Serialized Form
|
Package biggests.clustering |
numberOfGenes
int numberOfGenes
- The number of genes in the experiment.
numberOfConditions
int numberOfConditions
- The number of conditions (microarrays) in the experiment.
genesWeights
double[] genesWeights
- The weights of the genes.
conditionsWeights
double[] conditionsWeights
- The weights of the conditions.
genesOrder
double[] genesOrder
- The order of the genes in the data file.
conditionsOrder
double[] conditionsOrder
- The order of the conditions in the data file.
genesIndexes
int[] genesIndexes
- The indexes of the genes set by clustering method for file output.
conditionsIndexes
int[] conditionsIndexes
- The indexes of the conditions set by clustering method for file output.
uniqueID
java.lang.String uniqueID
- The name of the unique ID used to identify genes in the data file.
genesUniqueIDs
java.lang.String[] genesUniqueIDs
- Genes' unique IDs.
genesNames
java.lang.String[] genesNames
- Genes' names.
conditionsNames
java.lang.String[] conditionsNames
- Conditions' names.
expressionData
double[][] expressionData
- Expression data. Contains the expression values measured
for the genes in the experimental conditions.
missingsMask
int[][] missingsMask
- Missing values mask.
missingsMask[i][j] == 1 -> valid expression value in
expressionData[i][j]
missingsMask[i][j] == 0 -> missing expression value in
expressionData[i][j] (this means that the value in
expressionData[i][j] should not be used for calculations).
Mask is composed by integer values, not boolean, because these
values are sometimes used in calculation.
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.
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.
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.
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.
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
smadeira.biclustering.NodeObjectInterface nodeObject
- The object.
goFrontEnds
java.util.HashMap<K,V> goFrontEnds
- All computed GO frontends.
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
biggests.gui.MyTreeViewApp treeViewApp
- A Java TreeView application.
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
smadeira.biclustering.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
mainFrame
BiggestsFrame mainFrame
- The application's main frame.
expressionMatrix
smadeira.biclustering.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.
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
smadeira.biclustering.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.
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
smadeira.biclustering.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)
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.
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.
biclustering
smadeira.biclustering.Biclustering<T> 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.
mainFrame
BiggestsFrame mainFrame
- BiGGEsTS main window.
expressionMatrix
smadeira.biclustering.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.
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.
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).
missingValue
float missingValue
- The value that marks the cells which "contain" missing values.
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).
formatter
java.text.NumberFormat formatter
- The formatter which is used to format the float value.
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
smadeira.ontologizer.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.
formatter
java.text.NumberFormat formatter
- The formatter which is used to format the float value.
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).
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 Gon�alves
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 Gon�alves
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 Gon�alves
on 24-11-2006).
sortingColumns
java.util.ArrayList<E> sortingColumns
- The directives to sort columns.
postProcessed
boolean postProcessed
- States if this table sorter is for a table of functions of a
post-processed biclusters group or not.
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.
missingValue
char missingValue
- The value for marking missings.
goFrontEnd
smadeira.ontologizer.GOFrontEnd goFrontEnd
parent
java.awt.Component parent
formatter
java.text.NumberFormat formatter
- The formatter which is used to format the float value.
missingValue
float missingValue
- The value used to fill missing values.
serialVersionUID: -9150182590356849832L
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.
serialVersionUID: 3882987169020172801L
root
javax.swing.tree.DefaultMutableTreeNode root
- The root of the datasets tree, i.e., the "Datasets" node.
serialVersionUID: 7553487355938947549L
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
smadeira.biclustering.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;
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.