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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SamplePropertyMaster - Class in org.coolmap.core.data.entity.sampleProperty

SamplePropertyMaster() - Constructor for class org.coolmap.core.data.entity.sampleProperty.SamplePropertyMaster

SamplePropertyMatrix - Class in org.coolmap.core.data.entity.sampleProperty.model

This data object should be maintained during users modifying the order of properties thus generating the new ontology for properties

SamplePropertyMatrix(DataPropertyTable<String, String, String>, List<String>) - Constructor for class org.coolmap.core.data.entity.sampleProperty.model.SamplePropertyMatrix

saveCoolMapProject(File, boolean) - Static method in class org.coolmap.core.application.io.IOMaster

SaveDataDialog - Class in org.coolmap.core.application.ui.object

Created by Keqiang Li on 5/2/16.

SaveDataDialog(Window) - Constructor for class org.coolmap.core.application.ui.object.SaveDataDialog

saveOntologyToFile(CoolMapOntologyImpl, CoolMapOntologyFileFormatEnum, File) - Static method in class org.coolmap.core.application.io.IOHelper

SaveStateAction - Class in org.coolmap.core.application.state

SaveStateAction() - Constructor for class org.coolmap.core.application.state.SaveStateAction

saveStateBeforeOperation(String, CoolMapObject) - Static method in class org.coolmap.core.application.state.StateStorageMaster

saveStateForCoolMapObject(CoolMapObject, String) - Static method in class org.coolmap.core.application.state.StateStorageMaster

scrollToVisible(JTable, int, int) - Static method in class org.coolmap.core.canvas.ui.sidemaps.util.ExpandingControlDialog

search(String, Object...) - Static method in class org.coolmap.core.util.BrowserLauncher

SearchableTableRowFilter - Class in org.coolmap.core.application.ui.util

Created by Keqiang Li on 4/21/16.

SearchableTableRowFilter(String) - Constructor for class org.coolmap.core.application.ui.util.SearchableTableRowFilter

Selectable<T> - Interface in org.coolmap.core.canvas.ui.sidemaps

Created by Keqiang Li on 6/10/16.

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

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

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

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

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

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

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

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

selectViewNodesColumnTree(List<VNode>) - Method in class org.coolmap.core.data.CoolMapObject

selectViewNodesRowTree(List<VNode>) - Method in class org.coolmap.core.data.CoolMapObject

Session - Class in org.coolmap.core.application.utils

Session(String, String) - Constructor for class org.coolmap.core.application.utils.Session

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

setActiveCell(MatrixCell, MatrixCell) - Method in class org.coolmap.core.canvas.CoolMapView

setActiveColNodes(List<VNode>, boolean) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

replace the colnodes with new nodes, and remove all tree nodes;

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

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

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

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

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

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

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

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

setActiveRowNodes(List<VNode>, boolean) - Method in class org.coolmap.core.data.cmatrixview.model.VMatrix

set the active colNodes

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

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

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

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

setAggregator(CAggregator<BASE, VIEW>) - Method in class org.coolmap.core.data.CoolMapObject

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

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

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

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

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

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

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

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

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

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

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

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

setCategoryColor(String, Color) - Method in class org.coolmap.core.api.aggregation.SidePanelCategoricalValueAggregator

setCategoryColor(String, Color) - Method in class org.coolmap.core.api.aggregation.SidePanelCategoricalValueToColorMapper

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

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

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

setColIds(String[]) - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

setColumnIds(Set<String>) - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

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

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

setContPropGroup(String, ArrayList<Double>) - Method in class org.coolmap.core.data.entity.sampleProperty.model.SamplePropertyMatrix

setCoolMapObject(CoolMapObject, boolean) - Method in class org.coolmap.core.canvas.renderer.model.ViewRenderer

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

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

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

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

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

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

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

Set or change the description of this Ontology

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

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

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

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

setDisplayConverter(IdToSidePanelDisplayConverter<VALUE>) - Method in class org.coolmap.core.api.aggregation.AbstractSidePanelValueAggregator

setDisplayConverter(IdToSidePanelDisplayConverter<VALUE>) - Method in interface org.coolmap.core.api.aggregation.SidePanelValueAggregator

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setExporter(Class<? extends CoolMapMatrix>, InternalCoolMapMatrixExporter) - Static method in class org.coolmap.core.application.io.IOMaster

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

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

The foreground color of the button when the cell has focus

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

force drawing hover whenever active row/column is valid

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

setGroup(DataPropertyGroup<T>) - Method in class org.coolmap.core.data.entity.sampleProperty.model.DataProperty

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

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

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

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

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

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

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

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

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

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

setLabel(String) - Method in class org.coolmap.core.application.utils.TaskDialog

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

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

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

setLastSize(int) - Method in class org.coolmap.core.canvas.ui.sidemaps.SideMapDrawer.TargetDrawerContainerToggle

setLastSize(int) - Method in class org.coolmap.core.canvas.ui.sidemaps.SideMapDrawer.TargetDrawerToggle

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

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

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

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

Attempt to maximize view

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

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

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

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

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

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

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

The mnemonic to activate the button when the cell has focus

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

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

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

Set or rename the data matrix

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

Set or rename this Ontology

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

setRegions(Set<Rectangle>) - Method in class org.coolmap.core.canvas.ui.HighlightLayer

set the region on the map

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

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

setRowIds(Set<String>) - Method in class org.coolmap.core.data.cmatrix.impl.DataTableBackedCoolMapMatrix

setRowIds(String[]) - Method in class org.coolmap.core.data.cmatrix.model.AbstractCoolMapMatrix

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

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

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

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

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

setSelectedTreeNodes(Set<VNode>) - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnTree

setSelectedTreeNodes(Set<VNode>) - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowTree

setSelectedTreeNodes(Set<VNode>) - Method in interface org.coolmap.core.canvas.ui.sidemaps.SideTree

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

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

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

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

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

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

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

setSelectionRowIndices(Collection<Integer>) - Method in class org.coolmap.core.canvas.CoolMapView

setSelections(Collection<Rectangle>) - Method in class org.coolmap.core.canvas.CoolMapView

setSelectionsColumn(Collection<Range<Integer>>) - Method in class org.coolmap.core.canvas.CoolMapView

setSelectionsColumnIndices(Collection<Integer>) - Method in class org.coolmap.core.canvas.CoolMapView

setSelectionsRow(Collection<Range<Integer>>) - Method in class org.coolmap.core.canvas.CoolMapView

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

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

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

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

setSidePanelDisplayConverter(IdToSidePanelDisplayConverter<VIEW>) - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnHighlighter

setSidePanelDisplayConverter(IdToSidePanelDisplayConverter<VALUE>) - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowHighlighter

setSidePanelDisplayConverter(IdToSidePanelDisplayConverter<VALUE>) - Method in interface org.coolmap.core.canvas.ui.sidemaps.SidePanelHighlighter

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

a converter used to convert view matrix value into a short phrase for tool tip

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

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

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

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

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

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

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

setTitle(String, String) - Method in class org.coolmap.core.application.widget.Widget

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

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

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

this could result in Array Index of of bounds exception

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

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

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

setValueAggregator(SidePanelValueAggregator<VALUE, ?>) - Method in class org.coolmap.core.api.aggregation.AbstractIdToSidePanelDisplayConverterUseOntology

setValueMapper(SidePanelValueToColorMapper<VALUE>) - Method in class org.coolmap.core.api.aggregation.AbstractIdToSidePanelDisplayConverterNoOntology

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

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

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

setViewFilters(List<ViewFilter>) - Method in class org.coolmap.core.data.CoolMapObject

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

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

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

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

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

setViewRenderer(ViewRenderer<VIEW>, boolean) - Method in class org.coolmap.core.data.CoolMapObject

set view renderer maybe an event is needed to notify changed

setWithMarks(ArrayList<Double>) - Method in class org.coolmap.core.data.entity.sampleProperty.model.ContinuousDataPropertyGroupSetting

setWithNewGroups(ArrayList<DataPropertyGroup>) - Method in class org.coolmap.core.data.entity.sampleProperty.model.DataPropertyGroupSetting

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

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

it will only work when the view is valid

setZoomLevels(float, float) - Method in class org.coolmap.core.canvas.CoolMapView

showBusyDialog(String) - Method in class org.coolmap.core.application.CoolMapMainFrame

showErrorMessage(String, String) - Static method in class org.coolmap.core.application.utils.Messenger

showMessage(String, boolean) - Method in class org.coolmap.core.application.ui.util.ConfirmOrCancelDialog

showStackTrace(Exception, String) - Static method in class org.coolmap.core.application.utils.Messenger

showStackTrace(Exception, String, String) - Static method in class org.coolmap.core.application.utils.Messenger

showWarningMessage(String, String) - Static method in class org.coolmap.core.application.utils.Messenger

SideMap<BASE,VIEW> - Interface in org.coolmap.core.canvas.ui.sidemaps

Created by Keqiang Li on 6/9/16.

SideMapDrawer - Class in org.coolmap.core.canvas.ui.sidemaps

Created by Keqiang Li on 6/15/16.

SideMapDrawer(Point, CoolMapView) - Constructor for class org.coolmap.core.canvas.ui.sidemaps.SideMapDrawer

SideMapDrawer.DrawerHandle - Class in org.coolmap.core.canvas.ui.sidemaps

SideMapDrawer.TargetDrawerContainerToggle - Class in org.coolmap.core.canvas.ui.sidemaps

SideMapDrawer.TargetDrawerToggle - Class in org.coolmap.core.canvas.ui.sidemaps

sideMapLinkedToHandle - Variable in class org.coolmap.core.canvas.ui.sidemaps.SideMapDrawer.DrawerHandle

SidePanelCategoricalValueAggregator - Class in org.coolmap.core.api.aggregation

Created by Keqiang Li on 5/20/16.

SidePanelCategoricalValueAggregator(CategoricalValueAggregationMethod) - Constructor for class org.coolmap.core.api.aggregation.SidePanelCategoricalValueAggregator

SidePanelCategoricalValueToColorMapper - Class in org.coolmap.core.api.aggregation

Created by Keqiang Li on 5/23/16.

SidePanelCategoricalValueToColorMapper() - Constructor for class org.coolmap.core.api.aggregation.SidePanelCategoricalValueToColorMapper

SidePanelContinuousValueAggregator - Class in org.coolmap.core.api.aggregation

Created by Keqiang Li on 5/20/16.

SidePanelContinuousValueAggregator(ContinuousValueAggregationMethod, double, double) - Constructor for class org.coolmap.core.api.aggregation.SidePanelContinuousValueAggregator

SidePanelContinuousValueToColorMapper - Class in org.coolmap.core.api.aggregation

Created by Keqiang Li on 5/23/16.

SidePanelContinuousValueToColorMapper(double, double) - Constructor for class org.coolmap.core.api.aggregation.SidePanelContinuousValueToColorMapper

SidePanelHighlighter<BASE,VIEW,VALUE> - Interface in org.coolmap.core.canvas.ui.sidemaps

Created by Keqiang Li on 6/9/16.

SidePanelValueAggregator<VALUE,AggregationMethodEnum> - Interface in org.coolmap.core.api.aggregation

Created by Keqiang Li on 5/20/16.

SidePanelValueColorPair(VALUE, Color) - Constructor for class org.coolmap.core.api.aggregation.IdToSidePanelDisplayConverter.SidePanelValueColorPair

SidePanelValueToColorMapper<VALUE> - Interface in org.coolmap.core.api.aggregation

Created by Keqiang Li on 5/23/16.

SideTree - Interface in org.coolmap.core.canvas.ui.sidemaps

Created by Keqiang Li on 6/10/16.

SideTreeExpandingFinishedEvent - Class in org.coolmap.core.canvas.ui.sidemaps.listener

SideTreeExpandingFinishedEvent(Object, List<VNode>) - Constructor for class org.coolmap.core.canvas.ui.sidemaps.listener.SideTreeExpandingFinishedEvent

SideTreeNodeExpandingTask - Class in org.coolmap.core.canvas.ui.sidemaps.task

SideTreeNodeListExpandingListener - Interface in org.coolmap.core.canvas.ui.sidemaps.listener

SideTreeUtil - Class in org.coolmap.core.canvas.ui.sidemaps.util

SideTreeUtil() - Constructor for class org.coolmap.core.canvas.ui.sidemaps.util.SideTreeUtil

SimpleOBOEntry - Class in org.coolmap.core.util.bioparser.simpleobo

SimpleOBOEntry() - Constructor for class org.coolmap.core.util.bioparser.simpleobo.SimpleOBOEntry

SimpleOBOTree - Class in org.coolmap.core.util.bioparser.simpleobo

records the relationship between GO terms

SimpleOBOTree() - Constructor for class org.coolmap.core.util.bioparser.simpleobo.SimpleOBOTree

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

Created by Keqiang Li on 4/11/16.

SimpleTwoColumnFormatCoolMapOntologyImporter(File, FileDelimiterEnum, int, int) - Constructor for class org.coolmap.core.application.io.internal.contology.SimpleTwoColumnFormatCoolMapOntologyImporter

SnippetConverter - Class in org.coolmap.core.data.snippet

SnippetConverter() - Constructor for class org.coolmap.core.data.snippet.SnippetConverter

SnippetMaster - Class in org.coolmap.core.data.snippet

SnippetMaster() - Constructor for class org.coolmap.core.data.snippet.SnippetMaster

sort(Comparator<VNode>) - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.ColumnHighlighter

sort(Comparator<VNode>) - Method in class org.coolmap.core.canvas.ui.sidemaps.impl.RowHighlighter

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

sort(Comparator<VNode>) - Method in interface org.coolmap.core.canvas.ui.sidemaps.SidePanelHighlighter

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

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

sortColumnsBySelectedRows(List<Integer>, List<Boolean>) - Method in class org.coolmap.core.data.CoolMapObject

SortingConfigDialog - Class in org.coolmap.core.data.cmatrixview.utils

SortingConfigDialog(Frame, boolean, boolean, CoolMapObject) - Constructor for class org.coolmap.core.data.cmatrixview.utils.SortingConfigDialog

Creates new form SortingConfigDialog

sortRowsBySelectedColumns(List<Integer>, List<Boolean>) - Method in class org.coolmap.core.data.CoolMapObject

SortTracker - Class in org.coolmap.core.data.cmatrixview.utils

SortTracker() - Constructor for class org.coolmap.core.data.cmatrixview.utils.SortTracker

splashInit() - Static method in class org.coolmap.core.util.CoolMapSplashScreen

splashUpdate(String, int) - Static method in class org.coolmap.core.util.CoolMapSplashScreen

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

startNode - Variable in class org.coolmap.core.util.network.Edge

Start node.

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

StateQueue - Class in org.coolmap.core.application.state

StateQueue(String) - Constructor for class org.coolmap.core.application.state.StateQueue

StateSavable - Interface in org.coolmap.core.util

StateStorageMaster - Class in org.coolmap.core.application.state

StateStorageMaster() - Constructor for class org.coolmap.core.application.state.StateStorageMaster

StateStorageMasterListeners - Class in org.coolmap.core.application.state

StateStorageMasterListeners() - Constructor for class org.coolmap.core.application.state.StateStorageMasterListeners

stateToBeRestored(CoolMapObject, CoolMapState) - Method in interface org.coolmap.core.data.state.CObjectStateStoreListener

restore an object from the state; the source

stateToBeRestored(CoolMapObject, CoolMapState) - Method in class org.coolmap.core.data.state.misc.ZoomTracker

stateToBeSaved(CoolMapObject, CoolMapState) - Method in interface org.coolmap.core.data.state.CObjectStateStoreListener

This is only called when a config file is needed

stateToBeSaved(CoolMapObject, CoolMapState) - Method in class org.coolmap.core.data.state.misc.ZoomTracker

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

STRAIGHT - Static variable in interface org.coolmap.core.canvas.ui.sidemaps.SideTree

STRING_MENU_ANALYSIS - Static variable in class org.coolmap.core.application.CoolMapMainFrame

STRING_MENU_EDIT - Static variable in class org.coolmap.core.application.CoolMapMainFrame

STRING_MENU_FILE - Static variable in class org.coolmap.core.application.CoolMapMainFrame

STRING_MENU_HELP - Static variable in class org.coolmap.core.application.CoolMapMainFrame

STRING_MENU_PLUGIN - Static variable in class org.coolmap.core.application.CoolMapMainFrame

STRING_MENU_VIEW - Static variable in class org.coolmap.core.application.CoolMapMainFrame

stringArrowDown - Static variable in class org.coolmap.core.util.graphics.UI

stringArrowUp - Static variable in class org.coolmap.core.util.graphics.UI

stroke1 - Static variable in class org.coolmap.core.util.graphics.UI

stroke1_5 - Static variable in class org.coolmap.core.util.graphics.UI

stroke2 - Static variable in class org.coolmap.core.util.graphics.UI

stroke3 - Static variable in class org.coolmap.core.util.graphics.UI

stroke3_5 - Static variable in class org.coolmap.core.util.graphics.UI

stroke4 - Static variable in class org.coolmap.core.util.graphics.UI

stroke5 - Static variable in class org.coolmap.core.util.graphics.UI

stroke6 - Static variable in class org.coolmap.core.util.graphics.UI

stroke7 - Static variable in class org.coolmap.core.util.graphics.UI

stroke8 - Static variable in class org.coolmap.core.util.graphics.UI

strokeDash1_5 - Static variable in class org.coolmap.core.util.graphics.UI

strokeDash2 - Static variable in class org.coolmap.core.util.graphics.UI

strokeDash3 - Static variable in class org.coolmap.core.util.graphics.UI

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

SUBSET - Static variable in class org.coolmap.core.util.bioparser.geosoft.FieldConstants

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

Subset(String) - Constructor for class org.coolmap.core.util.bioparser.geosoft.Subset

subsetDatasetID - Static variable in class org.coolmap.core.util.bioparser.geosoft.FieldConstants

subsetDescription - Static variable in class org.coolmap.core.util.bioparser.geosoft.FieldConstants

subsetSampleID - Static variable in class org.coolmap.core.util.bioparser.geosoft.FieldConstants

subsetType - Static variable in class org.coolmap.core.util.bioparser.geosoft.FieldConstants

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