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Packages that use InvalidNodeObjectTypeException | |
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biggests.gui | |
biggests.tables | |
biggests.tree |
Uses of InvalidNodeObjectTypeException in biggests.gui |
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Methods in biggests.gui that throw InvalidNodeObjectTypeException | |
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static org.jfree.data.category.CategoryDataset |
PanelExpressionChart.createBiclusterDataset(smadeira.biclustering.Bicluster bicluster,
boolean pattern,
boolean normalize)
Creates an expression/pattern category dataset based on genes names, conditions names and expression values or pattern retrieved from the bicluster object. |
static PanelExpressionChart |
PanelExpressionChart.createExpressionAllTimePointsChart(smadeira.biclustering.Bicluster bicluster,
int width,
int height,
java.lang.String title,
boolean normalize)
Creates a new panel holding an all time points expression chart, with expression data retrieved from bicluster and
biclustering objects. |
static PanelExpressionChart |
PanelExpressionChart.createExpressionAllTimePointsChart(smadeira.biclustering.Bicluster bicluster,
java.lang.String title,
int width,
int height,
boolean normalize)
Creates a new panel holding an all time points expression chart, with expression data retrieved from bicluster and
biclustering objects. |
static PanelExpressionChart |
PanelExpressionChart.createExpressionBiclusterTimePointsChart(smadeira.biclustering.Bicluster bicluster,
int width,
int height,
boolean normalize,
boolean miniature)
Creates a new time points expression chart panel for a given bicluster . |
static PanelExpressionChart |
PanelExpressionChart.createExpressionBiclusterTimePointsChart(smadeira.biclustering.Bicluster bicluster,
int width,
int height,
java.lang.String title,
boolean normalize,
boolean miniature)
Creates a new time points expression chart panel for a given bicluster . |
PanelExpressionChart |
PanelExpressionChart.repaintTimePointsChart(int width,
int height,
boolean normalize)
Returns a new time points (bicluster or all time points) chart panel, repainted from the the current one. |
Constructors in biggests.gui that throw InvalidNodeObjectTypeException | |
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PanelExpressionChart(smadeira.biclustering.Bicluster bicluster,
boolean pattern,
int width,
int height,
java.lang.String title,
int minimumDrawWidth,
int minimumDrawHeight,
int maximumDrawWidth,
int maximumDrawHeight,
boolean useBuffer,
boolean properties,
boolean save,
boolean print,
boolean zoom,
boolean tooltips,
boolean shapesVisible,
boolean includeLegend,
boolean normalize)
Constructs a gene or pattern expression chart with the genes names, conditions names and gene expression data retrieved from the given bicluster . |
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PanelExpressionChart(java.lang.String[] genesNames,
java.lang.String[] conditionsNames,
float[][] expressionValues,
float missingValue,
int width,
int height,
java.lang.String title,
int minimumDrawWidth,
int minimumDrawHeight,
int maximumDrawWidth,
int maximumDrawHeight,
boolean useBuffer,
boolean properties,
boolean save,
boolean print,
boolean zoom,
boolean tooltips,
boolean shapesVisible,
boolean includeLegend,
boolean normalize)
Constructs a gene expression chart with the given genesNames , conditionsNames and respective
expressionValues |
Uses of InvalidNodeObjectTypeException in biggests.tables |
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Methods in biggests.tables that throw InvalidNodeObjectTypeException | |
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protected static java.lang.Object[] |
TableSymbolsWithMissingValues.constructColumnNames(smadeira.biclustering.DiscretizedExpressionMatrix discreteMatrix)
Constructs the column names' array with symbolic data retrieved from the given discretized expression matrix. |
protected static java.lang.Object[] |
TableSymbols.constructColumnNames(smadeira.biclustering.NodeObjectInterface nodeObject)
Constructs the column names' array with symbolic data retrieved from the node object's symbolic matrix. |
protected static java.lang.Object[] |
TableValues.constructColumnNames(smadeira.biclustering.NodeObjectInterface nodeObject)
Constructs the column names' array with data retrieved from the node object. |
protected static java.lang.Object[][] |
TableFunctionGroup.constructRowData(smadeira.biclustering.Biclustering biclustering,
java.util.Hashtable<java.lang.Integer,smadeira.utils.BiologicalRelevanceSummary> biologicalRelevanceSummary,
boolean postProcessed)
Constructs the row data matrix with data retrieved from the biclustering object. |
protected static java.lang.Object[][] |
TableSymbolsWithMissingValues.constructRowData(smadeira.biclustering.DiscretizedExpressionMatrix discreteMatrix)
Constructs the row data matrix with symbolic data retrieved from the node object's symbolic matrix. |
protected static java.lang.Object[][] |
TableSymbols.constructRowData(smadeira.biclustering.NodeObjectInterface nodeObject)
Constructs the row data matrix with symbolic data retrieved from the node object's symbolic matrix. |
protected static java.lang.Object[][] |
TableValues.constructRowData(smadeira.biclustering.NodeObjectInterface nodeObject)
Constructs the row data matrix with data retrieved from the node object. |
Constructors in biggests.tables that throw InvalidNodeObjectTypeException | |
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TableColors(smadeira.biclustering.NodeObjectInterface nodeObject)
Creates a new colored table with data from the the given node object's matrix. |
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TableColors(smadeira.biclustering.NodeObjectInterface nodeObject,
smadeira.ontologizer.GOFrontEnd go,
java.awt.Component parent)
Creates a new colored table with data from the the given node object's matrix. |
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TableColorsWithMissingValues(smadeira.biclustering.AbstractExpressionMatrix expressionMatrix)
Creates a new colored table with data from the given expression matrix with missing values. |
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TableColorsWithMissingValues(smadeira.biclustering.AbstractExpressionMatrix expressionMatrix,
smadeira.ontologizer.GOFrontEnd go,
java.awt.Component parent)
Creates a new colored table with data from the given expression matrix with missing values. |
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TableColorsWithMissingValues(smadeira.biclustering.Bicluster bicluster)
Creates a new colored table with data from the given bicluster with missing values. |
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TableColorsWithMissingValues(smadeira.biclustering.Bicluster bicluster,
smadeira.ontologizer.GOFrontEnd go,
java.awt.Component parent)
Creates a new colored table with data from the given bicluster with missing values. |
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TableColorsWithMissingValues(smadeira.biclustering.DiscretizedExpressionMatrix expressionMatrix)
Creates a new colored table with data from the given expression matrix with missing values. |
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TableColorsWithMissingValues(smadeira.biclustering.DiscretizedExpressionMatrix expressionMatrix,
smadeira.ontologizer.GOFrontEnd go,
java.awt.Component parent)
Creates a new colored table with data from the given expression matrix with missing values. |
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TableFunctionGroup(smadeira.biclustering.Biclustering biclustering,
java.util.Hashtable<java.lang.Integer,smadeira.utils.BiologicalRelevanceSummary> biologicalRelevanceSummary,
boolean postProcessed)
Creates a new function table from the data of a biclusters group object. |
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TableFunctionIndividual(smadeira.biclustering.Bicluster bicluster,
smadeira.ontologizer.GeneSetResult goProperties,
smadeira.ontologizer.GOFrontEnd go,
float pValueThreshold,
java.awt.Component parent)
Creates a new table of functions from the data of a bicluster object. |
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TableSymbols(smadeira.biclustering.NodeObjectInterface nodeObject)
Creates a new table of symbols with data from the the given node object's matrix. |
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TableSymbols(smadeira.biclustering.NodeObjectInterface nodeObject,
smadeira.ontologizer.GOFrontEnd go,
java.awt.Component parent)
Creates a new table of symbols with data from the the given node object's matrix. |
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TableSymbolsWithMissingValues(smadeira.biclustering.CCC_Bicluster bicluster)
Creates a new table of symbols with data from the given bicluster's matrix. |
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TableSymbolsWithMissingValues(smadeira.biclustering.CCC_Bicluster bicluster,
smadeira.ontologizer.GOFrontEnd go,
java.awt.Component parent)
Creates a new table of symbols with data from the the given bicluster. |
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TableSymbolsWithMissingValues(smadeira.biclustering.DiscretizedExpressionMatrix discreteMatrix)
Creates a new table of symbols with data from the the given discretized expression matrix. |
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TableSymbolsWithMissingValues(smadeira.biclustering.DiscretizedExpressionMatrix discreteMatrix,
smadeira.ontologizer.GOFrontEnd go,
java.awt.Component parent)
Creates a new table of symbols with data from the the given discretized expression matrix. |
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TableValues(smadeira.biclustering.NodeObjectInterface nodeObject)
Creates a new values table from the data of a node object. |
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TableValues(smadeira.biclustering.NodeObjectInterface nodeObject,
smadeira.ontologizer.GOFrontEnd go,
java.awt.Component parent)
Creates a new values table from the data of a node object. |
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TableValuesWithMissingValues(smadeira.biclustering.Bicluster bicluster)
Creates a new values table from the data of a bicluster with missing values. |
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TableValuesWithMissingValues(smadeira.biclustering.Bicluster bicluster,
smadeira.ontologizer.GOFrontEnd go,
java.awt.Component parent)
Creates a new values table from the data of a bicluster with missing values. |
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TableValuesWithMissingValues(smadeira.biclustering.IMatrix expressionMatrix)
Creates a new values table from the data of an expression matrix with missing values. |
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TableValuesWithMissingValues(smadeira.biclustering.IMatrix expressionMatrix,
smadeira.ontologizer.GOFrontEnd go,
java.awt.Component parent)
Creates a new values table from the data of an expression matrix with missing values. |
Uses of InvalidNodeObjectTypeException in biggests.tree |
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Methods in biggests.tree that throw InvalidNodeObjectTypeException | |
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javax.swing.tree.TreePath |
DatasetTree.addLoadedDataset(NodeInfo originalNodeInfo)
Adds the loaded dataset to the dataset tree and creates all additional nodes for preprocessed, discretized, biclustered and post-processed matrices of the dataset. |
javax.swing.tree.TreePath |
DatasetTree.addLoadedDataset(NodeInfo originalNodeInfo,
boolean setNewPath)
Adds the loaded dataset to the dataset tree and creates all additional nodes for preprocessed, discretized, biclustered and post-processed matrices of the dataset. |
javax.swing.tree.TreePath |
DatasetTree.addNewNode(NodeInfo nodeInfo,
javax.swing.tree.TreePath selectionPath,
boolean reload)
Adds a new node to the datasets tree, associated with a node information object. |
void |
DatasetTree.addNewNode(NodeInfo nodeInfo,
javax.swing.tree.TreePath selectionPath,
boolean setNewPath,
boolean reload)
Adds a new node to the datasets tree, associated with a node information object. |
int |
DatasetTree.generateNewNodeInfoId(int nodeObjectType,
javax.swing.tree.TreePath selectionPath,
boolean update)
Returns the next id for a new NodeInfo object to be
created in the dataset of the given selected path. |
int |
Dataset.generateNewNodeObjectTypeId(int nodeObjectType,
boolean update)
Generates a new id value (within this dataset) for a new node information object with the specified data type. |
Constructors in biggests.tree that throw InvalidNodeObjectTypeException | |
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NodeInfo(smadeira.biclustering.NodeObjectInterface nodeObject,
int nodeObjectType,
javax.swing.tree.TreePath selectionPath,
DatasetTree tree,
NodeInfo parent,
java.util.ArrayList<java.lang.String> infoStrings,
java.util.ArrayList<java.lang.String> infoStyles)
Constructs an object of type NodeInfo (with all the information about
a certain node, including a pointer for the node object itself. |
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NodeInfo(smadeira.biclustering.NodeObjectInterface nodeObject,
int nodeObjectType,
javax.swing.tree.TreePath selectionPath,
DatasetTree tree,
NodeInfo parent,
java.util.ArrayList<java.lang.String> infoStrings,
java.util.ArrayList<java.lang.String> infoStyles,
int index)
Constructs an object of type NodeInfo (with all the information about
a certain node, including a pointer for the node object itself. |
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