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Dataset
object.
NodeInfo
object to be
created in the dataset of the given selected path.
column
.
TableSorter
's getColumnClass
method.
TableSorter
's getColumnClass
method.
TableSorterValues
's getColumnClass
method.
TableSorter
's getColumnClass
method.
column
.
column
.
TableSorter
's getComparator
method.
TableSorter
's getComparator
method.
TableSorterValues
's getComparator
method.
TableSorter
's getComparator
method.
meanValue
to find the red or green
color component to colorize the cell.
Color
used to mark even rows that are not selected.
Color
used to mark even rows that are not selected.
GOFrontEnd
for the given
selectionPath
, if it exists, otherwise returns null.
GOFrontEnd
of
the given selectionPath
.
column
.
Color
used to mark highly significant terms.
NodeInfo
object.
- getInfo() -
Method in class biggests.tree.NodeInfo
- Returns a styled document containing information about this node.
- getInfoStrings() -
Method in class biggests.tree.NodeInfo
- Returns information strings.
- getInfoStyles() -
Method in class biggests.tree.NodeInfo
- Returns information styles.
- getInvalidDirectoryPaths() -
Method in class biggests.utils.FileFilterDirectory
- Returns this file filter invalid directory paths.
- getLabelContext() -
Method in class biggests.gui.BiggestsFrame
- Returns the context label, which displays tips about functionality
options to user.
- getLastBiclusterGroupId() -
Method in class biggests.tree.Dataset
- Returns the last id given to a bicluster group node information object
within the current dataset.
- getLastDiscretizedId() -
Method in class biggests.tree.Dataset
- Returns the last id given to a discretized node information object
within the current dataset.
- getLastPostprocessedGroupId() -
Method in class biggests.tree.Dataset
- Returns the last id given to a post-processed group node information
object within the current dataset.
- getLastPreprocessedId() -
Method in class biggests.tree.Dataset
- Returns the last id given to a preprocessed node information object
within the current dataset.
- getLeft() -
Method in class biggests.clustering.ClusterTreeNode
- Returns the index of the left element or node (left son).
- getMainFrame() -
Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
- Returns the application's main frame.
- getMainFrame() -
Method in class biggests.gui.PanelAnalyzingMatrixTables
- Returns the application's main frame.
- getMainFrame() -
Method in class biggests.gui.PanelBiclustering
- Returns the application's main frame.
- getMainFrame() -
Method in class biggests.gui.PanelExpression
- Returns the application's main frame, where this panel is being displayed.
- getMainFrame() -
Method in class biggests.gui.PanelFunctionAnalysis
- Returns the application's main frame.
- getMainFrame() -
Method in class biggests.gui.PanelPostProcessing
- Returns the frame of the application.
- getMainFrame() -
Method in class biggests.gui.PanelPreProcessing
- Returns the application's main frame.
- getMarkovChainOrderFilterTextField() -
Method in class biggests.gui.PanelPostProcessing
- Returns Markov chain order input text field.
- getMarkovChainOrderSortTextField() -
Method in class biggests.gui.PanelPostProcessing
- Returns Markov chain order input text field.
- getMeanValue() -
Method in class biggests.tables.TableColors
- Returns the mean value of the float values in the table.
- getMeanValueColor() -
Static method in class biggests.utils.HeatmapColorScheme
-
- getMenu() -
Method in class biggests.gui.BiggestsFrame
- Returns the application's menu bar.
- getMessageHistory() -
Method in class biggests.utils.ProgressBarFrame
- Returns message history.
- getMissingValue() -
Method in class biggests.tables.TableColorsWithMissingValues
- Returns the value used to mark cells which correspond to missing
values on the original gene expression data.
- getMissingValueColor() -
Static method in class biggests.utils.HeatmapColorScheme
-
- getMSRTextField() -
Method in class biggests.gui.PanelPostProcessing
- Returns MSR threshold input text field.
- getName() -
Method in class biggests.tree.Dataset
- Returns the name of this dataset.
- getName() -
Method in class biggests.tree.NodeInfo
- Returns the name of this node information object.
- getNeighborsECCCLabel() -
Method in class biggests.gui.PanelBiclustering
- Label for the number of neighbors on e-CCC-Biclustering algorithm.
- getNeighborsECCCTextField() -
Method in class biggests.gui.PanelBiclustering
- Text field for the input of number of neighbors for
e-CCC-Biclustering algorithm.
- getNodeInfo() -
Method in class biggests.gui.PanelAnalyzingMatrixTables
- Returns the node information object containing the object with the data
to display in the table.
- getNodeObject() -
Method in class biggests.gui.PanelAnalyzingFunctionTable
- Returns the bicluster group that is being processed.
- getNodeObject() -
Method in class biggests.tree.NodeInfo
- Returns the node object associated with the current node information object.
- getNodeObjectType() -
Method in class biggests.tree.NodeInfo
- Returns the node object type.
- getNormalize() -
Method in class biggests.gui.PanelExpression
- Returns the check box which allows the user to choose between an
expression chart with original or normalized data.
- getNormalizeButtonGroup() -
Method in class biggests.gui.PanelPreProcessing
- Returns normalize options button group.
- getNormalizeByGeneButton() -
Method in class biggests.gui.PanelPreProcessing
- Returns normalize by gene button.
- getNormalizeCheckBox() -
Method in class biggests.gui.PanelPreProcessing
- Returns normalize check box.
- getNormalizeMean0Std1Button() -
Method in class biggests.gui.PanelPreProcessing
- Returns normalize to mean 0 and std 1 button.
- getNormalizeMeanStdButtonGroup() -
Method in class biggests.gui.PanelPreProcessing
- Returns normalize to mean and std options button group.
- getNormalizeMeanStdValuesButton() -
Method in class biggests.gui.PanelPreProcessing
- Returns normalize by mean and std values button.
- getNormalizeMeanStdValuesLabel() -
Method in class biggests.gui.PanelPreProcessing
- Returns normalize to mean and std values label.
- getNormalizeMeanValueTextField() -
Method in class biggests.gui.PanelPreProcessing
- Return normalize mean input text field.
- getNormalizeOverallButton() -
Method in class biggests.gui.PanelPreProcessing
- Returns normalize overall values button.
- getNormalizeStdValueTextField() -
Method in class biggests.gui.PanelPreProcessing
- Returns normalize std input text field.
- getNumberOfDendrograms() -
Static method in class biggests.gui.PanelAnalyzingMatrixDendrogram
-
- getOddRowsColor() -
Method in class biggests.tables.TableFunctionGroup
- Returns the
Color
used to mark odd rows that are not selected.
- getOddRowsColor() -
Method in class biggests.tables.TableFunctionIndividual
- Returns the
Color
used to mark odd rows that are not selected.
- getOption() -
Method in class biggests.gui.PanelExpression
- Returns the combo box for the user to choose the number of biclusters
to display.
- getOrganism() -
Method in class biggests.gui.PanelFunctionAnalysis
- Returns the organism related with this function analysis.
- getOrganismLabel() -
Method in class biggests.gui.PanelFunctionAnalysis
- Returns the organism label.
- getPanelAnalyzingExpressionAllTimePoints() -
Method in class biggests.gui.BiggestsFrame
- Returns the expression analysis by all time points chart panel.
- getPanelAnalyzingFunctionSignificanceGraph() -
Method in class biggests.gui.BiggestsFrame
- Returns the function analysis - significance graph panel.
- getPanelAnalyzingFunctionTable() -
Method in class biggests.gui.BiggestsFrame
- Returns the function analysis - table panel.
- getPanelAnalyzingMatrixColors() -
Method in class biggests.gui.BiggestsFrame
- Returns the matrix analysis by colors panel.
- getPanelAnalyzingMatrixSymbols() -
Method in class biggests.gui.BiggestsFrame
- Returns the matrix analysis by symbols panel.
- getPanelAnalyzingMatrixValues() -
Method in class biggests.gui.BiggestsFrame
- Returns the matrix analysis by values panel.
- getPanelBiclustering() -
Method in class biggests.gui.BiggestsFrame
- Returns biclustering panel.
- getPanelContent() -
Method in class biggests.gui.BiggestsFrame
- Returns this frames' content panel.
- getPanelExpressionBiclusterPattern() -
Method in class biggests.gui.BiggestsFrame
- Returns the expression analysis by bicluster pattern chart panel.
- getPanelExpressionBiclusterTimePoints() -
Method in class biggests.gui.BiggestsFrame
- Returns the expression analysis by bicluster time points chart panel.
- getPanelLoading() -
Method in class biggests.gui.BiggestsFrame
- Returns the loading panel.
- getPanelPreProcessing() -
Method in class biggests.gui.BiggestsFrame
- Returns preprocessing panel.
- getPanelRight() -
Method in class biggests.gui.BiggestsFrame
- Returns the panel on the right, which holds the tabs and
visualization panels.
- getPanels() -
Method in class biggests.gui.PanelAnalyzingMatrixTables
- Returns the set of panels which holds the tables and their headers,
which are displayed in this panel (for
COLORS
and SYMBOLS
tableType
s only).
- getParentNodeInfo() -
Method in class biggests.tree.NodeInfo
- Returns parent node information object.
- getPathsToFolders() -
Method in class biggests.gui.BiggestsFrame
- Returns the paths to function results, gene ontology files and sessions.
- getPathToDatasets() -
Method in class biggests.gui.BiggestsFrame
- Returns the path to the directory with dataset files.
- getPathToDOT() -
Method in class biggests.gui.BiggestsFrame
- Returns the path to dot binary file.
- getPathToFunctionResults() -
Method in class biggests.gui.BiggestsFrame
- Returns the path to function results' folder/directory.
- getPathToGO_Files() -
Method in class biggests.gui.BiggestsFrame
- Returns the path to gene ontology files folder/directory.
- getPathToImage() -
Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
- Returns the path to image.
- getPathToSessions() -
Method in class biggests.gui.BiggestsFrame
- Returns the path to stored session files folder/directory.
- getPathToSvg() -
Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
- Returns the path to svg.
- getProgressBar() -
Method in class biggests.utils.ProgressBarFrame
- Returns the progress bar.
- getPvalueLabel() -
Method in class biggests.gui.PanelFunctionAnalysis
- Returns p-value label.
- getPvalueTextField() -
Method in class biggests.gui.PanelFunctionAnalysis
- Returns text field for the input of a p-value.
- getRestrictedErrorsECCCCheckBox() -
Method in class biggests.gui.PanelBiclustering
- Returns restricted errors for e-CCC-Biclustering algorithm check box.
- getRight() -
Method in class biggests.clustering.ClusterTreeNode
- Returns the index of the right element or node (right son).
- getRoot() -
Method in class biggests.tree.DatasetTree
- Returns the root node of the dataset tree.
- getRowCount() -
Method in class biggests.tables.TableSorter
- Returns the number of rows in the table model.
- getScrollAnalyzingExpressionAllTimePoints() -
Method in class biggests.gui.BiggestsFrame
- Returns the scroll pane which holds the expression
analysis - all time points chart panel.
- getScrollAnalyzingExpressionBiclusterPattern() -
Method in class biggests.gui.BiggestsFrame
- Returns the scroll pane which holds the expression
analysis - bicluster pattern chart panel.
- getScrollAnalyzingExpressionBiclusterTimePoints() -
Method in class biggests.gui.BiggestsFrame
- Returns the scroll pane which holds the expression
analysis - bicluster time points chart panel.
- getScrollAnalyzingFunctionSignificanceGraph() -
Method in class biggests.gui.BiggestsFrame
- Returns the scroll pane which holds the function
analysis - significance graph panel.
- getScrollAnalyzingFunctionTable() -
Method in class biggests.gui.BiggestsFrame
- Returns the scroll pane which holds the function
analysis - table of functions panel.
- getScrollAnalyzingMatrixColors() -
Method in class biggests.gui.BiggestsFrame
- Returns the scroll pane which holds the matrix analysis by colors panel.
- getScrollAnalyzingMatrixSymbols() -
Method in class biggests.gui.BiggestsFrame
- Returns the scroll pane which holds the matrix analysis by symbols panel.
- getScrollAnalyzingMatrixValues() -
Method in class biggests.gui.BiggestsFrame
- Returns the scroll pane which holds the matrix analysis by values panel.
- getScrollBiclustering() -
Method in class biggests.gui.BiggestsFrame
- Returns the scroll pane which scrolls biclustering panel.
- getScrollInfo() -
Method in class biggests.gui.BiggestsFrame
- Returns the scroll pane which scrolls information text pane.
- getScrollLoading() -
Method in class biggests.gui.BiggestsFrame
- Returns the scroll pane which scrolls loading panel.
- getScrollPreProcessing() -
Method in class biggests.gui.BiggestsFrame
- Returns the scroll pane which scrolls preprocessing panel.
- getScrolls() -
Method in class biggests.gui.PanelAnalyzingMatrixTables
- Returns the array with the scroll panes that hold the tables to be
displayed (for
VALUES
tableType
only).
- getScrollTree() -
Method in class biggests.gui.BiggestsFrame
- Returns the scroll pane which scrolls the dataset tree.
- getSelectedNode() -
Method in class biggests.tree.DatasetTree
-
- getSelectedNodeComponent() -
Method in class biggests.tree.DatasetTree
-
- getSelectionPath() -
Method in class biggests.gui.PanelAnalyzingFunctionTable
- Returns the tree selection path that corresponds to the bicluster
or bicluster group that is being processed.
- getSelectionPath() -
Method in class biggests.gui.PanelBiclustering
- Returns the dataset tree selected path which corresponds to the path of
the dataset which in turn leads to the node with the matrix on which
biclustering algorithm will be performed.
- getSelectionPath() -
Method in class biggests.gui.PanelFunctionAnalysis
- Returns the dataset tree selected path which corresponds to the path of
the dataset which in turn leads to the node with the matrix on which
biclustering algorithm will be performed.
- getSelectionPath() -
Method in class biggests.gui.PanelPostProcessing
- Rreturns the selected path in the dataset tree.
- getSelectionPath() -
Method in class biggests.gui.PanelPreProcessing
- Returns the path selected on the dataset tree.
- getSetOfBiclusters() -
Method in class biggests.gui.PanelAnalyzingMatrixTables
- Returns the set of biclusters from which the set of tables is constructed.
- getSetOfBiclusters() -
Method in class biggests.gui.PanelExpression
- Returns the set of biclusters retrieved from the group of
biclusters to display.
- getShiftsLabel() -
Method in class biggests.gui.PanelBiclustering
- Returns the label for number of shifts for CCC-Biclustering
and e-CCC-Biclustering algorithms.
- getShiftsTextField() -
Method in class biggests.gui.PanelBiclustering
- Returns the text field for the input of CCC-Biclustering
and e-CCC-Biclustering algorithms number of shifts.
- getSignificantColor() -
Method in class biggests.tables.TableFunctionGroup
- Returns the
Color
used to mark significant terms.
- getSignificantColor() -
Method in class biggests.tables.TableFunctionIndividual
- Returns the
Color
used to mark significant terms.
- getSignificantPValueThreshold() -
Method in class biggests.tables.TableFunctionIndividual
- Returns the p-value threshold for significant gene ontology terms.
- getSimilarityTextField() -
Method in class biggests.gui.PanelPostProcessing
- Returns the similarity threshold input text field.
- getSizeTextField() -
Method in class biggests.gui.PanelPostProcessing
- Returns the size threshold input text field.
- getSmoothCheckBox() -
Method in class biggests.gui.PanelPreProcessing
- Returns smooth check box.
- getSmoothWindowLabel() -
Method in class biggests.gui.PanelPreProcessing
- Returns smooth window label.
- getSmoothWindowTextField() -
Method in class biggests.gui.PanelPreProcessing
- Returns smooth window input text field.
- getSortCheckBox() -
Method in class biggests.gui.PanelPostProcessing
- Returns enabling/disabling sorting option check box.
- getSortCriteria() -
Method in class biggests.gui.PanelPostProcessing
-
- getSortCriteriaLabel() -
Method in class biggests.gui.PanelPostProcessing
- Returns the sorting criteria label.
- getSortCriteriaList() -
Method in class biggests.gui.PanelPostProcessing
- Returns sorting criteria list.
- getSortingStatus(int) -
Method in class biggests.tables.TableSorter
- Returns the sorting status of the given
column
:
DESCENDING
NOT_SORTED
ASCENDING
- getSortPanel() -
Method in class biggests.gui.PanelPostProcessing
- Returns the panel with the sorting options.
- getSplitLeftRight() -
Method in class biggests.gui.BiggestsFrame
- Returns the left-right split pane.
- getSplitTopBottom() -
Method in class biggests.gui.BiggestsFrame
- Returns the top-bottom split pane.
- getSpringLayout() -
Method in class biggests.gui.PanelBiclustering
- Returns the layout of this panel.
- getSpringLayout() -
Method in class biggests.gui.PanelPreProcessing
- Returns the layout of this panel.
- getStop() -
Static method in class biggests.gui.BiggestsIO
- Returns the value of stop flag.
- getString() -
Method in class biggests.utils.ProgressBarFrame
- Returns the message displayed by the progress bar.
- getSvgGraph() -
Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
- Returns the swing-based component which holds the svg graph.
- getTabbedPane() -
Method in class biggests.gui.BiggestsFrame
- Returns the main tabbed pane.
- getTabbedPaneAnalyzing() -
Method in class biggests.gui.BiggestsFrame
- Returns the analysis tabbed pane.
- getTabbedPaneAnalyzingExpression() -
Method in class biggests.gui.BiggestsFrame
- Returns the expression analysis tabbed pane.
- getTabbedPaneAnalyzingFunction() -
Method in class biggests.gui.BiggestsFrame
- Returns the function analysis tabbed pane.
- getTabbedPaneAnalyzingMatrix() -
Method in class biggests.gui.BiggestsFrame
- Returns the matrix analysis tabbed pane.
- getTableHeader() -
Method in class biggests.tables.TableSorter
- Returns the table header.
- getTableModel() -
Method in class biggests.tables.TableSorter
- Returns the table model.
- getTables() -
Method in class biggests.gui.PanelAnalyzingMatrixTables
- Returns the array which contains the tables to be displayed
(may contain
TableValues
s, TableColors
s
and TableSymbols
s, depending on the tableType
).
- getTableType() -
Method in class biggests.gui.PanelAnalyzingMatrixTables
- Returns the type of the tables presented in the panel.
- getTextPaneInfo() -
Method in class biggests.gui.BiggestsFrame
- Returns the information text pane, which displays informations about the
selected datasets, matrices or biclusters in the tree.
- getToolTipText(MouseEvent) -
Method in class biggests.tables.TableColorsWithMissingValues
- Overrides
TableValues
's getToolTipText
method
in order to allow the renderer's tips to be used if they have text set.
- getToolTipText(MouseEvent) -
Method in class biggests.tables.TableFunctionGroup
- Overrides
JTable
's getToolTipText
method
in order to allow the renderer's tips to be used if they have text set.
- getToolTipText(MouseEvent) -
Method in class biggests.tables.TableFunctionIndividual
- Overrides
JTable
's getToolTipText
method
in order to allow the renderer's tips to be used if they have text set.
- getToolTipText(MouseEvent) -
Method in class biggests.tables.TableHeader
- Overrides
JTableHeader
's getToolTipText method.
- getToolTipText(MouseEvent) -
Method in class biggests.tables.TableHeaderFunction
- Overrides
JTableHeader
's getToolTipText method.
- getToolTipText(MouseEvent) -
Method in class biggests.tables.TableValues
- Overrides
JTable
's getToolTipText
method
in order to allow the renderer's tips to be used if they have text set.
- getToolTipText(MouseEvent) -
Method in class biggests.tables.TableValuesWithMissingValues
- Overrides
TableValues
's getToolTipText
method
in order to allow the renderer's tips to be used if they have text set.
- getTree() -
Method in class biggests.gui.BiggestsFrame
- Returns the dataset tree object.
- getValidFileExtension() -
Method in class biggests.utils.FileFilterDirectory
- Returns this file filter valid file extension.
- getValidFileExtension() -
Method in class biggests.utils.FileFilterExtension
- Returns this file filter valid file extension.
- getValueAt(int, int) -
Method in class biggests.tables.TableSorter
- Returns the element in the cell at
row
and
column
indexes.
- getVisualizationOption() -
Method in class biggests.gui.PanelExpression
- Returns visualization options (number of biclusters to be displayed) to
include in a combo box when the expression type is either
BICLUSTER_TIME_POINTS or PATTERN and the corresponding object is a
group of biclusters.
- getZoom() -
Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
- Returns the current zoom scale factor.
- getZoomSlider() -
Method in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
- Returns the zoom slider.
- GIF -
Static variable in class biggests.gui.PanelAnalyzingFunctionSignificanceGraph
- GIF image type.
- goFrontEnd -
Variable in class biggests.tables.TableValues
-
- goFrontEndCheckBox_itemStateChanged(ItemEvent) -
Method in class biggests.gui.PanelFunctionAnalysis
-
- gunzipFile(File, File) -
Static method in class biggests.gui.BiggestsIO
- Gunzips the input archive.
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