Serialized Form


Package biggests.gui

Class biggests.gui.BiggestsFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

panelContent

javax.swing.JPanel panelContent
Main panel from main frame, which holds all other graphic components.


panelRight

javax.swing.JPanel panelRight
Right panel from main frame, which holds the tabbed pane and the context label.


tree

DatasetTree tree
Dataset matrices and biclusters tree.


textPaneInfo

javax.swing.JTextPane textPaneInfo
Information text pane - displays information about the current selected dataset, matrix or bicluster on the tree.


labelContext

javax.swing.JTextField labelContext
Context label, which contains information about what the user may do.


tabbedPane

javax.swing.JTabbedPane tabbedPane
Tabbed pane which contains the main functionalities of the application:
Loading;
Preprocessing;
Biclustering;
Analyzing;
Post-processing;
Comparing.


tabbedPaneAnalyzing

javax.swing.JTabbedPane tabbedPaneAnalyzing
Analyzing tabbed pane that contains the analyzing options:
Matrix analysis;
Expression analysis;
Function analysis.


tabbedPaneAnalyzingMatrix

javax.swing.JTabbedPane tabbedPaneAnalyzingMatrix
Matrix Analyzing tabbed pane which contains the matrix analyzing options:
Matrix analysis by values;
Matrix analysis by colors;
Matrix analysis by symbols.


tabbedPaneAnalyzingFunction

javax.swing.JTabbedPane tabbedPaneAnalyzingFunction
Shows function analysis options.


scrollTree

javax.swing.JScrollPane scrollTree
Tree scroll pane: scrolls tree view.


scrollInfo

javax.swing.JScrollPane scrollInfo
Info area scroll pane: scrolls the information text area.


scrollLoading

javax.swing.JScrollPane scrollLoading
Load scroll pane: scrolls the load panel.


scrollPreProcessing

javax.swing.JScrollPane scrollPreProcessing
Preprocessing scroll pane: scrolls the preprocessing panel.


scrollBiclustering

javax.swing.JScrollPane scrollBiclustering
Biclustering scroll pane: scrolls the biclustering panel.


scrollPostProcessing

javax.swing.JScrollPane scrollPostProcessing
Post-processing scroll pane: scrolls the post-processing panel.


scrollAnalyzingExpressionBiclusterTimePoints

javax.swing.JScrollPane scrollAnalyzingExpressionBiclusterTimePoints
Scrolls expression analysis - bicluster time points chart panel.


scrollAnalyzingExpressionAllTimePoints

javax.swing.JScrollPane scrollAnalyzingExpressionAllTimePoints
Scrolls expression analysis - all time points chart panel.


scrollAnalyzingExpressionBiclusterPattern

javax.swing.JScrollPane scrollAnalyzingExpressionBiclusterPattern
Scrolls expression analysis - bicluster pattern chart panel.


scrollAnalyzingFunctionTable

javax.swing.JScrollPane scrollAnalyzingFunctionTable
Scrolls function analysis - functions table panel.


scrollAnalyzingFunctionSignificanceGraph

javax.swing.JScrollPane scrollAnalyzingFunctionSignificanceGraph
Scrolls function analysis - significance graph panel.


scrollAnalyzingMatrixValues

javax.swing.JScrollPane scrollAnalyzingMatrixValues
Scrolls matrix analysis by values panel.


scrollAnalyzingMatrixColors

javax.swing.JScrollPane scrollAnalyzingMatrixColors
Scrolls matrix analysis by colors panel.


scrollAnalyzingMatrixSymbols

javax.swing.JScrollPane scrollAnalyzingMatrixSymbols
Scrolls matrix analysis by symbols panel.


scrollAnalyzingMatrixDendrogram

javax.swing.JScrollPane scrollAnalyzingMatrixDendrogram
Scrolls matrix analysis by dendrogram panel.


panelLoading

PanelLoading panelLoading
Loading panel: panel which contains the load options.


panelPreProcessing

PanelPreProcessing panelPreProcessing
Preprocessing panel: shows the options for preprocessing tasks.


panelBiclustering

PanelBiclustering panelBiclustering
Biclustering panel: shows all the options to apply biclustering algorithms.


panelPostProcessing

PanelPostProcessing panelPostProcessing
Post-processing panel: shows options to post-process biclusters.


tabbedPaneAnalyzingExpression

javax.swing.JTabbedPane tabbedPaneAnalyzingExpression
Shows expression analysis options.


panelAnalyzingExpressionBiclusterTimePoints

PanelExpression panelAnalyzingExpressionBiclusterTimePoints
Shows expression analysis of bicluster's genes in bicluster time points.


panelAnalyzingExpressionAllTimePoints

PanelExpression panelAnalyzingExpressionAllTimePoints
Shows expression analysis of bicluster's genes in all time points.


panelAnalyzingExpressionBiclusterPattern

PanelExpression panelAnalyzingExpressionBiclusterPattern
Shows expression analysis of bicluster's pattern.


panelAnalyzingMatrixValues

PanelAnalyzingMatrixTables panelAnalyzingMatrixValues
Shows matrix analysis by values.


panelAnalyzingMatrixColors

PanelAnalyzingMatrixTables panelAnalyzingMatrixColors
Shows matrix analysis by colors.


panelAnalyzingMatrixSymbols

PanelAnalyzingMatrixTables panelAnalyzingMatrixSymbols
Shows matrix analysis by symbols.


panelAnalyzingMatrixDendrogram

PanelAnalyzingMatrixDendrogram panelAnalyzingMatrixDendrogram
Shows matrix analysis by dendrogram.


panelAnalyzingFunctionTable

PanelAnalyzingFunctionTable panelAnalyzingFunctionTable
Shows function analysis - functions table.


panelAnalyzingFunctionSignificanceGraph

PanelAnalyzingFunctionSignificanceGraph panelAnalyzingFunctionSignificanceGraph
Shows function analysis - significant functions graph.


splitLeftRight

javax.swing.JSplitPane splitLeftRight
Left-right split pane: splits left and right sides of the main panel.


splitTopBottom

javax.swing.JSplitPane splitTopBottom
Top-bottom split pane: splits top and bottom in the left side panel of the main panel.


menu

javax.swing.JMenuBar menu
Application's menu bar.


session

javax.swing.JMenu session
Session menu.


sessionLoadDataset

javax.swing.JMenuItem sessionLoadDataset
Load dataset menu item.


sessionLoadSession

javax.swing.JMenuItem sessionLoadSession
Load session menu item.


sessionSaveSession

javax.swing.JMenuItem sessionSaveSession
Save session menu item.


sessionExit

javax.swing.JMenuItem sessionExit
Exit application menu item.


help

javax.swing.JMenu help
Help menu.


helpAbout

javax.swing.JMenuItem helpAbout
Help about menu item.


settings

javax.swing.JMenu settings
Settings menu.


settingsColors

javax.swing.JMenu settingsColors
Settings colors menu.


colorsRedGreen

javax.swing.JMenuItem colorsRedGreen
Red and green color scheme.


colorsYellowBlue

javax.swing.JMenuItem colorsYellowBlue
Blue and yellow color scheme.

Class biggests.gui.PanelAnalyzingFunctionSignificanceGraph extends javax.swing.JPanel implements Serializable

Serialized Fields

mainFrame

BiggestsFrame mainFrame
the application's main frame.


springLayout

javax.swing.SpringLayout springLayout
The layout of this panel.


pathToImage

java.lang.String pathToImage
The path to image file (currently .png image).


pathToSvg

java.lang.String pathToSvg
The path to svg file (.svg file).


zoomSlider

javax.swing.JSlider zoomSlider
A zoom slider to increase/decrease the size of the significance graph.


zoom

float zoom
The current zoom factor scale.


svgGraph

org.apache.batik.swing.svg.JSVGComponent svgGraph
The swing-based component which holds the svg graph.


svgBuilded

boolean svgBuilded
Flag which indicates when svg document has been fully parsed and its tree has been built.

Class biggests.gui.PanelAnalyzingFunctionTable extends javax.swing.JPanel implements Serializable

Serialized Fields

boxLayout

javax.swing.BoxLayout boxLayout
This panel's layout.


mainFrame

BiggestsFrame mainFrame
The application's main frame.


functionAnalysisPanel

PanelFunctionAnalysis functionAnalysisPanel
The function analysis panel.


selectionPath

javax.swing.tree.TreePath selectionPath
The selection path.


nodeObject

NodeObjectInterface nodeObject
The object.


goFrontEnds

java.util.HashMap<K,V> goFrontEnds
All computed GO frontends.

Class biggests.gui.PanelAnalyzingMatrixDendrogram extends javax.swing.JPanel implements Serializable

Serialized Fields

hierarchicalClusteringLabel

javax.swing.JLabel hierarchicalClusteringLabel
Hierarchical clustering label.


clusterGenesCheckBox

javax.swing.JCheckBox clusterGenesCheckBox
Cluster genes check box. Allows the user to choose if he/she wants to perform clustering on the genes dimension.


clusterConditionsCheckBox

javax.swing.JCheckBox clusterConditionsCheckBox
Cluster conditions check box. Allows the user to choose if he/she wants to perform clustering on the conditions dimension.


genesDistanceMetricLabel

javax.swing.JLabel genesDistanceMetricLabel
Genes distance metric label.


conditionsDistanceMetricLabel

javax.swing.JLabel conditionsDistanceMetricLabel
Conditions distance metric label.


genesDistanceMetricComboBox

javax.swing.JComboBox genesDistanceMetricComboBox
Genes distance metric combo box. Allows the user to select which similarity metric to use in genes dimension clustering.


conditionsDistanceMetricComboBox

javax.swing.JComboBox conditionsDistanceMetricComboBox
Conditions distance metric combo box. Allows the user to select which similarity metric to use in conditions dimension clustering.


clusteringMethodList

javax.swing.JList clusteringMethodList
Clustering methods list. Allows the user to select which clustering method to use.


clusteringMethodLabel

javax.swing.JLabel clusteringMethodLabel
Clustering methods label.


springLayout

javax.swing.SpringLayout springLayout
The layout manager for this panel.


applyButton

javax.swing.JButton applyButton
The apply button. When the user clicks it, hierarchical clustering is performed and the resulting dendrogram is presented in a new window.


hierarchicalClustering

HierarchicalClustering hierarchicalClustering
The hierarchical clustering object. It is initialized by paint with a given expression data matrix, over which hierarchical clustering will be performed.


frame

BiggestsFrame frame
The application's main frame.


treeViewApp

MyTreeViewApp treeViewApp
A Java TreeView application.

Class biggests.gui.PanelAnalyzingMatrixTables extends javax.swing.JPanel implements Serializable

Serialized Fields

tableType

int tableType
Indicates the type of tables to create. Valid types are:
PanelAnalyzingMatrixTables.VALUES
PanelAnalyzingMatrixTables.COLORS
PanelAnalyzingMatrixTables.SYMBOLS


mainFrame

BiggestsFrame mainFrame
The application's main frame.


tables

TableValues[] tables
The array which contains the tables to be displayed (may contain TableValuess, TableColorss and TableSymbolss, depending on the tableType).


scrolls

javax.swing.JScrollPane[] scrolls
The array with the scroll panes that hold the tables to be displayed (for VALUES tableType only).


panels

javax.swing.JPanel[] panels
The set of panels which holds the tables and their headers, which will be displayed in this panel (for COLORS and SYMBOLS tableTypes only).


biclustersNumberOption

javax.swing.JComboBox biclustersNumberOption
This combo box will only be initialized if the tables to show come from biclusters groups. If that happens, it is initialized with biclustersNumber options.


boxLayout

javax.swing.BoxLayout boxLayout
The layout of this panel.


setOfBiclusters

Bicluster[] setOfBiclusters
The set of biclusters. This will be only initialized if the tables to display come from bicluster matrices, i.e., if the object to display is either a group of biclusters or a group of post-processed biclusters.


nodeInfo

NodeInfo nodeInfo
The node information object which contains the object (expression matrix, preprocessed matrix, discretized matrix, bicluster, biclusters group, post-processed bicluster or post-processed biclusters group) to construct the tables from.


selectionPath

javax.swing.tree.TreePath selectionPath

Class biggests.gui.PanelBasicIOValidation extends javax.swing.JPanel implements Serializable

Class biggests.gui.PanelBiclustering extends PanelBasicIOValidation implements Serializable

Serialized Fields

mainFrame

BiggestsFrame mainFrame
The application's main frame.


expressionMatrix

NodeObjectInterface expressionMatrix
The node object which contains the original, preprocessed or discretized matrix on which biclustering algorithm will be performed.


selectionPath

javax.swing.tree.TreePath selectionPath
The dataset tree selected path which corresponds to the path of the dataset which leads to the node with the matrix on which biclustering algorithm will be performed.


springLayout

javax.swing.SpringLayout springLayout
The layout of this panel.


biclusteringAlgorithmsLabel

javax.swing.JLabel biclusteringAlgorithmsLabel
The biclustering algorithms label.


geneShiftsCheckBox

javax.swing.JCheckBox geneShiftsCheckBox
Gene shifts for CCC-Biclustering and e-CCC-Biclustering algorithms' check box. Allows the user to select/deselect gene shifts for these algorithms.


shiftsLabel

javax.swing.JLabel shiftsLabel
Label for number of shifts for CCC-Biclustering and e-CCC-Biclustering algorithms.


shiftsTextField

javax.swing.JTextField shiftsTextField
Text field for the input of CCC-Biclustering and e-CCC-Biclustering algorithm's number of shifts.


restrictedErrorsECCCCheckBox

javax.swing.JCheckBox restrictedErrorsECCCCheckBox
Restricted errors for e-CCC-Biclustering algorithm check box. Allows the user to select/deselect restricted errors for e-CCC-Biclustering algorithm.


signChangesCheckBox

javax.swing.JCheckBox signChangesCheckBox
Sign changes check box.


timeLagsCheckBox

javax.swing.JCheckBox timeLagsCheckBox
Time lags check box.


maxTimeLagTextField

javax.swing.JTextField maxTimeLagTextField
Maximum time lags text field.


maxTimeLagLabel

javax.swing.JLabel maxTimeLagLabel
Maximum time lags label.


neighborsECCCLabel

javax.swing.JLabel neighborsECCCLabel
Label for the number of neighbors on e-CCC-Biclustering algorithm.


neighborsECCCTextField

javax.swing.JTextField neighborsECCCTextField
Text field for the input of number of neighbors for e-CCC-Biclustering algorithm.


errorsNumberLabel

javax.swing.JLabel errorsNumberLabel
Label for the number of errors allowed in e-CCC-Biclustering algorithm.


errorsNumberTextField

javax.swing.JTextField errorsNumberTextField
Text field for the input of the number of errors allowed in e-CCC-Biclustering algorithm.


deltaLabel

javax.swing.JLabel deltaLabel
Delta input label;


deltaTextField

javax.swing.JTextField deltaTextField
Delta input text field.


alphaLabel

javax.swing.JLabel alphaLabel
Alpha input label.


alphaTextField

javax.swing.JTextField alphaTextField
Alpha input text field.


biclustersNumberLabel

javax.swing.JLabel biclustersNumberLabel
Number of biclusters label.


biclustersNumberTextField

javax.swing.JTextField biclustersNumberTextField
Number of biclusters input text field.


maxIterationsLabel

javax.swing.JLabel maxIterationsLabel
Maximum number of iterations label.


maxIterationsTextField

javax.swing.JTextField maxIterationsTextField
Maximum number of iterations input text field.


missingValuesLabel

javax.swing.JLabel missingValuesLabel

jumpMissingsButton

javax.swing.JRadioButton jumpMissingsButton

allowMissingsButton

javax.swing.JRadioButton allowMissingsButton

missingsButtonGroup

javax.swing.ButtonGroup missingsButtonGroup

biclusteringAlgorithmPanel

javax.swing.JPanel biclusteringAlgorithmPanel
Panel with biclustering algorithm name and parameters.


algorithmsList

javax.swing.JList algorithmsList
List with biclustering algorithms.


applyButton

javax.swing.JButton applyButton
The apply button. When the user clicks it, biclustering algorithms are applied to the matrix.


infoStrings

java.util.ArrayList<E> infoStrings
Information strings on the new bicluster group object.


infoStyles

java.util.ArrayList<E> infoStyles
Styles for the information strings on the new bicluster group object.

Class biggests.gui.PanelExpression extends javax.swing.JPanel implements Serializable

Serialized Fields

expressionType

int expressionType
The type of expression for this panel's chart. It may be:
PanelExpression.BICLUSTER_TIME_POINTS PanelExpression.ALL_TIME_POINTS PanelExpression.PATTERN


mainFrame

BiggestsFrame mainFrame
The application's main frame, where this panel is being displayed.


normalize

javax.swing.JCheckBox normalize
Check box which allows the user to choose between an expression chart with original or normalized data. To be used on BICLUSTER_TIME_POINTS and ALL_TIME_POINTS expression charts panel.


option

javax.swing.JComboBox option
Combo box for the user to choose the number of biclusters to display. To be used when the expression type is either BICLUSTER_TIME_POINTS or PATTERN and the corresponding object is a group of biclusters.


optionPanel

javax.swing.JPanel optionPanel

expressionChart

PanelExpressionChart expressionChart
The expression chart of a single bicluster. It can be a bicluster time points, an all time points or a pattern expression chart.


expressionCharts

PanelExpressionChart[] expressionCharts
The expression charts of a set of biclusters (which belong to a specific group of biclusters).


setOfBiclusters

Bicluster[] setOfBiclusters
The set of biclusters retrieved from the group of biclusters to display.


chartWidth

int chartWidth
The width of the expression chart.


chartHeight

int chartHeight
The height of the expression chart.

Class biggests.gui.PanelExpressionChart extends org.jfree.chart.ChartPanel implements Serializable

Serialized Fields

genesNames

java.lang.String[] genesNames
Holds the names of the genes for the expression chart for the following chart types: - matrix charts (ExpressionMatrix, PreProcessedExpressionMatrix, DiscretizedExpressionMatrix) - bicluster all time points charts (bicluster's genes * all conditions)


conditionsNames

java.lang.String[] conditionsNames
Holds the names of the conditions for the expression chart for the following chart types: - matrix charts (ExpressionMatrix, PreProcessedExpressionMatrix, DiscretizedExpressionMatrix) - bicluster all time points charts (bicluster's genes * all conditions)


expressionValues

float[][] expressionValues
Holds the expression values to be represented in the expression chart for the following chart types: - matrix charts (ExpressionMatrix, PreProcessedExpressionMatrix, DiscretizedExpressionMatrix) - bicluster all time points charts (bicluster's genes * all conditions)


missingValueFloat

float missingValueFloat

bicluster

Bicluster bicluster
Bicluster. It is null when this chart is a:
- bicluster all time points chart (bicluster's genes * all conditions)
- matrix chart (ExpressionMatrix, PreProcessedExpressionMatrix, DiscretizedExpressionMatrix)
It holds a Bicluster object (Bicluster, CCC_Bicluster, CCC_Bicluster_GeneShifts, CCC_Bicluster_SignChanges, CCC_Bicluster_Time_Lags, CCC_Bicluster_SignChanges_TimeLags, E_CCC_Bicluster, E_CCC_Bicluster_GeneShifts, E_CCC_Bicluster_RestrictedErrors, E_CCC_Bicluster_GeneShifts_RestrictedErrors) when chart is a:
- bicluster time points chart (bicluster's genes * bicluster's conditions)
- pattern chart (only for CCC_Bicluster and its subclasses)

Class biggests.gui.PanelFunctionAnalysis extends javax.swing.JPanel implements Serializable

Serialized Fields

mainFrame

BiggestsFrame mainFrame
Application's main frame.


selectionPath

javax.swing.tree.TreePath selectionPath
The selection path.


organism

java.lang.String organism
The organism related with this function analysis.


functionAnalysisLabel

javax.swing.JLabel functionAnalysisLabel
Function analysis label.


pvalueLabel

javax.swing.JLabel pvalueLabel
P-value label.


pvalueTextField

javax.swing.JTextField pvalueTextField
P-value text field.


organismLabel

javax.swing.JLabel organismLabel
Organism label.


filesFunctionAnalysisLabel

javax.swing.JLabel filesFunctionAnalysisLabel
Files to use on function analysis label.


geneOntologyFilePathLabel

javax.swing.JLabel geneOntologyFilePathLabel
Gene ontology file path label.


geneOntologyFilePathTextField

javax.swing.JTextField geneOntologyFilePathTextField
Gene ontology file path text field.


browseGeneOntologyFilePathButton

javax.swing.JButton browseGeneOntologyFilePathButton
Browse gene ontology file path button.


geneAssociationFilePathLabel

javax.swing.JLabel geneAssociationFilePathLabel
Gene association file path label.


geneAssociationFilePathTextField

javax.swing.JTextField geneAssociationFilePathTextField
Gene association file path text field.


browseGeneAssociationFilePathButton

javax.swing.JButton browseGeneAssociationFilePathButton
Browse gene association file path button.


downloadGeneOntologyFileButton

javax.swing.JButton downloadGeneOntologyFileButton
Download gene ontology file button.


downloadGeneAssociationFileButton

javax.swing.JButton downloadGeneAssociationFileButton
Download gene association file button.


springLayout

javax.swing.SpringLayout springLayout
The layout for this panel.


goFrontEndCheckBox

javax.swing.JCheckBox goFrontEndCheckBox
GO frontend check box.

Class biggests.gui.PanelLoading extends javax.swing.JPanel implements Serializable

Serialized Fields

mainFrame

BiggestsFrame mainFrame
The application's main frame.


springLayout

javax.swing.SpringLayout springLayout
The layout of this panel.


datasetFileLabel

javax.swing.JLabel datasetFileLabel
The information label of the dataset file input text field.


datasetFileTextField

javax.swing.JTextField datasetFileTextField
Dataset file input text field.


browseDatasetFileButton

javax.swing.JButton browseDatasetFileButton
Browse button.


organismList

javax.swing.JList organismList
Organisms' list.


organismLabel

javax.swing.JLabel organismLabel
Organisms' label.


datatypeLabel

javax.swing.JLabel datatypeLabel
Datatype label.


datatypeComboBox

javax.swing.JComboBox datatypeComboBox
Datatype combo box.


logTransformationCheckBox

javax.swing.JCheckBox logTransformationCheckBox
Log transformation check box.


conditionsNamesRowNumberLabel

javax.swing.JLabel conditionsNamesRowNumberLabel
Index of the row which holds conditions' names (label).


conditionsNamesRowNumberComboBox

javax.swing.JComboBox conditionsNamesRowNumberComboBox
Combo box with indexes of rows possibly holding conditions' names.


geneIDCheckBox

javax.swing.JCheckBox geneIDCheckBox
Check box to select/deselect gene ID.


geneIDColumnNumberLabel

javax.swing.JLabel geneIDColumnNumberLabel
Label for gene ID column index.


geneIDColumnNumberComboBox

javax.swing.JComboBox geneIDColumnNumberComboBox
Combo box to select gene ID column index.


probesetIDColumnNumberLabel

javax.swing.JLabel probesetIDColumnNumberLabel
Label for probeset ID column index.


probesetIDColumnNumberComboBox

javax.swing.JComboBox probesetIDColumnNumberComboBox
Combo box to select probeset ID column index.


conversionFileLabel

javax.swing.JLabel conversionFileLabel
Label for conversion file.


conversionFileTextField

javax.swing.JTextField conversionFileTextField
Input text field for conversion file.


browseConversionFileButton

javax.swing.JButton browseConversionFileButton
Browse button for conversion file.


previewTable

javax.swing.JTable previewTable
Table for data preview.


scrollTable

javax.swing.JScrollPane scrollTable
Scroll for data preview table.


expressionData

java.lang.Object[][] expressionData
Expression data read from file.


loadButton

javax.swing.JButton loadButton
Load button.

Class biggests.gui.PanelPostProcessing extends PanelBasicIOValidation implements Serializable

Serialized Fields

biclustering

Biclustering biclustering
Bicluster group object to post-process.


selectionPath

javax.swing.tree.TreePath selectionPath
The path of bicluster group object to post-process in the dataset tree.


springLayout

javax.swing.SpringLayout springLayout
The layout of this panel.


filterCheckBox

javax.swing.JCheckBox filterCheckBox
Filter check box. Allows the user to select/deselect filter post-processing option.


filterCriteriaLabel

javax.swing.JLabel filterCriteriaLabel
Filter criteria label. Displays a title for filter criteria list.


filterCriteriaList

javax.swing.JList filterCriteriaList
Filter criteria list. Contains available criteria to filter biclusters of a biclusters group.


sortCheckBox

javax.swing.JCheckBox sortCheckBox
Sort check box. Allows the user to select/deselect sort post-processing option.


sortCriteriaLabel

javax.swing.JLabel sortCriteriaLabel
Sort criteria label. Displays a title for sort criteria list.


sortCriteriaList

javax.swing.JList sortCriteriaList
Sort criteria list. Contains available criteria to sort biclusters of a biclusters group.


filterDescriptionLabel

javax.swing.JLabel filterDescriptionLabel
Filter description label. Displays a description of the selected filter criteria and the text fields so the user can enter filter parameters.


sortDescriptionLabel

javax.swing.JLabel sortDescriptionLabel
Sort description label. Displays a description of the selected sort criteria and the text fields so the user can enter sort parameters.


acvTextField

javax.swing.JTextField acvTextField
ACV text field. Allows the user to input average column variance threshold.


arvTextField

javax.swing.JTextField arvTextField
ARV text field. Allows the user to input average row variance threshold.


msrTextField

javax.swing.JTextField msrTextField
MSR text field. Allows the user to input mean squared residue threshold.


pValueTextField

javax.swing.JTextField pValueTextField
P-value text field. Allows the user to input the p-value threshold.


conditionsTextField

javax.swing.JTextField conditionsTextField
Number of conditions text field. Allows the user to input gene number threshold.


genesTextField

javax.swing.JTextField genesTextField
Number of genes text field. Allows the user to input gene number threshold.


similarityTextField

javax.swing.JTextField similarityTextField
Similarity text field. Allows the user to input similarity threshold.


sizeTextField

javax.swing.JTextField sizeTextField
Size text filed. Allows the user to input size threshold.


markovChainOrderFilterTextField

javax.swing.JTextField markovChainOrderFilterTextField

markovChainOrderSortTextField

javax.swing.JTextField markovChainOrderSortTextField
Markov chain order text field. Allows the user to input Markov chain order.


filterPanel

javax.swing.JPanel filterPanel
Filter panel. Contains information about filtering options.


filterPanelLayout

javax.swing.SpringLayout filterPanelLayout
The layout of the filter panel.


sortPanel

javax.swing.JPanel sortPanel
Sort panel. Contains information about soring options.


sortPanelLayout

javax.swing.SpringLayout sortPanelLayout
The layout of the sort panel.


ascendingButton

javax.swing.JRadioButton ascendingButton
Ascending sorting button. Allows the user to select sorting by the specified parameters in ascending order.


descendingButton

javax.swing.JRadioButton descendingButton
Descending sorting button. Allows the user to select sorting by the specified parameters in descending order.


group

javax.swing.ButtonGroup group
Button group. Groups ascending and descending sorting buttons, to ensure that only one of them is selected at any time.


applyButton

javax.swing.JButton applyButton
Apply button. When clicked, applies post-processing options to the selected biclusters group.


mainFrame

BiggestsFrame mainFrame
The application's main frame.

Class biggests.gui.PanelPreProcessing extends PanelBasicIOValidation implements Serializable

Serialized Fields

mainFrame

BiggestsFrame mainFrame
BiGGEsTS main window.


expressionMatrix

AbstractExpressionMatrix expressionMatrix
The original or preprocessed expression matrix in which preprocessing techniques will be performed.


selectionPath

javax.swing.tree.TreePath selectionPath
The path selected on the dataset tree. Corresponds to the path in the tree from the root node to the node that contains the original or preprocessed matrix to apply preprocessing techniques.


springLayout

javax.swing.SpringLayout springLayout
The layout of this panel.


filterCheckBox

javax.swing.JCheckBox filterCheckBox
Filter check box.


filterButtonGroup

javax.swing.ButtonGroup filterButtonGroup
Filter options button group.


filterAllGenesButton

javax.swing.JRadioButton filterAllGenesButton
Filter all genes with missing values button.


filterPercentGenesButton

javax.swing.JRadioButton filterPercentGenesButton
Filter genes with more than a % of missing values button.


filterPercentTextField

javax.swing.JTextField filterPercentTextField
Filter percent input text field.


filterPercentLabel

javax.swing.JLabel filterPercentLabel
Filter percent label.


fillCheckBox

javax.swing.JCheckBox fillCheckBox
Fill check box.


fillButtonGroup

javax.swing.ButtonGroup fillButtonGroup
Fill options button group.


fillValueButton

javax.swing.JRadioButton fillValueButton
Fill with a certain value button.


fillKNeighborsButton

javax.swing.JRadioButton fillKNeighborsButton
Fill with average over the k-neighbors button.


fillAverageRowButton

javax.swing.JRadioButton fillAverageRowButton
Fill with average over the same row button.


fillValueTextField

javax.swing.JTextField fillValueTextField
Fill with a certain value input text field.


fillKNeighborsTextField

javax.swing.JTextField fillKNeighborsTextField
Fill with average over the k-neighbors input text field.


fillKNeighborsLabel

javax.swing.JLabel fillKNeighborsLabel
Fill with average over the k-neighbors label.


normalizeCheckBox

javax.swing.JCheckBox normalizeCheckBox
Normalize check box.


normalizeButtonGroup

javax.swing.ButtonGroup normalizeButtonGroup
Normalize options button group.


normalizeOverallButton

javax.swing.JRadioButton normalizeOverallButton
Normalize overall values button.


normalizeByGeneButton

javax.swing.JRadioButton normalizeByGeneButton
Normalize by gene button.


normalizeMean0Std1Button

javax.swing.JRadioButton normalizeMean0Std1Button
Normalize to mean 0 and std 1 button.


normalizeMeanStdValuesButton

javax.swing.JRadioButton normalizeMeanStdValuesButton
Normalize by mean and std values button.


normalizeMeanValueTextField

javax.swing.JTextField normalizeMeanValueTextField
Normalize mean input text field.


normalizeStdValueTextField

javax.swing.JTextField normalizeStdValueTextField
Normalize std input text field.


normalizeMeanStdValuesLabel

javax.swing.JLabel normalizeMeanStdValuesLabel
Normalize to mean and std values label.


normalizeMeanStdButtonGroup

javax.swing.ButtonGroup normalizeMeanStdButtonGroup
Normalize to mean and std options button group.


smoothCheckBox

javax.swing.JCheckBox smoothCheckBox
Smooth check box.


smoothWindowLabel

javax.swing.JLabel smoothWindowLabel
Smooth window label.


smoothWindowTextField

javax.swing.JTextField smoothWindowTextField
Smooth window input text field.


discretizeCheckBox

javax.swing.JCheckBox discretizeCheckBox
Discretize check box.


discretizeLabel

javax.swing.JLabel discretizeLabel
Discretize label.


discretizeComboBox

javax.swing.JComboBox discretizeComboBox
Discretize combo box.


discretizeParameterTextField

javax.swing.JTextField discretizeParameterTextField
Discretize parameter input text field.


discretizeParameterLabel

javax.swing.JLabel discretizeParameterLabel
Discretize parameter label.


applyButton

javax.swing.JButton applyButton
Apply preprocessing options button.

Class biggests.gui.SaveChartImageDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

imageWidth

int imageWidth
The width of the image.


imageHeight

int imageHeight
The height of the image.


chartPanel

java.awt.Component chartPanel
Component(s) to export to image file(s).


imageSizeLabel

javax.swing.JLabel imageSizeLabel
Image size label.


fileLabel

javax.swing.JLabel fileLabel
File path label.


fileTextField

javax.swing.JTextField fileTextField
File path input text field.


browseButton

javax.swing.JButton browseButton
Browse file path button.


displayedSizeRadioButton

javax.swing.JRadioButton displayedSizeRadioButton
Displayed image size radio button.


customSizeRadioButton

javax.swing.JRadioButton customSizeRadioButton
Custom size radio button


widthLabel

javax.swing.JLabel widthLabel
Width label.


widthTextField

javax.swing.JTextField widthTextField
Width input text field.


heightLabel

javax.swing.JLabel heightLabel
Height label.


heightTextField

javax.swing.JTextField heightTextField
Height input text field.


sizeButtonGroup

javax.swing.ButtonGroup sizeButtonGroup
Size button group.


saveButton

javax.swing.JButton saveButton
Save button.


cancelButton

javax.swing.JButton cancelButton
Cancel button.


Package biggests.tables

Class biggests.tables.TableColors extends TableValues implements Serializable

Serialized Fields

meanValue

float meanValue
The mean of the node object matrix's values. It is used to calculate the red or green component value of each colored matrix's cell.
The mean value is calculated like this:
(maxValue + minValue)/2
in which the maxValue is the maximum value of all the node object matrix cells' values and the minValue is the minimum value of all.


divider

float divider
Used to calculate the red or green component value of each colored matrix's cell.
The divider value is calculated like this:
(maxValue - meanValue)/255
in which maxValue is the maximum value of all the node object matrix cells' values, the minValue is the minimum value of all and meanValue is the mean value (the value which is exactly in the middle between maximum and minimum values).

Class biggests.tables.TableColorsWithMissingValues extends TableColors implements Serializable

Serialized Fields

missingValue

float missingValue
The value that marks the cells which "contain" missing values.

Class biggests.tables.TableFunctionGroup extends javax.swing.JTable implements Serializable

Serialized Fields

postProcessed

boolean postProcessed
States if this function table is for a post-processed bicluster group or not.


significantColor

java.awt.Color significantColor
Color to mark rows that contain biclusters with significant terms.


evenRowsColor

java.awt.Color evenRowsColor
Color to mark even rows (when they are not selected).


oddRowsColor

java.awt.Color oddRowsColor
Color to mark odd rows (when they are not selected).

Class biggests.tables.TableFunctionGroup.FloatCellRenderer extends TableFunctionGroup.NumberCellRenderer implements Serializable

Serialized Fields

formatter

java.text.NumberFormat formatter
The formatter which is used to format the float value.

Class biggests.tables.TableFunctionGroup.NumberCellRenderer extends javax.swing.table.DefaultTableCellRenderer.UIResource implements Serializable

Class biggests.tables.TableFunctionIndividual extends javax.swing.JTable implements Serializable

Serialized Fields

highlySignificantPValueThreshold

float highlySignificantPValueThreshold
P-value threshold to mark highly significant terms.


significantPValueThreshold

float significantPValueThreshold
P-value threshold to mark significant terms.


highlySignificantColor

java.awt.Color highlySignificantColor
Color to mark rows that contain highly significant terms.


significantColor

java.awt.Color significantColor
Color to mark rows that contain significant terms.


evenRowsColor

java.awt.Color evenRowsColor
Color to mark even rows (when they are not selected).


oddRowsColor

java.awt.Color oddRowsColor
Color to mark odd rows (when they are not selected).


genesNames

java.lang.String[] genesNames
The genes names of the gene set (not the population set).


goFrontEnd

GOFrontEnd goFrontEnd
The GO Frontend with the GO graph of annotated terms.


parent

java.awt.Component parent
This table's parent GUI component. It's used to specify the location of the popup dialogs that display messages to the user.

Class biggests.tables.TableFunctionIndividual.FloatCellRenderer extends TableFunctionIndividual.NumberCellRenderer implements Serializable

Serialized Fields

formatter

java.text.NumberFormat formatter
The formatter which is used to format the float value.

Class biggests.tables.TableFunctionIndividual.NumberCellRenderer extends javax.swing.table.DefaultTableCellRenderer.UIResource implements Serializable

Class biggests.tables.TableHeader extends javax.swing.table.JTableHeader implements Serializable

Class biggests.tables.TableHeaderFunction extends javax.swing.table.JTableHeader implements Serializable

Class biggests.tables.TablePreview extends javax.swing.JTable implements Serializable

Serialized Fields

rowsWithNames

java.util.ArrayList<E> rowsWithNames
Indexes of rows which contain names (possibly conditions' names).


columnsWithNames

java.util.ArrayList<E> columnsWithNames
Indexes of columns which contain names (possibly genes' names).

Class biggests.tables.TableSorter extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

tableModel

javax.swing.table.TableModel tableModel
The table model.


viewToModel

biggests.tables.TableSorter.Row[] viewToModel
View to model indexes map.


modelToView

int[] modelToView
Model to view indexes map.


tableHeader

javax.swing.table.JTableHeader tableHeader
The header of the table. Set to protected access to be used by subclasses (by Joana Gonçalves on 24-11-2006)


mouseListener

java.awt.event.MouseListener mouseListener
The mouse listener of the table. Set to protected access to be used by subclasses (by Joana Gonçalves on 24-11-2006).


tableModelListener

javax.swing.event.TableModelListener tableModelListener
The table model listener.


columnComparators

java.util.HashMap<K,V> columnComparators
Hash map for the columns' comparators. Set to protected access to be used by subclasses (by Joana Gonçalves on 24-11-2006).


sortingColumns

java.util.ArrayList<E> sortingColumns
The directives to sort columns.

Class biggests.tables.TableSorterFunctionGroup extends TableSorter implements Serializable

Serialized Fields

postProcessed

boolean postProcessed
States if this table sorter is for a table of functions of a post-processed biclusters group or not.

Class biggests.tables.TableSorterFunctionIndividual extends TableSorter implements Serializable

Class biggests.tables.TableSorterSymbols extends TableSorterVerticalHeader implements Serializable

Class biggests.tables.TableSorterValues extends TableSorter implements Serializable

Class biggests.tables.TableSorterVerticalHeader extends TableSorterValues implements Serializable

Class biggests.tables.TableSymbols extends TableValues implements Serializable

Serialized Fields

alphabet

char[] alphabet
The alphabet with all discretization symbols used in the discretization technique that gave rise to the set of discrete values that may appear in this symbols table.


colors

java.awt.Color[] colors
The set of colors. Each position contains a color that corresponds to the symbol of the alphabet in the same position.

Class biggests.tables.TableSymbolsWithMissingValues extends TableSymbols implements Serializable

Serialized Fields

missingValue

char missingValue
The value for marking missings.

Class biggests.tables.TableValues extends javax.swing.JTable implements Serializable

Serialized Fields

goFrontEnd

GOFrontEnd goFrontEnd

parent

java.awt.Component parent

Class biggests.tables.TableValues.FloatCellRenderer extends TableValues.NumberCellRenderer implements Serializable

Serialized Fields

formatter

java.text.NumberFormat formatter
The formatter which is used to format the float value.

Class biggests.tables.TableValues.NumberCellRenderer extends javax.swing.table.DefaultTableCellRenderer.UIResource implements Serializable

Class biggests.tables.TableValuesWithMissingValues extends TableValues implements Serializable

Serialized Fields

missingValue

float missingValue
The value used to fill missing values.


Package biggests.tree

Class biggests.tree.Dataset extends java.lang.Object implements Serializable

serialVersionUID: -9150182590356849832L

Serialized Fields

name

java.lang.String name
The name of the dataset.


id

int id
The id value of the dataset.


lastPreprocessedId

int lastPreprocessedId
The last id given to a preprocessed node information object within the current dataset.


lastDiscretizedId

int lastDiscretizedId
The last id given to a discretized node information object within the current dataset.


lastBiclusterGroupId

int lastBiclusterGroupId
The last id given to a bicluster group node information object within the current dataset.


lastPostprocessedGroupId

int lastPostprocessedGroupId
The last id given to a post-processed group node information object within the current dataset.

Class biggests.tree.DatasetTree extends javax.swing.JTree implements Serializable

serialVersionUID: 3882987169020172801L

Serialized Fields

root

javax.swing.tree.DefaultMutableTreeNode root
The root of the datasets tree, i.e., the "Datasets" node.

Class biggests.tree.NodeInfo extends java.lang.Object implements Serializable

serialVersionUID: 7553487355938947549L

Serialized Fields

name

java.lang.String name
The name to be displayed with the id, as the tree node name.


id

int id
Id number to be displayed with the name, as the tree node name.


fakeID

int fakeID
Id number corresponding to the original bicluster id before post-processing operation.


nodeObjectType

int nodeObjectType
Node object type.
One of the following:
NodeInfo.ORIGINAL
NodeInfo.PREPROCESSED
NodeInfo.DISCRETIZED
NodeInfo.BICLUSTER_GROUP
NodeInfo.BICLUSTER_SINGLE
NodeInfo.POSTPROCESSED_GROUP
NodeInfo.POSTPROCESSED_SINGLE


dataType

boolean dataType
Type of data used in the matrix of the node object.
One of the two:
VALUES
SYMBOLS


geneID

boolean geneID
Type of genes' names.
true - genes' names are gene IDs (gene ontology names)
false - genes' names are probeset IDs (IDs used in the mRNA measurements


nodeObject

NodeObjectInterface nodeObject
The node object.


parentNodeInfo

NodeInfo parentNodeInfo
Parent node information object.


infoStrings

java.util.ArrayList<E> infoStrings
Information strings.


infoStyles

java.util.ArrayList<E> infoStyles
Information styles;


Package biggests.utils

Class biggests.utils.InvalidNodeObjectTypeException extends java.lang.Exception implements Serializable

Class biggests.utils.ProgressBarFrame extends javax.swing.JDialog implements Serializable

Serialized Fields

progressBar

javax.swing.JProgressBar progressBar
The progress bar.


messageHistory

javax.swing.JTextArea messageHistory
Message history of computation's progress.


cancelButton

javax.swing.JButton cancelButton
Abort/Cancel button.


workingThread

java.lang.Thread workingThread
Working thread.