A B C D E F G H I J L M N O P R S T U V W Z _

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generateGradient(CImageGradient.InterType) - Method in class org.coolmap.core.util.CImageGradient

generateOntology2ColumnFormat(String, String) - Static method in class org.coolmap.core.data.ontology.util.OntologyHelper

GenerateOntologyBaseOnSamplePropertyTask - Class in org.coolmap.core.data.entity.task

This task will generate an ontology based on passed in sample property table Created by Keqiang Li on 11/19/15.

GenerateOntologyBaseOnSamplePropertyTask(DataPropertyTable<String, String, String>, List<String>) - Constructor for class org.coolmap.core.data.entity.task.GenerateOntologyBaseOnSamplePropertyTask

GenerateOntologyFromDataPropertyTableDialog - Class in org.coolmap.core.application.ui.ontology

Created by Keqiang Li on 4/12/16.

GenerateOntologyFromDataPropertyTableDialog(Window) - Constructor for class org.coolmap.core.application.ui.ontology.GenerateOntologyFromDataPropertyTableDialog

GenerateOntologyFromDataPropertyTablePanel - Class in org.coolmap.core.application.ui.ontology

Created by Keqiang Li on 4/12/16.

generateOntologyFromOBOFormat(String, String) - Static method in class org.coolmap.core.data.ontology.util.OntologyHelper

GeoSOFT - Class in org.coolmap.core.util.bioparser.geosoft

GeoSOFT(Database, Dataset, Collection<Subset>, ArrayTable, Annotation) - Constructor for class org.coolmap.core.util.bioparser.geosoft.GeoSOFT

get(int, int) - Method in class org.coolmap.core.data.entity.model.DataPropertyTable

get(ROW, PROPERTY) - Method in class org.coolmap.core.data.entity.model.DataPropertyTable

get(String, String) - Method in class org.coolmap.core.util.TableCache

getActiveCell() - Method in class org.coolmap.core.canvas.CoolMapView

gets a copy of the active cell

getActiveColNode(int) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getActiveColumnNodes() - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getActiveColumnNodes(String) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getActiveCoolMapObject() - Static method in class org.coolmap.core.application.CoolMapMaster

getActiveCoolMapObjectListenerDelegate() - Static method in class org.coolmap.core.application.CoolMapMaster

getActiveFilters() - Method in class org.coolmap.core.data.CoolMapObject

getActiveNode(int, int) - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnTree

getActiveNode(int, int) - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowTree

getActiveNode(int, int) - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideTree

getActiveObject() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnTree

getActiveObject() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowTree

getActiveObject() - Method in interface org.coolmap.core.canvas.ui.sidemaps.Selectable

getActivePoint() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnTree

getActivePoint() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowTree

getActivePoint() - Method in interface org.coolmap.core.canvas.ui.sidemaps.Selectable

getActiveRowNode(int) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getActiveRowNodes() - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getActiveRowNodes(String) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getAggregation(BASE, Collection<CoolMapMatrix>, Integer, Integer) - Method in class org.coolmap.core.data.aggregator.CAggregator

getAggregation(Collection<BASE>, Collection<CoolMapMatrix>, Collection<Integer>, Collection<Integer>) - Method in class org.coolmap.core.data.aggregator.CAggregator

getAggregation(Double, Collection<CoolMapMatrix>, Integer, Integer) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleMax

getAggregation(Collection<Double>, Collection<CoolMapMatrix>, Collection<Integer>, Collection<Integer>) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleMax

getAggregation(Double, Collection<CoolMapMatrix>, Integer, Integer) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleMean

getAggregation(Collection<Double>, Collection<CoolMapMatrix>, Collection<Integer>, Collection<Integer>) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleMean

getAggregation(Double, Collection<CoolMapMatrix>, Integer, Integer) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleMedian

getAggregation(Collection<Double>, Collection<CoolMapMatrix>, Collection<Integer>, Collection<Integer>) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleMedian

getAggregation(Double, Collection<CoolMapMatrix>, Integer, Integer) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleMin

getAggregation(Collection<Double>, Collection<CoolMapMatrix>, Collection<Integer>, Collection<Integer>) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleMin

getAggregation(Double, Collection<CoolMapMatrix>, Integer, Integer) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleSD

getAggregation(Collection<Double>, Collection<CoolMapMatrix>, Collection<Integer>, Collection<Integer>) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleSD

getAggregation(Double, Collection<CoolMapMatrix>, Integer, Integer) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleSum

getAggregation(Collection<Double>, Collection<CoolMapMatrix>, Collection<Integer>, Collection<Integer>) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleSum

getAggregation(Double, Collection<CoolMapMatrix>, Integer, Integer) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleVariance

getAggregation(Collection<Double>, Collection<CoolMapMatrix>, Collection<Integer>, Collection<Integer>) - Method in class org.coolmap.core.data.aggregator.impl.DoubleDoubleVariance

getAggregation(Double, Collection<CoolMapMatrix>, Integer, Integer) - Method in class org.coolmap.core.data.aggregator.impl.DoubleToNetwork

getAggregation(Collection<Double>, Collection<CoolMapMatrix>, Collection<Integer>, Collection<Integer>) - Method in class org.coolmap.core.data.aggregator.impl.DoubleToNetwork

getAggregation(Object, Collection<CoolMapMatrix>, Integer, Integer) - Method in class org.coolmap.core.data.aggregator.impl.PassThrough

getAggregation(Collection<Object>, Collection<CoolMapMatrix>, Collection<Integer>, Collection<Integer>) - Method in class org.coolmap.core.data.aggregator.impl.PassThrough

getAggregation(VNode, VNode) - Method in class org.coolmap.core.data.aggregator.PropertyBasedAggregation

getAggregationMethod() - Method in class org.coolmap.core.api.aggregation.AbstractSidePanelValueAggregator

getAggregationMethod() - Method in interface org.coolmap.core.api.aggregation.SidePanelValueAggregator

getAggregator() - Method in class org.coolmap.core.data.CoolMapObject

getAllEntries() - Method in class org.coolmap.core.util.bioparser.simpleobo.SimpleOBOTree

getAllNodeIDs() - Method in class org.coolmap.core.util.bioparser.simpleobo.SimpleOBOTree

getAllNodesWithChildrenIds() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getAllNodesWithParentsIds() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getAllNodesWithParentsOrderedIds() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getAllTermIds() - Method in interface org.coolmap.core.api.data.ontology.CoolMapOntology

Get all term IDs

getAllTermIds() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getAllValues() - Method in class org.coolmap.core.data.entity.sampleProperty.model.CategorizedDataPropertyGroup

getAllWidgets() - Static method in class org.coolmap.core.application.widget.WidgetMaster

getAnchorX() - Method in class org.coolmap.core.canvas.ui.sidemaps.ColumnMap

getAnchorX() - Method in class org.coolmap.core.canvas.ui.sidemaps.RowMap

getAnchorX() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideMap

getAnchorY() - Method in class org.coolmap.core.canvas.ui.sidemaps.ColumnMap

getAnchorY() - Method in class org.coolmap.core.canvas.ui.sidemaps.RowMap

getAnchorY() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideMap

getAnnotation(VNode, VNode) - Method in class org.coolmap.core.data.annotation.AnnotationStorage

getAnnotation(String, String) - Method in class org.coolmap.core.data.annotation.AnnotationStorage

key = nodeName + ontologyID

getAnnotation() - Method in class org.coolmap.core.data.annotation.PointAnnotation

getAnnotations() - Method in class org.coolmap.core.data.annotation.AnnotationStorage

get all existing annotation

getAnnotationStorage() - Method in class org.coolmap.core.data.CoolMapObject

getAntiAliasing() - Method in class org.coolmap.core.canvas.renderer.model.ViewRenderer

getArrayTable() - Method in class org.coolmap.core.util.bioparser.geosoft.GeoSOFT

getAttachedCoolMapObject() - Method in class org.coolmap.core.canvas.ui.sidemaps.task.NewViewWithPropertyBasedAggregationTask

getAttachedCoolMapObject() - Method in class org.coolmap.core.data.aggregator.PropertyBasedAggregation

getAttachedDataPropertyTable() - Method in class org.coolmap.core.data.aggregator.PropertyBasedAggregation

getAttrbuteNames() - Method in class org.coolmap.core.data.ontology.model.COntologyAttribute

getAttribute(String, String) - Method in class org.coolmap.core.data.ontology.model.COntologyAttribute

getAttribute(String, String) - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getAttribute(String) - Method in class org.coolmap.core.data.ontology.util.edgeattributes.COntologyEdgeAttributeImpl

getAttribute(String) - Method in class org.coolmap.core.util.bioparser.geosoft.Dataset

getAttribute(String) - Method in class org.coolmap.core.util.bioparser.geosoft.Subset

getAttributeClass(String) - Method in class org.coolmap.core.data.ontology.model.COntologyAttribute

getAttributeNames() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getAttributeNamesSorted() - Method in class org.coolmap.core.data.ontology.model.COntologyAttribute

getAttributes() - Method in class org.coolmap.core.util.bioparser.geosoft.ArrayTable

getAvailableSubHeatMapSize() - Static method in class org.coolmap.core.canvas.CoolMapView

getBackgroundColor() - Method in class org.coolmap.core.data.annotation.PointAnnotation

getBaseClass() - Method in class org.coolmap.core.data.aggregator.CAggregator

getBaseClass() - Method in class org.coolmap.core.data.CoolMapObject

an aggregator must be assigned; otherwise the classes are unknown.

getBaseCMatrices() - Method in class org.coolmap.core.data.CoolMapObject

getBaseIndices(CoolMapMatrix, Integer, String) - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getBaseIndicesFromCOntology(CoolMapMatrix, Integer) - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getBaseValue(int, int, int) - Method in class org.coolmap.core.data.CoolMapObject

getBoldFont() - Method in class org.coolmap.core.canvas.ui.ZoomControl

getBorderColor() - Method in class org.coolmap.core.data.annotation.PointAnnotation

getBounds() - Method in class org.coolmap.core.canvas.CoolMapView

getCachedResult(String) - Method in class org.coolmap.core.api.aggregation.AbstractSidePanelValueAggregator

getCachedResult(String) - Method in class org.coolmap.core.api.aggregation.SidePanelCategoricalValueAggregator

getCachedResult(String) - Method in class org.coolmap.core.api.aggregation.SidePanelContinuousValueAggregator

getCanvas() - Method in class org.coolmap.core.application.widget.impl.ontology.OntologyBrowser

getCanvasDimension() - Method in class org.coolmap.core.canvas.CoolMapView

getCellEditorValue() - Method in class org.coolmap.core.application.ui.util.JTableButtonCell

getChildCoolMapObjects() - Method in class org.coolmap.core.data.CoolMapObject

getChildIndex() - Method in class org.coolmap.core.application.ui.ontology.ImportSimpleTwoColumnOntologyPanel

getChildNodes() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getChildNodes(String) - Method in class org.coolmap.core.util.bioparser.simpleobo.SimpleOBOTree

return all nodeIDs that are children of the given parentNodeID

getChildNodesInViewColumn(VNode) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

get all nodes associated with a certain tree node

getChildNodesInViewColumn(Collection<VNode>) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

get all leaf nodes associated with all the selected parent nodes visited -> for selections parent nodes will not be visited again

getChildNodesInViewColumnAll(Collection<VNode>) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

get all nodes associated w/ selected nodes

getChildNodesInViewRow(Collection<VNode>) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

get all left nodes associated with the selected parent nodes -> for selections

getChildNodesInViewRow(VNode) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getChildNodesInViewRowAll(Collection<VNode>) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

get all leaf nodes associated with the selected parent nodes

getChildren(String) - Method in class org.coolmap.core.data.entity.sampleProperty.model.CategorizedDataPropertyGroupSetting

getCMainFrame() - Static method in class org.coolmap.core.application.CoolMapMaster

getCMatrixByID(String) - Static method in class org.coolmap.core.application.CoolMapMaster

getCol() - Method in class org.coolmap.core.canvas.ui.MatrixCell

getColor(String) - Method in interface org.coolmap.core.api.aggregation.IdToSidePanelDisplayConverter

getColor() - Method in class org.coolmap.core.api.aggregation.IdToSidePanelDisplayConverter.SidePanelValueColorPair

getColorAt(int) - Method in class org.coolmap.core.util.graphics.GradientEditorPanel

getColorPositionAt(int) - Method in class org.coolmap.core.util.graphics.GradientEditorPanel

getColumnBaseNodes() - Method in class org.coolmap.core.data.state.CoolMapState

getColumnId(int) - Method in interface org.coolmap.core.api.data.matrix.CoolMapMatrix

Get column ID(label) at columnIndex

getColumnId(int) - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

getColumnId(int) - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

getColumnIds() - Method in interface org.coolmap.core.api.data.matrix.CoolMapMatrix

Get all column ids in a list ordered by column indices

getColumnIds() - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

getColumnIds() - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

getColumnKey() - Method in class org.coolmap.core.data.annotation.PointAnnotation

getColumnLabel(int) - Method in class org.coolmap.core.util.CoolMapDoubleMatrix

getColumnLabels() - Method in class org.coolmap.core.util.CoolMapDoubleMatrix

getColumnLeafNodeIds(VNode, CoolMapMatrix) - Static method in class org.coolmap.core.util.statistics.CoolMapDataUtil

getColumnMap(String) - Method in class org.coolmap.core.canvas.CoolMapView

getColumnMaps() - Method in class org.coolmap.core.canvas.CoolMapView

getColumnNames() - Method in class org.coolmap.core.util.bioparser.geosoft.ArrayTable

getColumnNodeName() - Method in class org.coolmap.core.data.annotation.PointAnnotation

getColumnNodeOntologyID() - Method in class org.coolmap.core.data.annotation.PointAnnotation

getColumnTreeNodes() - Method in class org.coolmap.core.data.state.CoolMapState

getComparator(boolean) - Method in interface org.coolmap.core.canvas.ui.sidemaps.SidePanelHighlighter

getConfig() - Method in class org.coolmap.core.data.state.CoolMapState

getConfigUI() - Method in class org.coolmap.core.canvas.renderer.impl.NumberToBar

getConfigUI() - Method in class org.coolmap.core.canvas.renderer.impl.NumberToBoxPlot

getConfigUI() - Method in class org.coolmap.core.canvas.renderer.impl.NumberToColor

getConfigUI() - Method in class org.coolmap.core.canvas.renderer.impl.NumberToSortedBar

getConfigUI() - Method in class org.coolmap.core.canvas.renderer.model.ViewRenderer

returns the UI for configuration

getConfigUI() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideMap

getConfigUI() - Method in class org.coolmap.core.data.aggregator.CAggregator

getContentPane() - Method in class org.coolmap.core.application.widget.Widget

getCOntologyByID(String) - Static method in class org.coolmap.core.application.CoolMapMaster

getCOntologyID() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getConverter(String) - Static method in class org.coolmap.core.data.snippet.SnippetMaster

getCoolMapObject() - Method in class org.coolmap.core.canvas.CoolMapView

getCoolMapObject() - Method in class org.coolmap.core.canvas.renderer.model.ViewRenderer

getCoolMapObject() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideMap

getCoolMapObject() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideTree

getCoolMapObjectByID(String) - Static method in class org.coolmap.core.application.CoolMapMaster

getCoolMapObjectID() - Method in class org.coolmap.core.data.state.CoolMapState

getCoolMapObjects() - Static method in class org.coolmap.core.application.CoolMapMaster

getCoolMapView() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideMap

getCoolMapView() - Method in class org.coolmap.core.data.CoolMapObject

getCopiedState() - Static method in class org.coolmap.core.application.state.StateStorageMaster

getCurProperty() - Method in class org.coolmap.core.data.aggregator.PropertyBasedAggregation

getCurrentCol(int) - Method in class org.coolmap.core.canvas.CoolMapView

getCurrentColSearchAll(int) - Method in class org.coolmap.core.canvas.CoolMapView

find the current Col using binary search -1 means left bound cols = right bound, null = undefined

getCurrentIdNonAggregatedValue(String) - Method in class org.coolmap.core.api.aggregation.AbstractIdToSidePanelDisplayConverterUseOntology

getCurrentIdNonAggregatedValue(String) - Method in class org.coolmap.core.api.aggregation.DefaultIdToSidePanelDisplayConverterUseOntology

getCurrentIdNonAggregatedValue(String) - Method in class org.coolmap.core.api.aggregation.PropertyBasedIdToSidePanelDisplayConverterUseOntology

getCurrentProjectFile() - Static method in class org.coolmap.core.application.io.IOMaster

getCurrentRedoOperationName() - Method in class org.coolmap.core.application.state.StateQueue

getCurrentRow(int) - Method in class org.coolmap.core.canvas.CoolMapView

getCurrentRowSearchAll(int) - Method in class org.coolmap.core.canvas.CoolMapView

getCurrentState() - Method in class org.coolmap.core.application.state.StateQueue

getCurrentState() - Method in class org.coolmap.core.application.widget.impl.console.WidgetConsole

getCurrentState() - Method in class org.coolmap.core.application.widget.impl.WidgetUserGroup

getCurrentState() - Method in class org.coolmap.core.application.widget.Widget

getCurrentState() - Method in class org.coolmap.core.canvas.renderer.impl.NumberToColor

getCurrentState() - Method in class org.coolmap.core.canvas.renderer.model.ViewRenderer

override this to save state to JSON

getCurrentState() - Method in class org.coolmap.core.data.aggregator.CAggregator

getCurrentState() - Method in class org.coolmap.core.data.snippet.SnippetConverter

getCurrentState() - Method in interface org.coolmap.core.util.StateSavable

state and be persisted using JSON

getCurrentUndoOperationName() - Method in class org.coolmap.core.application.state.StateQueue

getCurrentViewMultiplier() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getCurrentZoom() - Method in class org.coolmap.core.canvas.ui.ZoomControl

getCurrentZoomIndex() - Method in class org.coolmap.core.canvas.ui.ZoomControl

getCurrFilters() - Method in class org.coolmap.core.util.filter.impl.CombinationFilter

getCurSelectedDelimiterType() - Method in class org.coolmap.core.application.ui.util.DelimitedFilePreviewPanel

getCurSelectedFile() - Method in class org.coolmap.core.application.ui.util.DelimitedFilePreviewPanel

getCustomMultiFileChooser(FileFilter, String) - Static method in class org.coolmap.core.util.Tools

getCustomSingleFileChooser(FileFilter, String) - Static method in class org.coolmap.core.util.Tools

getData() - Method in class org.coolmap.core.util.CoolMapDoubleMatrix

getDataImporters() - Static method in class org.coolmap.core.util.CoolMapConfig

getDataImportingDialog(Window, DataImportingDialog.DataMatrixType) - Static method in class org.coolmap.core.application.ui.object.DataImportingDialog

getDataPropertyTables() - Static method in class org.coolmap.core.application.CoolMapMaster

getDefaultViewMultiplier() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getDelimiterString() - Method in enum org.coolmap.core.application.io.FileDelimiterEnum

getDepthOneTreeNodesCol() - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

returns only nodes with depth/1 in view

getDepthOneTreeNodesRow() - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

returns only the nodes w/ depth 1 in view

getDescription() - Method in interface org.coolmap.core.api.data.ontology.CoolMapOntology

Get the description of this Ontology

getDescription() - Method in class org.coolmap.core.canvas.renderer.model.ViewRenderer

getDescription() - Method in class org.coolmap.core.data.aggregator.CAggregator

getDescription() - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

getDescription() - Method in enum org.coolmap.core.data.ontology.CoolMapOntologyFileFormatEnum

getDescription() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getDescription(String) - Method in class org.coolmap.core.util.bioparser.gseagmt.GmtEntry

getDescription() - Method in class org.coolmap.core.util.FileOnlyExtensionFilter

getDescription() - Method in class org.coolmap.core.util.filter.ViewFilter

getDescription() - Method in class org.coolmap.core.util.statistics.test.TestResult

getDirection() - Method in class org.coolmap.core.canvas.ui.ColDrawer

getDirection() - Method in class org.coolmap.core.canvas.ui.RowDrawer

getDirection() - Method in class org.coolmap.core.canvas.ui.sidemaps.ColumnMap

getDirection() - Method in class org.coolmap.core.canvas.ui.sidemaps.RowMap

getDirection() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideMap

getDirection() - Method in class org.coolmap.core.canvas.ui.sidemaps.SideMapDrawer

getDisplayName() - Method in class org.coolmap.core.data.entity.sampleProperty.model.DataProperty

getDisplayName() - Method in class org.coolmap.core.data.entity.sampleProperty.model.DataPropertyGroup

getDisplayValue(String) - Method in interface org.coolmap.core.api.aggregation.IdToSidePanelDisplayConverter

getDockable() - Method in class org.coolmap.core.application.widget.Widget

getDrawerContainerHandlePanel() - Method in class org.coolmap.core.canvas.ui.ColDrawer

getDrawerContainerHandlePanel() - Method in class org.coolmap.core.canvas.ui.RowDrawer

getDrawerContainerHandlePanel() - Method in class org.coolmap.core.canvas.ui.sidemaps.SideMapDrawer

getDrawerSize() - Method in class org.coolmap.core.canvas.ui.sidemaps.SideMapDrawer.DrawerHandle

getDumpString() - Method in class org.coolmap.core.data.state.CoolMapState

getEdgeAttribute(String, String) - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getEdgeCount() - Method in class org.coolmap.core.util.network.LNetwork

getEdges() - Method in class org.coolmap.core.util.network.LNetwork

getEntry(String) - Method in class org.coolmap.core.util.bioparser.simpleobo.SimpleOBOTree

getExpandedNodes() - Method in class org.coolmap.core.canvas.ui.sidemaps.listener.SideTreeExpandingFinishedEvent

getFile() - Method in class org.coolmap.core.data.ontology.AbstractFileCoolMapOntologyImporter

getFileChooserTitle() - Method in class org.coolmap.core.application.ui.ontology.ImportSimpleTwoColumnOntologyPanel

getFileChooserTitle() - Method in class org.coolmap.core.application.ui.ontology.MappingFileSelectionPanel

getFileChooserTitle() - Method in class org.coolmap.core.application.ui.util.DelimitedFilePreviewPanel

getFileFilter() - Method in class org.coolmap.core.application.ui.ontology.ImportSimpleTwoColumnOntologyPanel

getFileFilter() - Method in class org.coolmap.core.application.ui.ontology.MappingFileSelectionPanel

getFileFilter() - Method in class org.coolmap.core.application.ui.util.DelimitedFilePreviewPanel

getFileNameExtensionFilter() - Method in interface org.coolmap.core.application.io.external.CoolMapObjectImporter

file name extension filter

getFileNameExtensionFilter() - Method in class org.coolmap.core.application.io.external.CoolMapObjectImporterFromGEOSOFT

getFileNameExtensionFilter() - Method in class org.coolmap.core.application.io.external.CoolMapObjectImporterFromXLS

getFilterMode() - Method in class org.coolmap.core.util.filter.impl.CombinationFilter

getFittingLevels(int) - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getFocusBorder() - Method in class org.coolmap.core.application.ui.util.JTableButtonCell

Get foreground color of the button when the cell has focus

getFontColor() - Method in class org.coolmap.core.data.annotation.PointAnnotation

getFormat() - Method in interface org.coolmap.core.api.aggregation.IdToSidePanelDisplayConverter

getGeneSetGenes(String) - Method in class org.coolmap.core.util.bioparser.gseagmt.GmtEntry

getGeneSetNames() - Method in class org.coolmap.core.util.bioparser.gseagmt.GmtEntry

getGeneSymbolToProbeIDMapping() - Method in class org.coolmap.core.util.bioparser.geosoft.ArrayTable

getGradientPaint() - Method in class org.coolmap.core.canvas.ui.sidemaps.SideMapDrawer.DrawerHandle

getGraphicsConfiguration() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideMap

getGroup() - Method in class org.coolmap.core.data.entity.sampleProperty.model.DataProperty

getGroup(String) - Method in class org.coolmap.core.data.entity.sampleProperty.model.DataPropertyGroupSetting

getGroupNum() - Method in class org.coolmap.core.data.entity.sampleProperty.model.DataPropertyGroupSetting

getGroups() - Method in class org.coolmap.core.data.entity.sampleProperty.model.DataPropertyGroupSetting

getGroupSetting(PROPERTY) - Method in class org.coolmap.core.data.entity.model.DataPropertyTable

getHeightDifference(String, String) - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getHighlightNodeColor() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnTree

getHighlightNodeColor() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowTree

getHighlightNodeColor() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideTree

getIcon() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideMap

getId() - Method in interface org.coolmap.core.api.data.matrix.CoolMapMatrix

Get the ID of the data matrix

getID() - Method in interface org.coolmap.core.api.data.ontology.CoolMapOntology

Get the ID of this Ontology

getID() - Method in class org.coolmap.core.data.aggregator.CAggregator

getId() - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

getId() - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

getID() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getID() - Method in class org.coolmap.core.data.CoolMapObject

getId() - Method in class org.coolmap.core.data.entity.model.DataPropertyTable

getID() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getID() - Method in class org.coolmap.core.util.bioparser.geosoft.Subset

getID() - Method in class org.coolmap.core.util.bioparser.simpleobo.SimpleOBOEntry

getImageIcon(String) - Static method in class org.coolmap.core.util.graphics.UI

getImmediateChildrenOrderedIds(String) - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getImmediateChildTermIds(String) - Method in interface org.coolmap.core.api.data.ontology.CoolMapOntology

Get all the immediate child terms of a specified parent term

getImmediateChildTermIds(String) - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getImmediateParentsOrderedIds(String) - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getImmediateParentTermIds(String) - Method in interface org.coolmap.core.api.data.ontology.CoolMapOntology

Get all the immediate parent terms of a specified child term

getImmediateParentTermIds(String) - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getImportedCOntology() - Method in interface org.coolmap.core.application.io.external.CoolMapObjectImporter

fetch the imported ontologies after the import operation

getImportedCOntology() - Method in class org.coolmap.core.application.io.external.CoolMapObjectImporterFromGEOSOFT

getImportedCOntology() - Method in class org.coolmap.core.application.io.external.CoolMapObjectImporterFromXLS

getImportedCoolMapObjects() - Method in interface org.coolmap.core.application.io.external.CoolMapObjectImporter

fetch the imported data after the import operation

getImportedCoolMapObjects() - Method in class org.coolmap.core.application.io.external.CoolMapObjectImporterFromGEOSOFT

getImportedCoolMapObjects() - Method in class org.coolmap.core.application.io.external.CoolMapObjectImporterFromXLS

getImportingValues() - Static method in enum org.coolmap.core.data.ontology.util.OntologySourceEnum

getIndexOfColumnById(String) - Method in interface org.coolmap.core.api.data.matrix.CoolMapMatrix

Given the ID of a column, looking for its index in the data matrix

getIndexOfColumnById(String) - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

getIndexOfColumnById(String) - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

getIndexOfRowById(String) - Method in interface org.coolmap.core.api.data.matrix.CoolMapMatrix

Given the ID of a row, looking for its index in the data matrix

getIndexOfRowById(String) - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

getIndexOfRowById(String) - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

getInstance() - Method in class org.coolmap.core.application.utils.Logger

getInstance() - Static method in class org.coolmap.core.application.utils.TaskEngine

getJSONConfig() - Static method in class org.coolmap.core.util.CoolMapConfig

getLabel() - Method in interface org.coolmap.core.application.io.external.CoolMapObjectImporter

get display label

getLabel() - Method in class org.coolmap.core.application.io.external.CoolMapObjectImporterFromGEOSOFT

getLabel() - Method in class org.coolmap.core.application.io.external.CoolMapObjectImporterFromXLS

getLabelColors() - Static method in interface org.coolmap.core.canvas.ui.sidemaps.SideTree

getLabels() - Method in class org.coolmap.core.data.ontology.model.COntologyPreset

getLabelToValue() - Method in class org.coolmap.core.canvas.ui.sidemaps.task.SideTreeNodeExpandingTask

getLeafNodes(VNode) - Static method in class org.coolmap.core.util.statistics.CoolMapDataUtil

getLeafTermIds() - Method in interface org.coolmap.core.api.data.ontology.CoolMapOntology

Get all leaf term IDs

getLeafTermIds() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getLegend() - Method in class org.coolmap.core.canvas.renderer.impl.NumberToBar

getLegend() - Method in class org.coolmap.core.canvas.renderer.impl.NumberToBoxPlot

getLegend() - Method in class org.coolmap.core.canvas.renderer.impl.NumberToColor

getLegend() - Method in class org.coolmap.core.canvas.renderer.impl.NumberToSortedBar

getLegend() - Method in class org.coolmap.core.canvas.renderer.model.ViewRenderer

getLinearGradientPaint(int, int, int, int) - Method in class org.coolmap.core.util.graphics.GradientEditorPanel

getLNetwork(Collection<Integer>, Collection<Integer>) - Method in class org.coolmap.core.data.cmatrix.model.NetworkCoolMapMatrix

getLoadedAggregationMethods() - Method in class org.coolmap.core.application.widget.impl.WidgetAggregator

getLoadedCMatrices() - Static method in class org.coolmap.core.application.CoolMapMaster

getLoadedCOntologies() - Static method in class org.coolmap.core.application.CoolMapMaster

getLoadedRenderers() - Method in class org.coolmap.core.application.widget.impl.WidgetViewRenderer

getMapAnchor() - Method in class org.coolmap.core.canvas.CoolMapView

get the anchoring point of the map all other node anchors are mapAnchor + view offset

getMapAnchor() - Method in class org.coolmap.core.data.state.CoolMapState

getMapBuffer() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideMap

getMapHeight() - Method in class org.coolmap.core.canvas.CoolMapView

getMapWidth() - Method in class org.coolmap.core.canvas.CoolMapView

getMax() - Method in class org.coolmap.core.data.entity.sampleProperty.model.ContinuousDataPropertyGroupSetting

getMax(Collection<Double>) - Static method in class org.coolmap.core.util.statistics.AggregationUtil

getMaxColInView() - Method in class org.coolmap.core.canvas.CoolMapView

max sub col, exclusive

getMaxRowInView() - Method in class org.coolmap.core.canvas.CoolMapView

max sub row, exclusive

getMean(Collection<Double>) - Static method in class org.coolmap.core.util.statistics.AggregationUtil

getMedian(Collection<Double>) - Static method in class org.coolmap.core.util.statistics.AggregationUtil

getMemberClass() - Method in interface org.coolmap.core.api.data.matrix.CoolMapMatrix

Get data type of the data matrix

getMemberClass() - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

getMemberClass() - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

getMessage() - Method in exception org.coolmap.core.application.exception.OntologyMalformedException

getMessageFont() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideMap

getMin() - Method in class org.coolmap.core.data.entity.sampleProperty.model.ContinuousDataPropertyGroupSetting

getMin(Collection<Double>) - Static method in class org.coolmap.core.util.statistics.AggregationUtil

getMinColInView() - Method in class org.coolmap.core.canvas.CoolMapView

getMinimalDepthFromLeaves(String) - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getMinRowInView() - Method in class org.coolmap.core.canvas.CoolMapView

returns the rectangle of viewport, anchors @ 0,0 returns the visible viewport area

getMnemonic() - Method in class org.coolmap.core.application.ui.util.JTableButtonCell

getMouseListener() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideTree

getMouseMotionListener() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideTree

getMouseXY() - Method in class org.coolmap.core.canvas.CoolMapView

get a copy of the current mouse location in view

getName() - Method in interface org.coolmap.core.api.data.matrix.CoolMapMatrix

Get data matrix name

getName() - Method in interface org.coolmap.core.api.data.ontology.CoolMapOntology

Get the name of this Ontology

getName() - Method in interface org.coolmap.core.api.io.data.CoolMapMatrixImporter

Name used to identify this data importer.

getName() - Method in interface org.coolmap.core.api.io.ontology.CoolMapOntologyImporter

Name of this Ontology importer.

getName() - Method in enum org.coolmap.core.application.io.FileDelimiterEnum

getName() - Method in class org.coolmap.core.application.io.internal.cmatrix.DoubleCoolMapMatrixImporter

getName() - Method in class org.coolmap.core.application.io.internal.contology.GMTFormatCoolMapOntologyImporter

getName() - Method in class org.coolmap.core.application.io.internal.contology.OWLOrOBOFormatCoolMapOntologyImporter

getName() - Method in class org.coolmap.core.application.io.internal.contology.SimpleTwoColumnFormatCoolMapOntologyImporter

getName() - Method in interface org.coolmap.core.application.plugin.CoolMapPlugin

getName() - Method in class org.coolmap.core.application.utils.LongTask

getName() - Method in class org.coolmap.core.application.widget.Widget

getName() - Method in enum org.coolmap.core.application.widget.Widget.WidgetGroup

getName() - Method in class org.coolmap.core.canvas.renderer.model.ViewRenderer

getName() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideMap

getName() - Method in class org.coolmap.core.canvas.ui.sidemaps.util.NodeListToExpand

getName() - Method in class org.coolmap.core.data.aggregator.CAggregator

getName() - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

getName() - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

getName() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getName() - Method in class org.coolmap.core.data.CoolMapObject

getName() - Method in class org.coolmap.core.data.entity.model.DataPropertyTable

getName() - Method in enum org.coolmap.core.data.ontology.CoolMapOntologyFileFormatEnum

getName() - Method in class org.coolmap.core.data.ontology.model.COntologyPreset

getName() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getName() - Method in class org.coolmap.core.util.bioparser.simpleobo.SimpleOBOEntry

getName() - Method in class org.coolmap.core.util.CoolMapDoubleMatrix

getName() - Method in class org.coolmap.core.util.filter.ViewFilter

getNamespace() - Method in class org.coolmap.core.util.bioparser.simpleobo.SimpleOBOEntry

getNearestZoomIndex(float) - Method in class org.coolmap.core.canvas.ui.ZoomControl

getNextZoom() - Method in class org.coolmap.core.canvas.ui.ZoomControl

zoom increase by 1

getNodeCount() - Method in class org.coolmap.core.util.network.LNetwork

getNodeNames() - Method in class org.coolmap.core.canvas.ui.sidemaps.util.NodeListToExpand

getNodeNameToExpand() - Method in class org.coolmap.core.canvas.ui.sidemaps.listener.NodeToExpandEvent

getNodePositionInView(VNode) - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnTree

getNodePositionInView(VNode) - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowTree

getNodePositionInView(VNode) - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideTree

getNodes() - Method in class org.coolmap.core.util.network.LNetwork

getNodeStrings() - Method in class org.coolmap.core.data.ontology.model.COntologyAttribute

getNodeStringSorted() - Method in class org.coolmap.core.data.ontology.model.COntologyAttribute

getNormalizedLength() - Method in class org.coolmap.core.data.ontology.util.edgeattributes.COntologyEdgeAttributeImpl

getNumberOfColumns() - Method in interface org.coolmap.core.api.data.matrix.CoolMapMatrix

Get number of columns in the data matrix

getNumberOfColumns() - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

getNumberOfColumns() - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

getNumberOfColumnsCanAccommodate() - Method in class org.coolmap.core.canvas.CoolMapView

getNumberOfRows() - Method in interface org.coolmap.core.api.data.matrix.CoolMapMatrix

Get number of rows in the data matrix

getNumberOfRows() - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

getNumberOfRows() - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

getNumberOfRowsCanAccommodate() - Method in class org.coolmap.core.canvas.CoolMapView

getNumCols() - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getNumColumns() - Method in class org.coolmap.core.util.CoolMapDoubleMatrix

getNumPoints() - Method in class org.coolmap.core.util.graphics.GradientEditorPanel

getNumRows() - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getNumRows() - Method in class org.coolmap.core.util.CoolMapDoubleMatrix

getOntology() - Method in class org.coolmap.core.api.aggregation.AbstractIdToSidePanelDisplayConverterUseOntology

getOntology() - Method in class org.coolmap.core.data.entity.sampleProperty.model.SamplePropertyMatrix

getOntologyProvider() - Method in class org.coolmap.core.application.ui.ontology.GenerateOntologyFromDataPropertyTablePanel

getOntologyProvider() - Method in class org.coolmap.core.application.ui.ontology.OntologyImportingPanel

getOntologyProvider() - Method in class org.coolmap.core.application.ui.ontology.OntologySelectionPanel

getOntologyProvider() - Method in interface org.coolmap.core.data.ontology.CanProduceOntology

getOntologyWithoutEmptyBranches() - Method in class org.coolmap.core.data.entity.sampleProperty.model.SamplePropertyMatrix

getOperationName() - Method in class org.coolmap.core.data.state.CoolMapState

returns the name of this operation

getOriginalValueAndColor(String) - Method in class org.coolmap.core.api.aggregation.AbstractIdToSidePanelDisplayConverterUseOntology

getOriginalValueAndColor(String) - Method in class org.coolmap.core.api.aggregation.DefaultIdToSidePanelDisplayConverterNoOntology

getOriginalValueAndColor(String) - Method in interface org.coolmap.core.api.aggregation.IdToSidePanelDisplayConverter

getOriginalValueAndColor(String) - Method in class org.coolmap.core.api.aggregation.PropertyBasedIdToSidePanelDisplayConverterNoOntology

getOtherAttributes() - Method in class org.coolmap.core.util.bioparser.simpleobo.SimpleOBOEntry

getParent() - Method in class org.coolmap.core.data.entity.sampleProperty.model.CategorizedDataPropertyGroup

getParentIndex() - Method in class org.coolmap.core.application.ui.ontology.ImportSimpleTwoColumnOntologyPanel

getParentNode() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getParentNodeIDs() - Method in class org.coolmap.core.util.bioparser.simpleobo.SimpleOBOTree

return all nodeIDs that have children

getPlainFont() - Method in class org.coolmap.core.canvas.ui.ZoomControl

getPopupMenu() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SidePanelHighlighter

getPopupMenu() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideTree

getPreferredLocation() - Method in class org.coolmap.core.application.widget.Widget

getPreferredSize() - Method in class org.coolmap.core.application.ui.util.ConfirmOrCancelDialog

getPresets() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getPreviousZoom() - Method in class org.coolmap.core.canvas.ui.ZoomControl

getProperty() - Method in class org.coolmap.core.data.entity.sampleProperty.model.DataPropertyGroupSetting

getProperty(String) - Static method in class org.coolmap.core.util.CoolMapConfig

getPropertyBasedAggregation() - Method in class org.coolmap.core.canvas.CoolMapView

getPropertyBasedAggregationDirection() - Method in class org.coolmap.core.canvas.CoolMapView

getPropertyByName(String) - Method in class org.coolmap.core.canvas.ui.sidemaps.util.NodeListToExpand

getPropertyContinuityType(PROPERTY) - Method in class org.coolmap.core.data.entity.model.DataPropertyTable

getPropertyList() - Method in class org.coolmap.core.data.entity.model.DataPropertyTable

getPropertyNames() - Method in class org.coolmap.core.canvas.ui.sidemaps.util.NodeListToExpand

getPropertyNumber() - Method in class org.coolmap.core.data.entity.model.DataPropertyTable

getPValue() - Method in class org.coolmap.core.util.statistics.test.TestResult

getRenderedFullMap(CoolMapObject<?, VIEW>, float, float) - Method in class org.coolmap.core.canvas.renderer.model.ViewRenderer

getRenderedFullMap(CoolMapObject<?, VIEW>, float) - Method in class org.coolmap.core.canvas.renderer.model.ViewRenderer

getRenderedMap(CoolMapObject<?, VIEW>, int, int, int, int, float, float) - Method in class org.coolmap.core.canvas.renderer.model.ViewRenderer

GetRootTermIds() - Method in interface org.coolmap.core.api.data.ontology.CoolMapOntology

Get all root term IDs

GetRootTermIds() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getRootVNodes() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getRootVNodesOrdered() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getRow() - Method in class org.coolmap.core.canvas.ui.MatrixCell

getRowBaseNodes() - Method in class org.coolmap.core.data.state.CoolMapState

getRowCount() - Method in class org.coolmap.core.application.ui.util.DataMatrixTableRowHeader

getRowHeight(int) - Method in class org.coolmap.core.application.ui.util.DataMatrixTableRowHeader

getRowId(int) - Method in interface org.coolmap.core.api.data.matrix.CoolMapMatrix

Get row ID(label) at rowIndex

getRowId(int) - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

getRowId(int) - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

getRowIds() - Method in interface org.coolmap.core.api.data.matrix.CoolMapMatrix

Get all row ids in a list ordered by row indices

getRowIds() - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

getRowIds() - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

getRowKey() - Method in class org.coolmap.core.data.annotation.PointAnnotation

getRowLabel(int) - Method in class org.coolmap.core.util.CoolMapDoubleMatrix

getRowLabels() - Method in class org.coolmap.core.util.CoolMapDoubleMatrix

getRowLeafNodeIds(VNode, CoolMapMatrix) - Static method in class org.coolmap.core.util.statistics.CoolMapDataUtil

getRowList() - Method in class org.coolmap.core.data.entity.model.DataPropertyTable

getRowMap(String) - Method in class org.coolmap.core.canvas.CoolMapView

getRowMaps() - Method in class org.coolmap.core.canvas.CoolMapView

getRowNames() - Method in class org.coolmap.core.util.bioparser.geosoft.ArrayTable

getRowNodeName() - Method in class org.coolmap.core.data.annotation.PointAnnotation

getRowNodeOntologyID() - Method in class org.coolmap.core.data.annotation.PointAnnotation

getRowSymbols() - Method in class org.coolmap.core.util.bioparser.geosoft.ArrayTable

getRowTreeNodes() - Method in class org.coolmap.core.data.state.CoolMapState

getSampleAttribute(String) - Method in class org.coolmap.core.util.bioparser.geosoft.Dataset

getSamplePropertyMatrices(DataPropertyTable) - Static method in class org.coolmap.core.data.entity.sampleProperty.SamplePropertyMaster

getSelectedCell() - Method in class org.coolmap.core.canvas.CoolMapView

getSelectedColumnLeafNodeNames() - Static method in class org.coolmap.core.util.statistics.CoolMapDataUtil

getSelectedColumnLeafNodeValues() - Static method in class org.coolmap.core.util.statistics.CoolMapDataUtil

getSelectedColumns() - Method in class org.coolmap.core.canvas.CoolMapView

getSelectedColumnViewNodeNames() - Static method in class org.coolmap.core.util.statistics.CoolMapDataUtil

getSelectedColumnViewNodeValues() - Static method in class org.coolmap.core.util.statistics.CoolMapDataUtil

getSelectedLeafNodeNames() - Static method in class org.coolmap.core.util.statistics.CoolMapDataUtil

getSelectedMatrices() - Method in class org.coolmap.core.application.widget.impl.WidgetCMatrix

getSelectedNodes() - Method in class org.coolmap.core.canvas.ui.sidemaps.task.NewViewWithPropertyBasedAggregationTask

getSelectedObjects() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnTree

getSelectedObjects() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowTree

getSelectedObjects() - Method in interface org.coolmap.core.canvas.ui.sidemaps.Selectable

getSelectedRegion() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnTree

getSelectedRegion() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowTree

getSelectedRegion() - Method in interface org.coolmap.core.canvas.ui.sidemaps.Selectable

getSelectedRowLeafNodeNames() - Static method in class org.coolmap.core.util.statistics.CoolMapDataUtil

getSelectedRowLeafNodeValues() - Static method in class org.coolmap.core.util.statistics.CoolMapDataUtil

getSelectedRows() - Method in class org.coolmap.core.canvas.CoolMapView

getSelectedRowViewNodeNames() - Static method in class org.coolmap.core.util.statistics.CoolMapDataUtil

getSelectedRowViewNodeValues() - Static method in class org.coolmap.core.util.statistics.CoolMapDataUtil

getSelectionEndPoint() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnTree

getSelectionEndPoint() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowTree

getSelectionEndPoint() - Method in interface org.coolmap.core.canvas.ui.sidemaps.Selectable

getSelections() - Method in class org.coolmap.core.canvas.CoolMapView

getSelections() - Method in class org.coolmap.core.data.state.CoolMapState

getSelectionsColumn() - Method in class org.coolmap.core.data.state.CoolMapState

getSelectionsRow() - Method in class org.coolmap.core.data.state.CoolMapState

getSelectionStartPoint() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnTree

getSelectionStartPoint() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowTree

getSelectionStartPoint() - Method in interface org.coolmap.core.canvas.ui.sidemaps.Selectable

getSelectionsUnion() - Method in class org.coolmap.core.canvas.CoolMapView

returns the outer bounds of all selections

getSession() - Static method in class org.coolmap.core.application.CoolMapMaster

getSessionName() - Method in class org.coolmap.core.application.utils.Session

getSessionURI() - Method in class org.coolmap.core.application.utils.Session

getSideMap(String) - Method in class org.coolmap.core.canvas.ui.sidemaps.SideMapDrawer

getSideMaps() - Method in class org.coolmap.core.canvas.ui.sidemaps.SideMapDrawer

getSidePanelDisplayConverter() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnHighlighter

getSidePanelDisplayConverter() - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowHighlighter

getSidePanelDisplayConverter() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SidePanelHighlighter

getSnippetConverter() - Method in class org.coolmap.core.data.CoolMapObject

getSortTracker() - Method in class org.coolmap.core.data.CoolMapObject

getSourceActions(JComponent) - Method in class org.coolmap.core.application.ui.util.TableRowTransferHandler

getStatesForCoolMapObject(CoolMapObject) - Static method in class org.coolmap.core.application.state.StateStorageMaster

getStdDev(Collection<Double>) - Static method in class org.coolmap.core.util.statistics.AggregationUtil

getSubHeatMap(VNode, VNode, List<String>, List<String>, int) - Method in class org.coolmap.core.canvas.renderer.impl.NumberToColor

getSubHeatMapCellSize() - Static method in class org.coolmap.core.canvas.CoolMapView

getSubMapDimension() - Method in class org.coolmap.core.canvas.CoolMapView

returns the x,y,width,height of submapbuffer

getSubsets() - Method in class org.coolmap.core.util.bioparser.geosoft.GeoSOFT

getSubTip(CoolMapObject, VNode, VNode, float, float, int, int) - Method in class org.coolmap.core.canvas.renderer.impl.NumberToBoxPlot

getSubTip(CoolMapObject, VNode, VNode, float, float, int, int) - Method in class org.coolmap.core.canvas.renderer.impl.NumberToColor

getSubTip(CoolMapObject, VNode, VNode, float, float, int, int) - Method in class org.coolmap.core.canvas.renderer.impl.NumberToSeries

getSubTip(CoolMapObject, VNode, VNode, float, float, int, int) - Method in class org.coolmap.core.canvas.renderer.impl.NumberToSortedBar

getSubTip(CoolMapObject, VNode, VNode, float, float, int, int) - Method in class org.coolmap.core.canvas.renderer.model.ViewRenderer

getSum(Collection<Double>) - Static method in class org.coolmap.core.util.statistics.AggregationUtil

getSupportedFileExtensions() - Method in enum org.coolmap.core.application.io.FileDelimiterEnum

getSupportedFileExtensions() - Method in enum org.coolmap.core.data.ontology.CoolMapOntologyFileFormatEnum

getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.coolmap.core.application.ui.util.JTableButtonCell

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.coolmap.core.application.ui.util.JTableButtonCell

getTagColor(String) - Static method in class org.coolmap.core.util.graphics.UI

getTipName() - Method in class org.coolmap.core.data.aggregator.CAggregator

getTitle() - Method in class org.coolmap.core.util.statistics.test.TestResult

getToBeExpandedIndices() - Method in class org.coolmap.core.data.ontology.model.COntologyPreset

getToggleAnimator() - Method in class org.coolmap.core.canvas.ui.sidemaps.SideMapDrawer.DrawerHandle

getToggleTarget() - Method in class org.coolmap.core.canvas.ui.sidemaps.SideMapDrawer.DrawerHandle

getTree() - Method in class org.coolmap.core.util.bioparser.simpleobo.SimpleOBOTree

returns the go tree - not a copy, for efficiency and economy concerns

getTreeNodeOffset(VNode, CoolMapObject) - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnTree

getTreeNodeOffset(VNode, CoolMapObject) - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowTree

getTreeNodeOffset(VNode, CoolMapObject) - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideTree

getTreeNodesColumn(float, float) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getTreeNodesColumn() - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getTreeNodesRow(float, float) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getTreeNodesRow() - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getType() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getUniqueID() - Method in class org.coolmap.core.data.entity.sampleProperty.model.CategorizedDataPropertyGroup

getUniqueID() - Method in class org.coolmap.core.data.entity.sampleProperty.model.ContinuousDataPropertyGroup

getUniqueID() - Method in class org.coolmap.core.data.entity.sampleProperty.model.DataPropertyGroup

getUniqueName() - Method in class org.coolmap.core.data.entity.sampleProperty.model.CategorizedDataPropertyGroup

getUniqueValueAsListByProperty(PROPERTY) - Method in class org.coolmap.core.data.entity.model.DataPropertyTable

getValue() - Method in class org.coolmap.core.api.aggregation.IdToSidePanelDisplayConverter.SidePanelValueColorPair

getValue(int, int) - Method in interface org.coolmap.core.api.data.matrix.CoolMapMatrix

Get value at (rowIndex, columnIndex) from the data matrix

getValue(int, int) - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

getValue(int, int) - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

getValue(int, int) - Method in class org.coolmap.core.data.cmatrix.model.Model2DCMatrix

getValue(int, int) - Method in class org.coolmap.core.data.cmatrix.model.NetworkCoolMapMatrix

getValue(int, int, CAggregator<BASE, VIEW>, List<CoolMapMatrix<BASE>>) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

getValue(int, int) - Method in class org.coolmap.core.util.bioparser.geosoft.ArrayTable

getValue(int, int) - Method in class org.coolmap.core.util.CoolMapDoubleMatrix

getValueAggregator() - Method in class org.coolmap.core.api.aggregation.AbstractIdToSidePanelDisplayConverterNoOntology

getValueAggregator() - Method in class org.coolmap.core.api.aggregation.AbstractIdToSidePanelDisplayConverterUseOntology

getValueAggregator() - Method in interface org.coolmap.core.api.aggregation.IdToSidePanelDisplayConverter

getValueAsListByProperty(PROPERTY) - Method in class org.coolmap.core.data.entity.model.DataPropertyTable

getValueAsListByRow(ROW) - Method in class org.coolmap.core.data.entity.model.DataPropertyTable

getValueAsString() - Method in class org.coolmap.core.data.entity.sampleProperty.model.CategorizedDataProperty

getValueAsString() - Method in class org.coolmap.core.data.entity.sampleProperty.model.ContinuousDataProperty

getValueAsString() - Method in class org.coolmap.core.data.entity.sampleProperty.model.DataProperty

getValueAt(int, int) - Method in class org.coolmap.core.application.ui.util.DataMatrixTableRowHeader

getValueMapper() - Method in class org.coolmap.core.api.aggregation.AbstractIdToSidePanelDisplayConverterNoOntology

getValueMapper() - Method in class org.coolmap.core.api.aggregation.AbstractIdToSidePanelDisplayConverterUseOntology

getValueMapper() - Method in interface org.coolmap.core.api.aggregation.IdToSidePanelDisplayConverter

getVariance(Collection<Double>) - Static method in class org.coolmap.core.util.statistics.AggregationUtil

getViewCanvas() - Method in class org.coolmap.core.canvas.CoolMapView

returns the JComponent that displays CoolMap

getViewClass() - Method in class org.coolmap.core.data.aggregator.CAggregator

getViewClass() - Method in class org.coolmap.core.data.CoolMapObject

getViewColor() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getViewColor() - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getViewFrame() - Method in class org.coolmap.core.canvas.CoolMapView

getViewHeightDiffFromParent() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getViewHeightInTree() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getViewIndex() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getViewLabel() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getViewNodeColumn(int) - Method in class org.coolmap.core.data.CoolMapObject

getViewNodeRow(int) - Method in class org.coolmap.core.data.CoolMapObject

getViewNodesColumn(String) - Method in class org.coolmap.core.data.CoolMapObject

returns all view base nodes that has the name in column

getViewNodesColumn() - Method in class org.coolmap.core.data.CoolMapObject

getViewNodesColumn(VNode) - Method in class org.coolmap.core.data.CoolMapObject

returns all child nodes in view to this parent

getViewNodesColumnFromTreeNodesAll(Collection<VNode>) - Method in class org.coolmap.core.data.CoolMapObject

get all nodes associated with the selected tree nodes

getViewNodesColumnFromTreeNodesLeafOnly(Collection<VNode>) - Method in class org.coolmap.core.data.CoolMapObject

get leaft nodes from seleted tree nodes in row

getViewNodesColumnSelected() - Method in class org.coolmap.core.data.CoolMapObject

getViewNodesColumnTree(float, float) - Method in class org.coolmap.core.data.CoolMapObject

returns a subset of tree nodes that currently have view index between fromViewIndex and toViewIndex

getViewNodesRow(String) - Method in class org.coolmap.core.data.CoolMapObject

returns all view base nodes that has the name in row

getViewNodesRow() - Method in class org.coolmap.core.data.CoolMapObject

getViewNodesRow(VNode) - Method in class org.coolmap.core.data.CoolMapObject

getViewNodesRowFromTreeNodesAll(Collection<VNode>) - Method in class org.coolmap.core.data.CoolMapObject

get all nodes associated with the selected tree nodes

getViewNodesRowFromTreeNodesLeafOnly(Collection<VNode>) - Method in class org.coolmap.core.data.CoolMapObject

get all leaf nodes from selected tree nodes in row

getViewNodesRowSelected() - Method in class org.coolmap.core.data.CoolMapObject

getViewNodesRowTree(float, float) - Method in class org.coolmap.core.data.CoolMapObject

returns a subset of tree nodes that currently have view index between fromViewIndex and toViewIndex

getViewNumColumns() - Method in class org.coolmap.core.data.CoolMapObject

getViewNumRows() - Method in class org.coolmap.core.data.CoolMapObject

getViewOffset() - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getViewOffset(float) - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getViewOffsetCenter(float) - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getViewPanel() - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideMap

getViewport() - Static method in class org.coolmap.core.application.widget.WidgetMaster

getViewRenderer() - Method in class org.coolmap.core.data.CoolMapObject

getViewSizeInMap(float) - Method in class org.coolmap.core.data.cmatrixview.model.VNode

getViewTreeNodesColumn() - Method in class org.coolmap.core.data.CoolMapObject

obtains the nodes in tree

getViewTreeNodesRow() - Method in class org.coolmap.core.data.CoolMapObject

obtains a copy of nodes in row

getViewValue(int, int) - Method in class org.coolmap.core.data.CoolMapObject

get view cache directly from underlying view matrix used for rendering

getViewValueAsSnippet(int, int) - Method in class org.coolmap.core.data.CoolMapObject

getVNodeById(String) - Method in class org.coolmap.core.data.ontology.model.CoolMapOntologyImpl

getWidget(String) - Static method in class org.coolmap.core.application.widget.WidgetMaster

getWidgetGroup() - Method in class org.coolmap.core.application.widget.Widget

getZoom(int) - Method in class org.coolmap.core.canvas.ui.ZoomControl

getZoomControlX() - Method in class org.coolmap.core.canvas.CoolMapView

getZoomControlY() - Method in class org.coolmap.core.canvas.CoolMapView

getZoomX() - Method in class org.coolmap.core.canvas.CoolMapView

getZoomY() - Method in class org.coolmap.core.canvas.CoolMapView

GmtEntry - Class in org.coolmap.core.util.bioparser.gseagmt

GmtEntry(String, GmtEntry.ID_TYPE) - Constructor for class org.coolmap.core.util.bioparser.gseagmt.GmtEntry

GmtEntry.ID_TYPE - Enum in org.coolmap.core.util.bioparser.gseagmt

GMTFormatCoolMapOntologyImporter - Class in org.coolmap.core.application.io.internal.contology

Created by Keqiang Li on 4/11/16.

GMTFormatCoolMapOntologyImporter(File) - Constructor for class org.coolmap.core.application.io.internal.contology.GMTFormatCoolMapOntologyImporter

googleScholarURL - Static variable in class org.coolmap.core.util.BrowserLauncher

googleSearchURL - Static variable in class org.coolmap.core.util.BrowserLauncher

GradientEditorPanel - Class in org.coolmap.core.util.graphics

GradientEditorPanel() - Constructor for class org.coolmap.core.util.graphics.GradientEditorPanel

GraphFrame - Class in org.coolmap.core.util.network

Dialog with a simple graph visualization, displaying graph nodes as circles of specified sizes and colors at specified positions.

GraphFrame(Map<Node, double[]>, Map<Node, Integer>) - Constructor for class org.coolmap.core.util.network.GraphFrame

Constructs the dialog.

gridChanged(CoolMapObject) - Method in enum org.coolmap.core.application.utils.ActiveCoolMapObjectListenerTunnel

gridChanged(CoolMapObject) - Method in class org.coolmap.core.application.widget.impl.WidgetPointAnnotation

gridChanged(CoolMapObject) - Method in class org.coolmap.core.application.widget.impl.WidgetSyncer

gridChanged(CoolMapObject) - Method in class org.coolmap.core.canvas.listeners.CViewAdaptor

gridChanged(CoolMapObject) - Method in interface org.coolmap.core.canvas.listeners.CViewListener

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