheProperties
          org.eclipse.swt.widgets.Label lblSetTheProperties
        • matrix
          ExpressionMatrix matrix
        • textName
          org.eclipse.swt.widgets.Text textName
        • txtCutoff1
          org.eclipse.swt.widgets.Text txtCutoff1
        • txtCutoff2
          org.eclipse.swt.widgets.Text txtCutoff2

    • Class bacnet.table.gui.FilterExpressionMatrixDialog

      class FilterExpressionMatrixDialog extends org.eclipse.jface.dialogs.TitleAreaDialog implements Serializable
      serialVersionUID:
      8526381730648269264L

      • Serialized Fields

        • btnCreateNew
          org.eclipse.swt.widgets.Button btnCreateNew
        • btnEdit
          org.eclipse.swt.widgets.Button btnEdit
        • btnRemove
          org.eclipse.swt.widgets.Button btnRemove
        • composite_1
          org.eclipse.swt.widgets.Composite composite_1
        • filters
          FilterList filters
        • label
          org.eclipse.swt.widgets.Label label
        • lblElementname
          org.eclipse.swt.widgets.Label lblElementname
        • lblName
          org.eclipse.swt.widgets.Label lblName
        • lblRoworcolumn
          org.eclipse.swt.widgets.Label lblRoworcolumn
        • lblType
          org.eclipse.swt.widgets.Label lblType
        • listFilter
          org.eclipse.swt.widgets.List listFilter
        • shell
          org.eclipse.swt.widgets.Shell shell

    • Class bacnet.table.gui.HideExpressionMatrixDialog

      class HideExpressionMatrixDialog extends org.eclipse.jface.dialogs.TitleAreaDialog implements Serializable
      serialVersionUID:
      -6890471316308295477L

      • Serialized Fields

        • btnAddColumn
          org.eclipse.swt.widgets.Button btnAddColumn
        • btnAddRow
          org.eclipse.swt.widgets.Button btnAddRow
        • btnHideColumn
          org.eclipse.swt.widgets.Button btnHideColumn
        • btnHideRow
          org.eclipse.swt.widgets.Button btnHideRow
        • btnLoadColumn
          org.eclipse.swt.widgets.Button btnLoadColumn
        • btnLoadRow
          org.eclipse.swt.widgets.Button btnLoadRow
        • btnSelectGenes
          org.eclipse.swt.widgets.Button btnSelectGenes
        • btnSignaturesLoader
          org.eclipse.swt.widgets.Button btnSignaturesLoader
        • genome
          Genome genome
        • hideDialogExcludeColumn
          ArrayList<String> hideDialogExcludeColumn
        • hideRow
          ArrayList<String> hideRow
        • listAddColumn
          org.eclipse.swt.widgets.List listAddColumn
        • listAddRow
          org.eclipse.swt.widgets.Table listAddRow
        • listHideColumn
          org.eclipse.swt.widgets.List listHideColumn
        • listHideRow
          org.eclipse.swt.widgets.Table listHideRow
        • matrix
          ExpressionMatrix matrix
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • shell
          org.eclipse.swt.widgets.Shell shell
        • showRow
          ArrayList<String> showRow

    • Class bacnet.table.gui.TableFilter

      class TableFilter extends org.eclipse.jface.viewers.ViewerFilter implements Serializable
      serialVersionUID:
      -7621715116380436406L

      • Serialized Fields

        • searchString
          String searchString

  • Package bacnet.utils

  • Package bacnet.views

    • Class bacnet.views.BannerView

      class BannerView extends Object implements Serializable
      serialVersionUID:
      3803453895078156914L

      • Serialized Fields

        • canvas
          org.eclipse.swt.widgets.Canvas canvas
          In this Canvas we will draw the Banner of the website/software
        • tltmAbout
          org.eclipse.swt.widgets.ToolItem tltmAbout
        • tltmGenomics
          org.eclipse.swt.widgets.ToolItem tltmGenomics
        • tltmProteomics
          org.eclipse.swt.widgets.ToolItem tltmProteomics
        • tltmTranscriptomics
          org.eclipse.swt.widgets.ToolItem tltmTranscriptomics

    • Class bacnet.views.CoExprNetworkView

      class CoExprNetworkView extends Object implements Serializable
      serialVersionUID:
      -4429010895850129342L

      • Serialized Fields

        • browserGraph
          org.eclipse.swt.browser.Browser browserGraph
        • btnCorrMinus
          org.eclipse.swt.widgets.Button btnCorrMinus
        • btnCorrPlus
          org.eclipse.swt.widgets.Button btnCorrPlus
        • btnHelp
          org.eclipse.swt.widgets.Button btnHelp
        • btnSelectGenomeElements
          org.eclipse.swt.widgets.Button btnSelectGenomeElements
        • comboGenome
          org.eclipse.swt.widgets.Combo comboGenome
        • composite
          org.eclipse.swt.widgets.Composite composite
        • filteredNetwork
          Network filteredNetwork
        • focused
          boolean focused
          Indicates if we focus the view, so we can pushState navigation
        • generalNetwork
          Network generalNetwork
        • genome
          Genome genome
        • genomeName
          String genomeName
        • listGenomeElements
          ArrayList<String> listGenomeElements
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • shell
          org.eclipse.swt.widgets.Shell shell
        • tabFolder
          org.eclipse.swt.widgets.TabFolder tabFolder
        • tableGenes
          org.eclipse.swt.widgets.Table tableGenes
        • tbtmGraphVisualization
          org.eclipse.swt.widgets.TabItem tbtmGraphVisualization
        • textCutOff
          org.eclipse.swt.widgets.Text textCutOff
        • txtSearch
          org.eclipse.swt.widgets.Text txtSearch

    • Class bacnet.views.CRISPRPredictView

      class CRISPRPredictView extends Object implements Serializable
      serialVersionUID:
      4263354745027835111L

      • Serialized Fields

        • btnRunPredicition
          org.eclipse.swt.widgets.Button btnRunPredicition
        • btnRunTest
          org.eclipse.swt.widgets.Button btnRunTest
        • btnTxt
          org.eclipse.swt.widgets.Button btnTxt
        • btnUploadFastaFile
          org.eclipse.swt.widgets.Button btnUploadFastaFile
        • columnNames
          ArrayList<String> columnNames
        • combo
          org.eclipse.swt.widgets.Combo combo
        • DEFAULT_MODEL
          String DEFAULT_MODEL
        • MODEL_CAS9
          String MODEL_CAS9
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • PYTHON_PATH
          String PYTHON_PATH
        • PYTHON_SERVER
          String PYTHON_SERVER
        • results
          String[][] results
        • SCRIPT_PATH
          String SCRIPT_PATH
        • SCRIPT_SERVER
          String SCRIPT_SERVER
        • shell
          org.eclipse.swt.widgets.Shell shell
        • SINGULARITY_PATH
          String SINGULARITY_PATH
        • table
          org.eclipse.swt.widgets.Table table
        • tableViewer
          org.eclipse.jface.viewers.TableViewer tableViewer
        • text
          org.eclipse.swt.widgets.Text text

    • Class bacnet.views.CRISPRPredictView2

      class CRISPRPredictView2 extends Object implements Serializable
      serialVersionUID:
      3931172856313756769L

      • Serialized Fields

        • btnRunPredicition
          org.eclipse.swt.widgets.Button btnRunPredicition
        • btnRunTest
          org.eclipse.swt.widgets.Button btnRunTest
        • btnUploadFastaFile
          org.eclipse.swt.widgets.Button btnUploadFastaFile
        • columnNames
          ArrayList<String> columnNames
        • combo
          org.eclipse.swt.widgets.Combo combo
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService
        • PYTHON_PATH
          String PYTHON_PATH
        • PYTHON_SERVER
          String PYTHON_SERVER
        • SCRIPT_PATH
          String SCRIPT_PATH
        • shell
          org.eclipse.swt.widgets.Shell shell
        • SINGULARITY_PATH
          String SINGULARITY_PATH
        • table
          org.eclipse.swt.widgets.Table table
        • tableViewer
          org.eclipse.jface.viewers.TableViewer tableViewer
        • text
          org.eclipse.swt.widgets.Text text

    • Class bacnet.views.InitView

      class InitView extends Object implements Serializable
      serialVersionUID:
      -2416453633652904396L

      • Serialized Fields

        • btnBHI37
          org.eclipse.swt.widgets.Button btnBHI37
        • btnIntracellular
          org.eclipse.swt.widgets.Button btnIntracellular
        • btnSrnas
          org.eclipse.swt.widgets.Button btnSrnas
        • btnStat
          org.eclipse.swt.widgets.Button btnStat
        • partService
          org.eclipse.e4.ui.workbench.modeling.EPartService partService

  • Package org.biojava3.core.exceptions

  • Package org.biojava3.genome.parsers.gff