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A

actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignment.swingx.ErrorDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColorSequenceDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignment.ui.EditLineAnnDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignment.ui.EditSeqAnnBaseDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignment.ui.EditSeqAnnDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignment.ui.EditSequenceDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignment.ui.EditSequenceNameDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
activityBackgroundChanged(DisplayProperties) - Method in interface org.processmining.plugins.tracealignment.ui.DisplayPropertiesListener
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
ActivityOverFlowException - Exception in org.processmining.plugins.tracealignment.util
 
ActivityOverFlowException() - Constructor for exception org.processmining.plugins.tracealignment.util.ActivityOverFlowException
 
addClipboardBindings(JTextComponent) - Static method in class org.processmining.plugins.tracealignment.swingx.Utils
 
addColumn() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
addColumnFilter(ColumnFilter, int) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
addColumnFilter(ColumnFilter, int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
addColumnSort(ColumnSort, int) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
addColumnSort(ColumnSort, int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
addDuplicateProcessInstance(String) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
addLayoutComponent(Component, Object) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
addLayoutComponent(String, Component) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
addLineAnnotation(String, String) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
addLineAnnotation(Sequence.LineAnnotation) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
addListener(AlignmentListener) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
addListener(ColorSchemeListener) - Method in interface org.processmining.plugins.tracealignment.ui.ColorScheme
 
addListener(DisplayPropertiesListener) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
Add a listener
addListener(SequenceListener) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
addRulerAnnotation() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
addToGridBag(Container, GridBagLayout, Component, int, int, int, int, int, int, int, int) - Static method in class org.processmining.plugins.tracealignment.swingx.Utils
 
addToGridBag(Container, GridBagLayout, Component, int, int, int, int, int, int, int, int, Insets) - Static method in class org.processmining.plugins.tracealignment.swingx.Utils
 
AgglomerativeHierarchicalClustering - Class in org.processmining.plugins.tracealignment.clustering
 
AgglomerativeHierarchicalClustering(float[][], AgglomerativeHierarchicalClustering.ClusterType, AgglomerativeHierarchicalClustering.ClusterCriteria) - Constructor for class org.processmining.plugins.tracealignment.clustering.AgglomerativeHierarchicalClustering
 
AgglomerativeHierarchicalClustering.Cluster - Class in org.processmining.plugins.tracealignment.clustering
 
AgglomerativeHierarchicalClustering.ClusterCriteria - Enum in org.processmining.plugins.tracealignment.clustering
 
AgglomerativeHierarchicalClustering.ClusterType - Enum in org.processmining.plugins.tracealignment.clustering
 
Alignment - Class in org.processmining.plugins.tracealignment.ui
 
Alignment(int, Sequence[]) - Constructor for class org.processmining.plugins.tracealignment.ui.Alignment
 
alignment - Variable in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
alignment - Variable in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
alignment - Variable in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
alignment - Variable in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
Alignment.RulerAnnotation - Class in org.processmining.plugins.tracealignment.ui
 
AlignmentFrame - Class in org.processmining.plugins.tracealignment
 
AlignmentFrame(UIPluginContext, XLog) - Constructor for class org.processmining.plugins.tracealignment.AlignmentFrame
 
alignmentFrame - Variable in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
alignmentFrame - Variable in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
AlignmentFrameVisualization - Class in org.processmining.plugins.tracealignment
 
AlignmentFrameVisualization() - Constructor for class org.processmining.plugins.tracealignment.AlignmentFrameVisualization
 
AlignmentListener - Interface in org.processmining.plugins.tracealignment.ui
 
alignmentNameChanged(Alignment) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
alignmentNameChanged(Alignment) - Method in interface org.processmining.plugins.tracealignment.ui.AlignmentListener
 
alignmentNameChanged(Alignment) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
alignmentNameChanged(Alignment) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
alignmentNameChanged(Alignment) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
alignmentNameChanged(Alignment) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
alignmentNameChanged(Alignment) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
alignmentNameChanged(Alignment) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
AlignmentNamePanel - Class in org.processmining.plugins.tracealignment.ui
 
AlignmentNamePanel(AlignmentFrame, Alignment, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
AlignmentPanel - Class in org.processmining.plugins.tracealignment.ui
 
AlignmentPanel(AlignmentFrame, Alignment, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in interface org.processmining.plugins.tracealignment.ui.AlignmentListener
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in interface org.processmining.plugins.tracealignment.ui.AlignmentListener
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
alignmentSeqInserted(Alignment, int) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
alignmentSeqInserted(Alignment, int) - Method in interface org.processmining.plugins.tracealignment.ui.AlignmentListener
 
alignmentSeqInserted(Alignment, int) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
alignmentSeqInserted(Alignment, int) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
alignmentSeqInserted(Alignment, int) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
alignmentSeqInserted(Alignment, int) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
alignmentSeqInserted(Alignment, int) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
alignmentSeqInserted(Alignment, int) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
alignmentSeqSwapped(Alignment, int, int) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
alignmentSeqSwapped(Alignment, int, int) - Method in interface org.processmining.plugins.tracealignment.ui.AlignmentListener
 
alignmentSeqSwapped(Alignment, int, int) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
alignmentSeqSwapped(Alignment, int, int) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
alignmentSeqSwapped(Alignment, int, int) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
alignmentSeqSwapped(Alignment, int, int) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
alignmentSeqSwapped(Alignment, int, int) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
alignmentSeqSwapped(Alignment, int, int) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
AlignmentSorter - Class in org.processmining.plugins.tracealignment.ui
 
AlignmentSorter(Alignment, Comparator<Sequence>) - Constructor for class org.processmining.plugins.tracealignment.ui.AlignmentSorter
 
ArrayMatrixFileIO - Class in org.processmining.plugins.tracealignment.util
 
ArrayMatrixFileIO() - Constructor for class org.processmining.plugins.tracealignment.util.ArrayMatrixFileIO
 
assignPriority(int) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 

C

cachedValue - Variable in class org.processmining.plugins.tracealignment.swingx.LazyBoundedRangeModel
 
calcSortValueBasedOnColumnSorts(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
caretPositionChanged(InputMethodEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterDialog
 
caretPositionChanged(InputMethodEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortDialog
 
caretUpdate(CaretEvent) - Method in class org.processmining.plugins.tracealignment.ui.EditActivityAnnDialog
 
caretUpdate(CaretEvent) - Method in class org.processmining.plugins.tracealignment.ui.EditSeqAnnBaseDialog
 
clear() - Method in class org.processmining.plugins.tracealignment.swingx.ConsolePane
Clear the document.
clearHighlights() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
clearLastActivityIndexSelected() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
clearLastColumnIndexSelected() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
clearLastRulerAnnIndexSelected() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
clearRefSequence() - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
clearSelections() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
Deselect all sequences
close() - Method in class org.processmining.plugins.tracealignment.swingx.DocumentWriter
Close the stream, flushing it first.
Cluster(float[]) - Constructor for class org.processmining.plugins.tracealignment.clustering.AgglomerativeHierarchicalClustering.Cluster
 
Cluster(AgglomerativeHierarchicalClustering.Cluster, AgglomerativeHierarchicalClustering.Cluster, float[]) - Constructor for class org.processmining.plugins.tracealignment.clustering.AgglomerativeHierarchicalClustering.Cluster
 
collapsed - Variable in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
ColorScheme - Interface in org.processmining.plugins.tracealignment.ui
 
colorSchemeChanged(ColorScheme) - Method in interface org.processmining.plugins.tracealignment.ui.ColorSchemeListener
 
colorSchemeChanged(ColorScheme) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
ColorSchemeListener - Interface in org.processmining.plugins.tracealignment.ui
 
ColorSequenceDialog - Class in org.processmining.plugins.tracealignment.ui
 
ColorSequenceDialog(AlignmentFrame, Sequence) - Constructor for class org.processmining.plugins.tracealignment.ui.ColorSequenceDialog
 
ColumnAnnotation(int, String, String, Color, boolean) - Constructor for class org.processmining.plugins.tracealignment.ui.Sequence.ColumnAnnotation
 
ColumnAnnotationComponent - Class in org.processmining.plugins.tracealignment.ui
 
ColumnAnnotationComponent(Alignment, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
ColumnFilter - Class in org.processmining.plugins.tracealignment.ui
 
ColumnFilter(AlignmentFrame, int, String) - Constructor for class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
ColumnFilter(AlignmentFrame, String) - Constructor for class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
ColumnFilterComponent - Class in org.processmining.plugins.tracealignment.ui
 
ColumnFilterComponent(AlignmentFrame, Alignment, DisplayProperties, AlignmentFrame) - Constructor for class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
ColumnFilterDialog - Class in org.processmining.plugins.tracealignment.ui
 
ColumnFilterDialog(AlignmentFrame, DisplayProperties, int, ColumnFilter, Point) - Constructor for class org.processmining.plugins.tracealignment.ui.ColumnFilterDialog
 
columnFiltering - Variable in class org.processmining.plugins.tracealignment.AlignmentFrame
 
ColumnSort - Class in org.processmining.plugins.tracealignment.ui
 
ColumnSort(AlignmentFrame, int, String, int) - Constructor for class org.processmining.plugins.tracealignment.ui.ColumnSort
 
ColumnSort(AlignmentFrame, String, int) - Constructor for class org.processmining.plugins.tracealignment.ui.ColumnSort
 
ColumnSort(AlignmentFrame, String) - Constructor for class org.processmining.plugins.tracealignment.ui.ColumnSort
 
ColumnSortComponent - Class in org.processmining.plugins.tracealignment.ui
 
ColumnSortComponent(Frame, Alignment, DisplayProperties, AlignmentFrame) - Constructor for class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
ColumnSortDialog - Class in org.processmining.plugins.tracealignment.ui
 
ColumnSortDialog(AlignmentFrame, DisplayProperties, int, ColumnSort, Point) - Constructor for class org.processmining.plugins.tracealignment.ui.ColumnSortDialog
 
columnSorting - Variable in class org.processmining.plugins.tracealignment.AlignmentFrame
 
compare(Sequence, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
ConsensusComponent - Class in org.processmining.plugins.tracealignment.ui
 
ConsensusComponent(ConsensusSequence, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
ConsensusSequence - Class in org.processmining.plugins.tracealignment.ui
 
ConsensusSequence(AlignmentFrame, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignment.ui.ConsensusSequence
 
ConsensusSequence(AlignmentFrame, DisplayProperties, Sequence[]) - Constructor for class org.processmining.plugins.tracealignment.ui.ConsensusSequence
 
ConsolePane - Class in org.processmining.plugins.tracealignment.swingx
 
ConsolePane() - Constructor for class org.processmining.plugins.tracealignment.swingx.ConsolePane
 
createDir(String) - Method in class org.processmining.plugins.tracealignment.util.ArrayMatrixFileIO
 
createDir(String) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
createPrintStream(AttributeSet) - Method in class org.processmining.plugins.tracealignment.swingx.ConsolePane
Create a PrintStream that will display in the console using the given attributes.
createPrintWriter(AttributeSet) - Method in class org.processmining.plugins.tracealignment.swingx.ConsolePane
Create a PrintWriter that will display in the console using the given attributes.

D

decrementNumColumnSorts() - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
deleteActivity(int) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
deleteAnnotation() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
deletes sequence annotations
deleteLineAnnotation(String) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
Deletes the specified line annotation
deleteLineAnnotation(int) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
deselectAllColumns(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
deselectAllColumns(DisplayProperties, boolean) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
deselectAllRulerSelections() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in interface org.processmining.plugins.tracealignment.ui.DisplayPropertiesListener
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
displayColorSchemeChanged(DisplayProperties, ColorScheme) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
displayColorSchemeChanged(DisplayProperties, ColorScheme) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
displayColorSchemeChanged(DisplayProperties, ColorScheme) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
displayColorSchemeChanged(DisplayProperties, ColorScheme) - Method in interface org.processmining.plugins.tracealignment.ui.DisplayPropertiesListener
 
displayColorSchemeChanged(DisplayProperties, ColorScheme) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
displayColorSchemeChanged(DisplayProperties, ColorScheme) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
displayColorSchemeChanged(DisplayProperties, ColorScheme) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
displayColorSchemeChanged(DisplayProperties, ColorScheme) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
displayColorSchemeChanged(DisplayProperties, ColorScheme) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
displayedAnnotationButtonGroup - Variable in class org.processmining.plugins.tracealignment.ui.EditSeqAnnBaseDialog
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
displayFontChanged(DisplayProperties) - Method in interface org.processmining.plugins.tracealignment.ui.DisplayPropertiesListener
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
displayGroupEditingChanged(DisplayProperties) - Method in interface org.processmining.plugins.tracealignment.ui.DisplayPropertiesListener
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in interface org.processmining.plugins.tracealignment.ui.DisplayPropertiesListener
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in interface org.processmining.plugins.tracealignment.ui.DisplayPropertiesListener
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
displayOverwriteChanged(DisplayProperties) - Method in interface org.processmining.plugins.tracealignment.ui.DisplayPropertiesListener
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
displayProperties - Variable in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
displayProperties - Variable in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
displayProperties - Variable in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
displayProperties - Variable in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
DisplayProperties - Class in org.processmining.plugins.tracealignment.ui
 
DisplayProperties(int, Alignment, Font, FontMetrics, boolean, boolean) - Constructor for class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
displayProperties - Variable in class org.processmining.plugins.tracealignment.ui.EditSeqAnnBaseDialog
 
DisplayPropertiesListener - Interface in org.processmining.plugins.tracealignment.ui
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
displayRenderGapsChanged(DisplayProperties) - Method in interface org.processmining.plugins.tracealignment.ui.DisplayPropertiesListener
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in interface org.processmining.plugins.tracealignment.ui.DisplayPropertiesListener
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
DocumentOutputStream - Class in org.processmining.plugins.tracealignment.swingx
An OutputStream implementation that places it's output in a swing text model (Document).
DocumentOutputStream(Document, AttributeSet) - Constructor for class org.processmining.plugins.tracealignment.swingx.DocumentOutputStream
Constructs an output stream that will output to the given document with the given set of character attributes.
DocumentOutputStream(Document) - Constructor for class org.processmining.plugins.tracealignment.swingx.DocumentOutputStream
Constructs an output stream that will output to the given document with whatever the default attributes are.
DocumentWriter - Class in org.processmining.plugins.tracealignment.swingx
An Writer implementation that places it's output in a swing text model (Document).
DocumentWriter(Document, AttributeSet) - Constructor for class org.processmining.plugins.tracealignment.swingx.DocumentWriter
Constructs an output stream that will output to the given document with the given set of character attributes.
DocumentWriter(Document) - Constructor for class org.processmining.plugins.tracealignment.swingx.DocumentWriter
Constructs an output stream that will output to the given document with whatever the default attributes are.

E

edit(Point) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
edit(Point) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
Double clickable sequence name
EditActivityAnnDialog - Class in org.processmining.plugins.tracealignment.ui
 
EditActivityAnnDialog(AlignmentFrame, DisplayProperties, Alignment, Sequence, int) - Constructor for class org.processmining.plugins.tracealignment.ui.EditActivityAnnDialog
 
EditLineAnnDialog - Class in org.processmining.plugins.tracealignment.ui
 
EditLineAnnDialog(Frame, Sequence, DisplayProperties, int) - Constructor for class org.processmining.plugins.tracealignment.ui.EditLineAnnDialog
 
EditSeqAnnBaseDialog - Class in org.processmining.plugins.tracealignment.ui
 
EditSeqAnnBaseDialog(AlignmentFrame, String, DisplayProperties, Sequence) - Constructor for class org.processmining.plugins.tracealignment.ui.EditSeqAnnBaseDialog
 
EditSeqAnnDialog - Class in org.processmining.plugins.tracealignment.ui
 
EditSeqAnnDialog(AlignmentFrame, DisplayProperties, Sequence) - Constructor for class org.processmining.plugins.tracealignment.ui.EditSeqAnnDialog
 
EditSequenceDialog - Class in org.processmining.plugins.tracealignment.ui
 
EditSequenceDialog(AlignmentFrame, Sequence) - Constructor for class org.processmining.plugins.tracealignment.ui.EditSequenceDialog
 
EditSequenceDialog(AlignmentFrame, Sequence, Alignment, int) - Constructor for class org.processmining.plugins.tracealignment.ui.EditSequenceDialog
Allows user to create and edit a NEW sequence
EditSequenceNameDialog - Class in org.processmining.plugins.tracealignment.ui
 
EditSequenceNameDialog(AlignmentFrame, DisplayProperties, Sequence) - Constructor for class org.processmining.plugins.tracealignment.ui.EditSequenceNameDialog
 
encode(String[]) - Method in class org.processmining.plugins.tracealignment.util.EncodeActivitySet
 
encode(String[], String[]) - Method in class org.processmining.plugins.tracealignment.util.EncodeActivitySet
 
encode(String[], String[], String[]) - Method in class org.processmining.plugins.tracealignment.util.EncodeActivitySet
 
EncodeActivitySet - Class in org.processmining.plugins.tracealignment.util
 
EncodeActivitySet(Set<String>) - Constructor for class org.processmining.plugins.tracealignment.util.EncodeActivitySet
This method encodes a set of elements passed to it; The elements can be the set of activities along with the trace identifier.
EncodeTraces - Class in org.processmining.plugins.tracealignment.util
 
EncodeTraces(Map<String, String>, XLog) - Constructor for class org.processmining.plugins.tracealignment.util.EncodeTraces
 
encodingLength - Variable in class org.processmining.plugins.tracealignment.ui.Alignment
 
EncodingNotFoundException - Exception in org.processmining.plugins.tracealignment.util
 
enforceDisabledElements() - Method in class org.processmining.plugins.tracealignment.swingx.JListX
 
equals(Object) - Method in class org.processmining.plugins.tracealignment.ui.Sequence.LineAnnotation
 
EqualsThisLetter - Static variable in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
EqualsThisLetter - Static variable in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
EquivalenceClass - Class in org.processmining.plugins.tracealignment.util
 
EquivalenceClass() - Constructor for class org.processmining.plugins.tracealignment.util.EquivalenceClass
 
ErrorDialog - Class in org.processmining.plugins.tracealignment.swingx
 
EuclideanDistance - Class in org.processmining.plugins.tracealignment.util
 
EuclideanDistance(int, List<String>, Set<String>, EuclideanDistance.Normalization) - Constructor for class org.processmining.plugins.tracealignment.util.EuclideanDistance
 
EuclideanDistance(int, List<String>, Map<Set<String>, Set<String>>, EuclideanDistance.Normalization) - Constructor for class org.processmining.plugins.tracealignment.util.EuclideanDistance
 
EuclideanDistance(float[][], EuclideanDistance.Normalization) - Constructor for class org.processmining.plugins.tracealignment.util.EuclideanDistance
This constructor is used when a feature matrix is provided
EuclideanDistance.Normalization - Enum in org.processmining.plugins.tracealignment.util
 

F

FeatureExtraction - Class in org.processmining.plugins.tracealignment.util
 
FeatureExtraction() - Constructor for class org.processmining.plugins.tracealignment.util.FeatureExtraction
 
FeatureExtraction(int, List<String>, Map<String, String>, FeatureExtraction.FeatureType) - Constructor for class org.processmining.plugins.tracealignment.util.FeatureExtraction
 
FeatureExtraction(int, List<String>, FeatureExtraction.FeatureType, int) - Constructor for class org.processmining.plugins.tracealignment.util.FeatureExtraction
 
FeatureExtraction.FeatureType - Enum in org.processmining.plugins.tracealignment.util
 
FeatureMatrix - Class in org.processmining.plugins.tracealignment.util
 
FeatureMatrix(int, List<String>, Set<String>) - Constructor for class org.processmining.plugins.tracealignment.util.FeatureMatrix
 
FeatureMatrix(int, List<String>, Set<String>, FeatureSelection.FilterType) - Constructor for class org.processmining.plugins.tracealignment.util.FeatureMatrix
Cater to feature matrix generation with consideration of non-overlaps
FeatureMatrix(int, List<String>, Map<Set<String>, Set<String>>) - Constructor for class org.processmining.plugins.tracealignment.util.FeatureMatrix
 
FeatureSelection - Class in org.processmining.plugins.tracealignment.util
 
FeatureSelection(int) - Constructor for class org.processmining.plugins.tracealignment.util.FeatureSelection
 
FeatureSelection(int, Set<String>) - Constructor for class org.processmining.plugins.tracealignment.util.FeatureSelection
 
FeatureSelection(int, List<String>) - Constructor for class org.processmining.plugins.tracealignment.util.FeatureSelection
 
FeatureSelection.FilterType - Enum in org.processmining.plugins.tracealignment.util
 
FileIO - Class in org.processmining.plugins.tracealignment.util
 
FileIO() - Constructor for class org.processmining.plugins.tracealignment.util.FileIO
 
findColumn(int, int) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
findColumn(int, int) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
findColumn(int, int) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
Return the column number based on the coordinate location; Only the x-coordinate value is required to determine the column number
findLeftDiverseNodes() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
Assess the left diversity (property) of nodes A node v is called left diverse if at least two leaves in v's subtree have different left symbols; So, check for the leftSymbolSet to be of at least size 2; If the node qualifies to be leftDiverse, then set all its ancestors also as leftDiverse;
findLineAnnotation(int, int) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
findMouseColumn(int) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
fireDisplayHighlightsChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
fireDisplayHighlightsChanged(Sequence[]) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
fireSeqSelect(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
FixedWidthTextField - Class in org.processmining.plugins.tracealignment.swingx
JTextField which always uses a fixed width font, good for having sequences line up, etc.
FixedWidthTextField(String, int) - Constructor for class org.processmining.plugins.tracealignment.swingx.FixedWidthTextField
 
flush() - Method in class org.processmining.plugins.tracealignment.swingx.DocumentWriter
Flush the stream.

G

get3GramSet() - Method in class org.processmining.plugins.tracealignment.util.IndelSubstitutionMatrix
 
getActivityCharMap() - Method in class org.processmining.plugins.tracealignment.util.EncodeActivitySet
 
getActivityHeight() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getActivityIndex(int) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getActivityIndexArray() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getActivityList() - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
getActivityPosition(int) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
Get the coordinate location of an activity given the activity column (position) number
getActivityWidth() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getAlignment() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getAlignments(int) - Method in class org.processmining.plugins.tracealignment.msa.MSA
 
getAllSelected() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getAllSelected(boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getAllSequences() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getAlphabetEquivalenceClassMap(int, Set<String>) - Method in class org.processmining.plugins.tracealignment.util.EquivalenceClass
 
getAlphabetFeatureFeatureCountMapTracesList() - Method in class org.processmining.plugins.tracealignment.util.EuclideanDistance
 
getAlphabetFeatureList() - Method in class org.processmining.plugins.tracealignment.util.FeatureMatrix
 
getAlphabetFeatureSetMap() - Method in class org.processmining.plugins.tracealignment.util.FeatureExtraction
 
getAnnotation() - Method in class org.processmining.plugins.tracealignment.ui.Sequence.ColumnAnnotation
 
getAnnotation() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getAnnotation() - Method in class org.processmining.plugins.tracealignment.ui.Sequence.LineAnnotation
 
getAnnView(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getArrayFromString(String) - Static method in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
getArrayFromString(String) - Static method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
getBackgroundColor(Sequence, int) - Method in interface org.processmining.plugins.tracealignment.ui.ColorScheme
 
getBaseFeatureSet(Set<String>) - Method in class org.processmining.plugins.tracealignment.util.FeatureSelection
 
getBaseFileName(File) - Static method in class org.processmining.plugins.tracealignment.swingx.Utils
 
getCharActivityMap() - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
getCharActivityMap() - Method in class org.processmining.plugins.tracealignment.util.EncodeActivitySet
 
getCharStreamList() - Method in class org.processmining.plugins.tracealignment.util.EncodeTraces
 
getCharWidth() - Method in class org.processmining.plugins.tracealignment.swingx.FixedWidthTextField
 
getClusterItems(int) - Method in class org.processmining.plugins.tracealignment.msa.MSA
 
getClusters() - Method in class org.processmining.plugins.tracealignment.clustering.AgglomerativeHierarchicalClustering
 
getCmdOptionChar() - Static method in class org.processmining.plugins.tracealignment.swingx.Utils
 
getCollapsed() - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
getCollapsed() - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
getColor() - Method in class org.processmining.plugins.tracealignment.ui.Alignment.RulerAnnotation
 
getColor() - Method in class org.processmining.plugins.tracealignment.ui.Sequence.ColumnAnnotation
 
getColor() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getColumn() - Method in class org.processmining.plugins.tracealignment.ui.Sequence.ColumnAnnotation
 
getColumnAnnotation(int) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getColumnAnnotations() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getColumnAnnotationsCount() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getColumnFilter(Integer) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getColumnFilterColumnIterator() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getColumnFilterCurrentColumn() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getColumnFiltering() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getColumnLocationRelativeToOwner(int) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
getColumnLocationRelativeToOwner(int) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
getColumnSort(Integer) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getColumnSortColumnIterator() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getColumnSortCurrentColumn() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getColumnSorting() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getColumnsSize() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
Returns the total number of columns in the alignment
getComplexAlphabetTandemRepeatMap() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
getComplexTandemRepeats() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
getConsensusColorAt(int) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
getConservationScoreAtColumnIndex(int) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
getCurrentColumnFilter() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getCurrentColumnSort() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getCursorColumn() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getCursorRow() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getDisplayCustom() - Static method in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
getDisplayCustom() - Static method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
getDisplayCustomOpNames() - Static method in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
getDisplayCustomOpNames() - Static method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
getDisplayedAnnotation() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getDisplayedAnnotationName() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getDisplayNone() - Static method in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
getDisplayNone() - Static method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
getDisplayOpNames() - Static method in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
getDisplayOpNames() - Static method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
getDisplayProperties() - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
getDisplayText() - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
getDisplayText() - Method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
getDistanceMatrix() - Method in class org.processmining.plugins.tracealignment.util.EuclideanDistance
 
getDuplicateProcessInstanceNameList() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getEncodedActivity(int) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getEncodedActivityColorMap() - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
getEncodingLength() - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
getEncodingLength() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getEncodingLength() - Method in class org.processmining.plugins.tracealignment.util.EncodeActivitySet
 
getF2Score(int[][]) - Method in class org.processmining.plugins.tracealignment.util.TraceSimilarity
 
getFeatureFeatureCountMapTracesList() - Method in class org.processmining.plugins.tracealignment.util.EuclideanDistance
 
getFeatureMatrix() - Method in class org.processmining.plugins.tracealignment.util.FeatureMatrix
 
getFilterActivitiesString() - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
getFilterActivitiesString() - Method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
getFilteredAlphabetFeatureSet(Map<Set<String>, Set<String>>, FeatureSelection.FilterType, int, int) - Method in class org.processmining.plugins.tracealignment.util.FeatureSelection
 
getFilteredAlphabetFeatureSet(Map<Set<String>, Set<String>>, FeatureSelection.FilterType, float, float) - Method in class org.processmining.plugins.tracealignment.util.FeatureSelection
 
getFilteredMaximalRepeats() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
getFilteredNearSuperMaximalRepeats() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
getFilteredSequenceFeatureSet(Set<String>, FeatureSelection.FilterType) - Method in class org.processmining.plugins.tracealignment.util.FeatureSelection
 
getFilteredSequenceFeatureSet(Set<String>, FeatureSelection.FilterType, int, int) - Method in class org.processmining.plugins.tracealignment.util.FeatureSelection
 
getFilteredSequenceFeatureSet(Set<String>, FeatureSelection.FilterType, float, float) - Method in class org.processmining.plugins.tracealignment.util.FeatureSelection
 
getFilteredSuperMaximalRepeats() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
getFirstColumnSelected() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getFont() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getFontMetrics() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getFontSize() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getFontXOffset() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getFontYOffset() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getForegroundColor(Sequence, int) - Method in interface org.processmining.plugins.tracealignment.ui.ColorScheme
 
getFormattedAnnotationInfo(Sequence, StringBuffer) - Method in class org.processmining.plugins.tracealignment.ui.Sequence.ColumnAnnotation
 
getFScore(Set<String>, Collection<String>) - Method in class org.processmining.plugins.tracealignment.util.TraceSimilarity
 
getFScore(int[][]) - Method in class org.processmining.plugins.tracealignment.util.TraceSimilarity
 
getHgap() - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
getHiddenLineAnnotations() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getHiddenLineAnnotations(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
Get a list of the line annotations that are hidden for the given sequence
getHighlights(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
Identify the column positions (activities) that are highlighted in the given sequence
getIndelLeftGivenRightScoreMap() - Method in class org.processmining.plugins.tracealignment.util.IndelSubstitutionMatrix
 
getIndelRightGivenLeftScoreMap() - Method in class org.processmining.plugins.tracealignment.util.IndelSubstitutionMatrix
 
getIndex(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getInformationInColumnGapsExcluded() - Method in class org.processmining.plugins.tracealignment.ui.ConsensusSequence
 
getInformationInColumnGapsIncluded() - Method in class org.processmining.plugins.tracealignment.ui.ConsensusSequence
 
getInverseRowIndex(int) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
getItemElements(int, int) - Method in class org.processmining.plugins.tracealignment.msa.MSA
 
getItemsJoined() - Method in class org.processmining.plugins.tracealignment.clustering.AgglomerativeHierarchicalClustering
 
getLastActivityIndexSelected() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getLastActivityRowSelected() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getLastColumnIdxSelected() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getLastColumnSelected() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getLayoutAlignmentX(Container) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
getLayoutAlignmentY(Container) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
getLeaves(SuffixNode) - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
getLeftDiverseNodes(SuffixNode) - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
getLengthWithGaps() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getLengthWithoutGaps() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getLetter() - Method in class org.processmining.plugins.tracealignment.ui.Alignment.RulerAnnotation
 
getLineAnnotation(int) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getLineAnnotation(String) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getLineAnnotations() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getLineAnnotationsCount() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getListCellRenderer() - Method in class org.processmining.plugins.tracealignment.swingx.ItemSelectionDialog
 
getListCellRenderer() - Method in class org.processmining.plugins.tracealignment.ui.LineAnnotationSelectionDialog
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class org.processmining.plugins.tracealignment.ui.LineAnnotationListCellRenderer
 
getMatches(String) - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
getMaximalRepeats() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
Get the maximal repeat strings (not necessarily tandem) in the input string for which the suffix tree is constructed The algorithm is of Gusfield's; Determine the maximal repeats; A string alpha labeling a path to a node v of T is a maximal repeat iff v is leftDiverse Retrieve all leftDiverseNodes and print the paths leading to that node from the root The path information is stored in the class attributes pathPosition and edgeLabelEnd; Returns a HashSet of maximal Repeats; Assumes that the parent method calling this would have invoked findLeftDiverseNodes();
getMaximumActivityLength() - Method in class org.processmining.plugins.tracealignment.util.EncodeActivitySet
 
getMaximumSize() - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
getMaximumSize() - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
getMaximumSize() - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
getMaximumSize() - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
getMaxLength() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getMaxPriority() - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
getMinimumSize() - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
getMinimumSize() - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
getMinimumSize() - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
getMinimumSize() - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
getName() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getName() - Method in interface org.processmining.plugins.tracealignment.ui.ColorScheme
 
getName() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getName() - Method in class org.processmining.plugins.tracealignment.ui.Sequence.LineAnnotation
 
getNearSuperMaximalRepeats() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
Find NearSuperMaximal Repeats; A left diverse internal node v represents a near super maximal repeat alpha if and only if one of v's children is a leaf and its left character is the left character of no other leaf below v Assumes that the parent method calling this would have already invoked findLeftDiverseNodes();
getNextFreePriority() - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
getNoDuplicates() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getNoSequences() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getNumberOfColumnsSelected() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getNumColumnSorts() - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
getNumVisibleRows() - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
getOSDirectoryName() - Static method in class org.processmining.plugins.tracealignment.swingx.Utils
 
getOutputArea() - Method in class org.processmining.plugins.tracealignment.swingx.ConsolePane
Fetch the component used for the output.
getPairWiseGlobalAlign(String, String) - Method in class org.processmining.plugins.tracealignment.msa.SequenceAlignment
 
getPairWiseSemiGlobalAlign(String, String) - Method in class org.processmining.plugins.tracealignment.msa.SequenceAlignment
 
getPreferredScrollableViewportSize() - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
getPrevCursorColumn() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getPrevCursorRow() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getPrimitiveTandemRepeats() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
Simple Cases
getPriority() - Method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
getProfileProfileGlobalAlign(String[], String[]) - Method in class org.processmining.plugins.tracealignment.msa.SequenceAlignment
 
getProfileProfileSemiGlobalAlign(String[], String[]) - Method in class org.processmining.plugins.tracealignment.msa.SequenceAlignment
 
getProfileSequenceGlobalAlign(String[], String) - Method in class org.processmining.plugins.tracealignment.msa.SequenceAlignment
 
getRefSequence() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getRepeatAlphabetFeatureTypeFeatureSetMap(int, List<String>, Map<String, String>, List<FeatureExtraction.FeatureType>) - Method in class org.processmining.plugins.tracealignment.util.FeatureExtraction
 
getRepeatAlphabetFeatureTypeFeatureSetMap(int, String, List<FeatureExtraction.FeatureType>) - Method in class org.processmining.plugins.tracealignment.util.FeatureExtraction
 
getRepeatFeatureTypeFeatureSetMap(int, List<String>, Map<String, String>, List<FeatureExtraction.FeatureType>) - Method in class org.processmining.plugins.tracealignment.util.FeatureExtraction
 
getRepeatFeatureTypeFeatureSetMap(int, String, List<FeatureExtraction.FeatureType>) - Method in class org.processmining.plugins.tracealignment.util.FeatureExtraction
 
getRowIndex(int) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
Determine the actual row given visible row index; When sequences are hidden, the cursor based row index (visible row) need to be adjusted for the actual sequence in order to perform any operations on the sequence
getRulerAnnotation(int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getScrollableBlockIncrement(Rectangle, int, int) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
getScrollableTracksViewportHeight() - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
getScrollableTracksViewportWidth() - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
getScrollableUnitIncrement(Rectangle, int, int) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
getSelectedCount() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getSelectedItems() - Method in class org.processmining.plugins.tracealignment.swingx.ItemSelectionDialog
 
getSelectedLineAnnotations() - Method in class org.processmining.plugins.tracealignment.ui.LineAnnotationSelectionDialog
 
getSelectedOption() - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
getSelectedOption() - Method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
getSeqColor() - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
getSeqSelect(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getSequence(int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getSequence(String) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getSequence() - Method in class org.processmining.plugins.tracealignment.ui.Sequence.LineAnnotation
 
getSequence() - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
getSequence() - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
getSequence() - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
getSequenceComponent(int) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
getSequenceComponent(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
getSequenceFeatureList() - Method in class org.processmining.plugins.tracealignment.util.FeatureMatrix
 
getSequenceFeatureSet() - Method in class org.processmining.plugins.tracealignment.util.FeatureExtraction
 
getSequenceIndex(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
getSequenceNameComponent(int) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
getSequenceWithGaps() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getSequenceWithoutGaps() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getSequenceWithoutGapsString() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getSize() - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
getSize() - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
getSize() - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
getSortValue() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getSpacingWidth() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getStartSymbolEquivalenceClassAlphabetMap(int, Set<String>) - Method in class org.processmining.plugins.tracealignment.util.EquivalenceClass
 
getStartSymbolEquivalenceClassMap(int, Set<String>) - Method in class org.processmining.plugins.tracealignment.util.EquivalenceClass
 
getSubstitutionScoreMap() - Method in class org.processmining.plugins.tracealignment.util.IndelSubstitutionMatrix
 
getSuperMaximalRepeats() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
Find SuperMaximal Repeats; A left diverse internal node v represents a super maximal repeat alpha if and only if all of v's children are leaves, and each has a distinct left character Assumes that the parent method calling this would have already invoked findLeftDiverseNodes();
getSymbol() - Method in class org.processmining.plugins.tracealignment.ui.Sequence.ColumnAnnotation
 
getSymbol(int) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
getTandemRepeats() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
getToolTipText(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
getToolTipText(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
getUniqueActivitiesInColumn(int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getUniqueActivityCounts(int, String[]) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getUniqueActivityCounts(int, String[], Sequence[]) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
getVerticalScrollBar() - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableViewport
 
getVgap() - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
getVisibleLineAnnotations(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
Get a list of the line annotations that are visible for the given sequence.
getXForColumn(int) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
getXYForRowColumn(int, int) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 

H

hasAnyActivities(String) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterDialog
 
hasAnyActivities(String) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortDialog
 
HasAnyOfTheseLetters - Static variable in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
HasAnyOfTheseLetters - Static variable in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
hasCached - Variable in class org.processmining.plugins.tracealignment.swingx.LazyBoundedRangeModel
 
hasCollapsedRows() - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
hashCode() - Method in class org.processmining.plugins.tracealignment.ui.Sequence.LineAnnotation
 
HasNoneOfTheseLetters - Static variable in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
HasNoneOfTheseLetters - Static variable in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
hours() - Method in class org.processmining.plugins.tracealignment.util.Watch
 

I

incrementalVerticalScroll(int) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
incrementLikeSubstitutions(int) - Method in class org.processmining.plugins.tracealignment.msa.SequenceAlignment
 
incrementNumColumnSorts() - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
IndelSubstitutionMatrix - Class in org.processmining.plugins.tracealignment.util
 
IndelSubstitutionMatrix(int, List<String>) - Constructor for class org.processmining.plugins.tracealignment.util.IndelSubstitutionMatrix
 
init(Component, String, String, Object[], int[]) - Method in class org.processmining.plugins.tracealignment.swingx.ItemSelectionDialog
 
init() - Method in class org.processmining.plugins.tracealignment.swingx.JListX
 
initialize(String, String[]) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
inputMethodTextChanged(InputMethodEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterDialog
 
inputMethodTextChanged(InputMethodEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortDialog
 
invalidateLayout(Container) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
inverseRGB(Color) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
isActivityBackgroundSquare() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
isAnnotationPopupEnabled() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
isColumnSelected() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
isColumnSelected(int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
isElementEnabled(int) - Method in class org.processmining.plugins.tracealignment.swingx.JListX
 
isEncodedActivityRendered() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
isGapRendered() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
isGroupEditing() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
isLazy - Variable in class org.processmining.plugins.tracealignment.swingx.LazyBoundedRangeModel
 
isMapping() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
isRulerAnnotationSelected() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
isSelected() - Method in class org.processmining.plugins.tracealignment.ui.Alignment.RulerAnnotation
 
isSeqAnnEditing() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
isSeqHighlight(Sequence, int) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
isSequenceHidden(int) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
isShown() - Method in class org.processmining.plugins.tracealignment.ui.Sequence.ColumnAnnotation
 
ItemSelectionDialog - Class in org.processmining.plugins.tracealignment.swingx
Dialog for selection of (generic) items.
ItemSelectionDialog(Frame, String, String, String, Object[], int[]) - Constructor for class org.processmining.plugins.tracealignment.swingx.ItemSelectionDialog
 
ItemSelectionDialog(Dialog, String, String, String, Object[], int[]) - Constructor for class org.processmining.plugins.tracealignment.swingx.ItemSelectionDialog
 

J

JListX - Class in org.processmining.plugins.tracealignment.swingx
Extended functionality JList.
JListX() - Constructor for class org.processmining.plugins.tracealignment.swingx.JListX
Constructs a JList with an empty model.
JListX(ListModel) - Constructor for class org.processmining.plugins.tracealignment.swingx.JListX
Constructs a JList that displays the elements in the specified, non-null model.
JListX(Object[]) - Constructor for class org.processmining.plugins.tracealignment.swingx.JListX
Constructs a JList that displays the elements in the specified array.
JListX(Vector) - Constructor for class org.processmining.plugins.tracealignment.swingx.JListX
Constructs a JList that displays the elements in the specified Vector.

K

keyPressed(KeyEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
keyReleased(KeyEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
keyTyped(KeyEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
kill() - Method in class org.processmining.plugins.tracealignment.clustering.AgglomerativeHierarchicalClustering.Cluster
 

L

layoutContainer(Container) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
LazyBoundedRangeModel - Class in org.processmining.plugins.tracealignment.swingx
Model for ScrollBar's which do not fire events while adjusting.
LazyBoundedRangeModel(boolean) - Constructor for class org.processmining.plugins.tracealignment.swingx.LazyBoundedRangeModel
 
LineAnnotation(String, String, Sequence) - Constructor for class org.processmining.plugins.tracealignment.ui.Sequence.LineAnnotation
 
LineAnnotationListCellRenderer - Class in org.processmining.plugins.tracealignment.ui
 
LineAnnotationListCellRenderer() - Constructor for class org.processmining.plugins.tracealignment.ui.LineAnnotationListCellRenderer
 
LineAnnotationSelectionDialog - Class in org.processmining.plugins.tracealignment.ui
 
LineAnnotationSelectionDialog(Dialog, String, String, String, Sequence.LineAnnotation[], int[]) - Constructor for class org.processmining.plugins.tracealignment.ui.LineAnnotationSelectionDialog
 
LineAnnotationSelectionDialog(Frame, String, String, String, Sequence.LineAnnotation[], int[]) - Constructor for class org.processmining.plugins.tracealignment.ui.LineAnnotationSelectionDialog
 
live() - Method in class org.processmining.plugins.tracealignment.clustering.AgglomerativeHierarchicalClustering.Cluster
 
log2(double) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusSequence
 
LZDecomposition() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 

M

main(String[]) - Static method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
makeRoom(int) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
maximumLayoutSize(Container) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
maxLength() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
minimumLayoutSize(Container) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
mins() - Method in class org.processmining.plugins.tracealignment.util.Watch
 
mouseClicked(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
mouseClicked(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
mouseClicked(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
mouseClicked(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
mouseClicked(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
mouseClicked(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
mouseDragged(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
mouseEntered(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
mouseEntered(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
mouseEntered(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
mouseEntered(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
mouseEntered(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
mouseEntered(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
mouseExited(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
mouseExited(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
mouseExited(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
mouseExited(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
mouseExited(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
mouseExited(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
mouseMoved(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
mousePressed(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
mousePressed(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
mousePressed(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
mousePressed(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
mousePressed(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
mousePressed(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
mouseReleased(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
mouseReleased(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
mouseReleased(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
mouseReleased(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
mouseReleased(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
mouseReleased(MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
mouseWheelMoved(MouseWheelEvent) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
MSA - Class in org.processmining.plugins.tracealignment.msa
 
MSA(int, List<String>, int[][], Map<String, Integer>, Map<String, Integer>, int, float, int, float) - Constructor for class org.processmining.plugins.tracealignment.msa.MSA
 
msecs() - Method in class org.processmining.plugins.tracealignment.util.Watch
 

N

noMatches(String) - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
noOptions - Static variable in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
noOptions - Static variable in class org.processmining.plugins.tracealignment.ui.ColumnSort
 

O

optionNames - Static variable in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
optionNames - Static variable in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
optionTest(String) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
optionTest(String) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
optionTestGetPriorityBit(String) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
org.processmining.plugins.tracealignment - package org.processmining.plugins.tracealignment
 
org.processmining.plugins.tracealignment.clustering - package org.processmining.plugins.tracealignment.clustering
 
org.processmining.plugins.tracealignment.msa - package org.processmining.plugins.tracealignment.msa
 
org.processmining.plugins.tracealignment.swingx - package org.processmining.plugins.tracealignment.swingx
 
org.processmining.plugins.tracealignment.ui - package org.processmining.plugins.tracealignment.ui
 
org.processmining.plugins.tracealignment.util - package org.processmining.plugins.tracealignment.util
 
owner - Variable in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
owner - Variable in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
owner - Variable in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
owner - Variable in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
owner - Variable in class org.processmining.plugins.tracealignment.ui.EditSeqAnnBaseDialog
 

P

paint(Graphics) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
paint(Graphics) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
paint(Graphics) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
paint(Graphics) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
paint(Graphics) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
paintComponent(Graphics) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
paintComponent(Graphics) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
paintComponent(Graphics) - Method in class org.processmining.plugins.tracealignment.ui.RulerComponent
 
paintComponent(Graphics) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
pause() - Method in class org.processmining.plugins.tracealignment.util.Watch
 
pointInExpandBox(Point) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
popupMenuCanceled(PopupMenuEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
popupMenuCanceled(PopupMenuEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
popupMenuWillBecomeInvisible(PopupMenuEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
popupMenuWillBecomeInvisible(PopupMenuEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
popupMenuWillBecomeVisible(PopupMenuEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilterComponent
 
popupMenuWillBecomeVisible(PopupMenuEvent) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSortComponent
 
preferredLayoutSize(Container) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
printArray(T[]) - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
printTree() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 

R

readEquivalenceClassMapFromFile(String, String, String) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
readFile(String, String) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
readFileAsSet(String, String) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
readFloatMatrixFromFile(String, String) - Method in class org.processmining.plugins.tracealignment.util.ArrayMatrixFileIO
 
readFloatMatrixFromFile(String, String) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
readIntMatrixFromFile(String, String) - Method in class org.processmining.plugins.tracealignment.util.ArrayMatrixFileIO
 
readIntMatrixFromFile(String, String) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
readMapFromFile(String, String, String) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
readMapSetIntegerFromFile(String, String, String) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
readMapSetStringFromFile(String, String, String) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
readMapStringIntegerFromFile(String, String, String) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
readSetFromFile(String, String) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
rebuildGUI() - Method in class org.processmining.plugins.tracealignment.ui.EditSeqAnnBaseDialog
 
rebuildGUI() - Method in class org.processmining.plugins.tracealignment.ui.EditSeqAnnDialog
 
rebuildGUI() - Method in class org.processmining.plugins.tracealignment.ui.EditSequenceNameDialog
 
recalc() - Method in class org.processmining.plugins.tracealignment.ui.ConsensusSequence
 
removeAllGapColumns() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
removeColumnFilter(int) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
removeColumnFilter(int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
removeColumnFromEnd() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
removeColumnRange(int, int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
removeColumnSort(int) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
removeColumnSort(int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
removed(int) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
removed() - Method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
removeLayoutComponent(Component) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
removeListener(ColorSchemeListener) - Method in interface org.processmining.plugins.tracealignment.ui.ColorScheme
 
removeListener(DisplayPropertiesListener) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
Remove a listener
removeListener(SequenceListener) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
removeRulerAnnotationFromEnd() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
removeRulerAnnotationRange(int, int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
revalidateAndRepaintAll() - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
RulerAnnotation(String, Color, boolean) - Constructor for class org.processmining.plugins.tracealignment.ui.Alignment.RulerAnnotation
 
RulerAnnotationComponent - Class in org.processmining.plugins.tracealignment.ui
 
RulerAnnotationComponent(Alignment, DisplayProperties, AlignmentFrame) - Constructor for class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
rulerAnnotationsSize() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
RulerComponent - Class in org.processmining.plugins.tracealignment.ui
 
RulerComponent(Alignment, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignment.ui.RulerComponent
 

S

ScrollableGridLayout - Class in org.processmining.plugins.tracealignment.swingx
LayoutManager which is like a grid, but fixes the sizes of certain rows and columns to their preferred size.
ScrollableGridLayout(Container, int, int, int, int) - Constructor for class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
ScrollableViewport - Class in org.processmining.plugins.tracealignment.swingx
JViewport that can sync (horizontally or vertically) to scrollbars or other viewports.
ScrollableViewport() - Constructor for class org.processmining.plugins.tracealignment.swingx.ScrollableViewport
 
scrollTo(int, int, float, float) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
scrollTo(int, int, float, float, boolean) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
secs() - Method in class org.processmining.plugins.tracealignment.util.Watch
 
sequence - Variable in class org.processmining.plugins.tracealignment.ui.EditSeqAnnBaseDialog
 
Sequence - Class in org.processmining.plugins.tracealignment.ui
 
Sequence() - Constructor for class org.processmining.plugins.tracealignment.ui.Sequence
 
Sequence(int, String, List<String>, String[]) - Constructor for class org.processmining.plugins.tracealignment.ui.Sequence
 
Sequence.ColumnAnnotation - Class in org.processmining.plugins.tracealignment.ui
 
Sequence.LineAnnotation - Class in org.processmining.plugins.tracealignment.ui
 
sequenceActivityChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
sequenceActivityChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
sequenceActivityChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
sequenceActivityChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
sequenceActivityChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
sequenceActivityChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
sequenceActivityChanged(Sequence) - Method in interface org.processmining.plugins.tracealignment.ui.SequenceListener
 
sequenceActivityChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
SequenceAlignment - Class in org.processmining.plugins.tracealignment.msa
 
SequenceAlignment(int, Map<String, Integer>, Map<String, Integer>, float) - Constructor for class org.processmining.plugins.tracealignment.msa.SequenceAlignment
 
SequenceAlignment.TraceBack - Enum in org.processmining.plugins.tracealignment.msa
 
SequenceAnnComponent - Class in org.processmining.plugins.tracealignment.ui
 
SequenceAnnComponent(AlignmentFrame, Sequence, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
sequenceAnnotationChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
sequenceAnnotationChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
sequenceAnnotationChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
sequenceAnnotationChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
sequenceAnnotationChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
sequenceAnnotationChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
sequenceAnnotationChanged(Sequence) - Method in interface org.processmining.plugins.tracealignment.ui.SequenceListener
 
sequenceAnnotationChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
sequenceColorChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
sequenceColorChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
sequenceColorChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
sequenceColorChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
sequenceColorChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
sequenceColorChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
sequenceColorChanged(Sequence) - Method in interface org.processmining.plugins.tracealignment.ui.SequenceListener
 
sequenceColorChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
sequenceColumnAnnotationsChanged(Sequence, int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
sequenceColumnAnnotationsChanged(Sequence, int) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
sequenceColumnAnnotationsChanged(Sequence, int) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
sequenceColumnAnnotationsChanged(Sequence, int) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
sequenceColumnAnnotationsChanged(Sequence, int) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
sequenceColumnAnnotationsChanged(Sequence, int) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
sequenceColumnAnnotationsChanged(Sequence, int) - Method in interface org.processmining.plugins.tracealignment.ui.SequenceListener
 
sequenceColumnAnnotationsChanged(Sequence, int) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
SequenceComponent - Class in org.processmining.plugins.tracealignment.ui
 
SequenceComponent(AlignmentFrame, Sequence, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
sequenceLineAnnotationsChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
sequenceLineAnnotationsChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
sequenceLineAnnotationsChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
sequenceLineAnnotationsChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
sequenceLineAnnotationsChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
sequenceLineAnnotationsChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
sequenceLineAnnotationsChanged(Sequence) - Method in interface org.processmining.plugins.tracealignment.ui.SequenceListener
 
sequenceLineAnnotationsChanged(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
SequenceListener - Interface in org.processmining.plugins.tracealignment.ui
 
sequenceNameChanged(Sequence, String) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
sequenceNameChanged(Sequence, String) - Method in class org.processmining.plugins.tracealignment.ui.ColumnAnnotationComponent
 
sequenceNameChanged(Sequence, String) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
sequenceNameChanged(Sequence, String) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
sequenceNameChanged(Sequence, String) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
sequenceNameChanged(Sequence, String) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
sequenceNameChanged(Sequence, String) - Method in interface org.processmining.plugins.tracealignment.ui.SequenceListener
 
sequenceNameChanged(Sequence, String) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
SequenceNameComponent - Class in org.processmining.plugins.tracealignment.ui
 
SequenceNameComponent(AlignmentFrame, Sequence, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
sequenceTextField - Variable in class org.processmining.plugins.tracealignment.ui.EditSeqAnnBaseDialog
 
setActivity(String[]) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
setActivityBackgroundSquare(boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
setAligmentRecentlyEdited(boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
setAllSequenceCollapsed(boolean, boolean) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
setAllSequenceCollapsed(boolean, boolean) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
setAllSequenceCollapsed(boolean, boolean) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
setAllSequencesHidden(boolean) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
setAnnotation(String) - Method in class org.processmining.plugins.tracealignment.ui.Sequence.LineAnnotation
 
setAnnView(Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
setChanged(boolean) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
setCollapsed(boolean) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
setCollapsed(boolean) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
setCollapsed(boolean) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
setColor(Color) - Method in class org.processmining.plugins.tracealignment.ui.Alignment.RulerAnnotation
 
setColor(Color) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
setColumnFilterCurrentColumn(int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
setColumnFiltering(boolean) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
setColumnFiltering(boolean, boolean) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
setColumnFiltering(boolean) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
setColumnFixed(int, boolean) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
setColumnSelected(int, boolean, DisplayProperties) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
setColumnSort(int, ColumnSort) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
setColumnSortCurrentColumn(int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
setColumnSorting(boolean) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
setColumnSorting(boolean, boolean) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
setColumnSorting(boolean) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
setConsensus(ConsensusSequence) - Method in class org.processmining.plugins.tracealignment.ui.ConsensusComponent
 
setCursorHidden(boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
setElementEnabled(int, boolean) - Method in class org.processmining.plugins.tracealignment.swingx.JListX
 
setFilterActivities(int, String) - Method in class org.processmining.plugins.tracealignment.ui.ColumnFilter
 
setFilterActivities(int, String) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
setGapPenalty(int) - Method in class org.processmining.plugins.tracealignment.msa.SequenceAlignment
 
setHiddenLineAnnotation(Sequence, Sequence.LineAnnotation) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
setHorizontalScrollbar(JScrollBar) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableViewport
 
setHorizontalViewport(ScrollableViewport) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableViewport
 
setIndelRightGivenLeftScoreScaleFactor(Map<String, Integer>, float) - Method in class org.processmining.plugins.tracealignment.msa.SequenceAlignment
 
setLastActivityIndexSelected(int, int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
setLastColumnIdxSelected(int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
setLastRulerAnnIdxSelected(int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
setLazy(boolean) - Method in class org.processmining.plugins.tracealignment.swingx.LazyBoundedRangeModel
 
setLengthRatioThreshold(float) - Method in class org.processmining.plugins.tracealignment.msa.SequenceAlignment
 
setLetter(String) - Method in class org.processmining.plugins.tracealignment.ui.Alignment.RulerAnnotation
 
setLineAnnotation(int, String, String) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
setName(String) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
setPosition(Component, int, int) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
setPriority(int) - Method in class org.processmining.plugins.tracealignment.ui.ColumnSort
 
setRangeProperties(int, int, int, int, boolean) - Method in class org.processmining.plugins.tracealignment.swingx.LazyBoundedRangeModel
 
setRefSequence(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
setRefSequence(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
setRenderEncodedActivity(boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
setRenderGaps(boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
setRowFixed(int, boolean) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableGridLayout
 
setRulerEditing(boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
setSelected(boolean) - Method in class org.processmining.plugins.tracealignment.ui.Alignment.RulerAnnotation
 
setSeqAnnEditing(boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
setSeqHidden(Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
setSeqHighlight(Sequence, int, boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
setSeqHighlight(Sequence, int, boolean, boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
setSeqSelect(Sequence, boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
setSequence(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.Sequence.LineAnnotation
 
setSequence(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceAnnComponent
 
setSequence(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceComponent
 
setSequence(Sequence) - Method in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
setSequenceCollapsed(int, boolean, boolean) - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
setSequenceCollapsed(int, boolean, boolean) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentNamePanel
 
setSequenceCollapsed(int, boolean, boolean) - Method in class org.processmining.plugins.tracealignment.ui.AlignmentPanel
 
setSortValue(int) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
setVerticalScrollbar(JScrollBar) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableViewport
 
setVerticalViewport(ScrollableViewport) - Method in class org.processmining.plugins.tracealignment.swingx.ScrollableViewport
 
setVisibleLineAnnotation(Sequence, Sequence.LineAnnotation) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
shiftActivity(int, int, boolean) - Method in class org.processmining.plugins.tracealignment.ui.Sequence
 
showActivityAnnPanel() - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
showDialog(AlignmentFrame, DisplayProperties, int, ColumnFilter, Point) - Static method in class org.processmining.plugins.tracealignment.ui.ColumnFilterDialog
 
showDialog(AlignmentFrame, DisplayProperties, int, ColumnSort, Point) - Static method in class org.processmining.plugins.tracealignment.ui.ColumnSortDialog
 
showErrorDialog(Component, String, Throwable) - Static method in class org.processmining.plugins.tracealignment.swingx.ErrorDialog
 
showErrorDialog(Component, String) - Static method in class org.processmining.plugins.tracealignment.swingx.ErrorDialog
 
shown - Variable in class org.processmining.plugins.tracealignment.ui.Sequence.ColumnAnnotation
 
showPopup(JPopupMenu, Component, int, int) - Static method in class org.processmining.plugins.tracealignment.swingx.Utils
 
sign(int) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
sign(int) - Method in class org.processmining.plugins.tracealignment.ui.RulerAnnotationComponent
 
singleStringTest() - Method in class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
sort() - Method in class org.processmining.plugins.tracealignment.ui.AlignmentSorter
 
sortBasedOnColumnSorts() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
sortBasedOnSortValue() - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 
Spacing - Static variable in class org.processmining.plugins.tracealignment.ui.SequenceNameComponent
 
start() - Method in class org.processmining.plugins.tracealignment.util.Watch
 
swapSequence(int, int) - Method in class org.processmining.plugins.tracealignment.ui.Alignment
 

T

toString() - Method in class org.processmining.plugins.tracealignment.ui.Sequence
Returns sequence (with gaps) as a string
toString() - Method in exception org.processmining.plugins.tracealignment.util.EncodingNotFoundException
 
traceAlignment(UIPluginContext, XLog) - Static method in class org.processmining.plugins.tracealignment.TraceAlignmentPlugin
 
TraceAlignmentConnection - Class in org.processmining.plugins.tracealignment
 
TraceAlignmentConnection(AlignmentFrame) - Constructor for class org.processmining.plugins.tracealignment.TraceAlignmentConnection
 
TraceAlignmentPlugin - Class in org.processmining.plugins.tracealignment
 
TraceAlignmentPlugin() - Constructor for class org.processmining.plugins.tracealignment.TraceAlignmentPlugin
 
TraceSimilarity - Class in org.processmining.plugins.tracealignment.util
 
TraceSimilarity(int) - Constructor for class org.processmining.plugins.tracealignment.util.TraceSimilarity
 
trimEnd(StringBuffer) - Method in class org.processmining.plugins.tracealignment.ui.EditLineAnnDialog
 

U

UkkonenSuffixTree - Class in org.processmining.plugins.tracealignment.util
 
UkkonenSuffixTree(int, String) - Constructor for class org.processmining.plugins.tracealignment.util.UkkonenSuffixTree
 
updateCollapsed() - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
updateCursor(int, int) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
updateCursor(int, int, MouseEvent) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
updateCursor(int, int, boolean, boolean) - Method in class org.processmining.plugins.tracealignment.ui.DisplayProperties
 
updateSort() - Method in class org.processmining.plugins.tracealignment.AlignmentFrame
 
Utils - Class in org.processmining.plugins.tracealignment.swingx
Some miscellaneous utilities.
Utils() - Constructor for class org.processmining.plugins.tracealignment.swingx.Utils
 

V

valueChanged(ListSelectionEvent) - Method in class org.processmining.plugins.tracealignment.swingx.JListX
 
valueOf(String) - Static method in enum org.processmining.plugins.tracealignment.clustering.AgglomerativeHierarchicalClustering.ClusterCriteria
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.processmining.plugins.tracealignment.clustering.AgglomerativeHierarchicalClustering.ClusterType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.processmining.plugins.tracealignment.msa.SequenceAlignment.TraceBack
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.processmining.plugins.tracealignment.util.EuclideanDistance.Normalization
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.processmining.plugins.tracealignment.util.FeatureExtraction.FeatureType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.processmining.plugins.tracealignment.util.FeatureSelection.FilterType
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.processmining.plugins.tracealignment.clustering.AgglomerativeHierarchicalClustering.ClusterCriteria
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.processmining.plugins.tracealignment.clustering.AgglomerativeHierarchicalClustering.ClusterType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.processmining.plugins.tracealignment.msa.SequenceAlignment.TraceBack
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.processmining.plugins.tracealignment.util.EuclideanDistance.Normalization
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.processmining.plugins.tracealignment.util.FeatureExtraction.FeatureType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.processmining.plugins.tracealignment.util.FeatureSelection.FilterType
Returns an array containing the constants of this enum type, in the order they are declared.
visualize(PluginContext, AlignmentFrame) - Method in class org.processmining.plugins.tracealignment.AlignmentFrameVisualization
 

W

Watch - Class in org.processmining.plugins.tracealignment.util
 
Watch() - Constructor for class org.processmining.plugins.tracealignment.util.Watch
 
write(int) - Method in class org.processmining.plugins.tracealignment.swingx.DocumentOutputStream
Writes the specified byte to this output stream.
write(byte[], int, int) - Method in class org.processmining.plugins.tracealignment.swingx.DocumentOutputStream
Writes len bytes from the specified byte array starting at offset off to this output stream.
write(char[], int, int) - Method in class org.processmining.plugins.tracealignment.swingx.DocumentWriter
Write a portion of an array of characters.
write(String, int, int) - Method in class org.processmining.plugins.tracealignment.swingx.DocumentWriter
Write a portion of a string.
write(String) - Method in class org.processmining.plugins.tracealignment.swingx.DocumentWriter
Write a string.
writeToFile(String, String, float[][]) - Method in class org.processmining.plugins.tracealignment.util.ArrayMatrixFileIO
 
writeToFile(String, String, int[][]) - Method in class org.processmining.plugins.tracealignment.util.ArrayMatrixFileIO
 
writeToFile(String, String, Map<T, E>, String) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
writeToFile(String, String, Collection<T>) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
writeToFile(String, String, T[][]) - Method in class org.processmining.plugins.tracealignment.util.FileIO
 
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