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A

actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColorEditor
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColorSequenceDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSeqAnnBaseDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSequenceDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSequenceNameDialog
 
actionPerformed(ActionEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
activityBackgroundChanged(DisplayProperties) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.DisplayPropertiesListener
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
activityBackgroundChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
ActivityCharEncodingTable - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
ActivityCharEncodingTable(Map<String, String>, String) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.ActivityCharEncodingTable
 
activityColorChanged(String, Color) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.ActivityColorListener
 
activityColorChanged(String, Color) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ActivityCharEncodingTable
 
activityColorChanged(String, Color) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
ActivityColorListener - Interface in org.processmining.plugins.tracealignmentwithguidetree.listeners
 
activityColorMappingChanged(Color) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.ActivityColorListener
 
activityColorMappingChanged(Color) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ActivityCharEncodingTable
 
activityColorMappingChanged(Color) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
ActivityNotFoundException - Exception in org.processmining.plugins.tracealignmentwithguidetree.exceptions
 
ActivityNotFoundException(String) - Constructor for exception org.processmining.plugins.tracealignmentwithguidetree.exceptions.ActivityNotFoundException
 
addClipboardBindings(JTextComponent) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.Utils
 
addColumn() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
addColumnFilter(ColumnFilter, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
addColumnFilter(ColumnFilter, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
addColumnSort(ColumnSort, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
addColumnSort(ColumnSort, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
addLayoutComponent(Component, Object) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
addLayoutComponent(String, Component) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
addListener(AlignmentListener) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
addListener(DisplayPropertiesListener) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
addListener(SequenceListener) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
addRulerAnnotation() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
addToGridBag(Container, GridBagLayout, Component, int, int, int, int, int, int, int, int) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.Utils
 
addToGridBag(Container, GridBagLayout, Component, int, int, int, int, int, int, int, int, Insets) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.Utils
 
Alignment - Class in org.processmining.plugins.tracealignmentwithguidetree.datatypes
 
Alignment(int, AlignmentFrame, Sequence[]) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
alignment - Variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
Alignment.RulerAnnotation - Class in org.processmining.plugins.tracealignmentwithguidetree.datatypes
 
AlignmentAlgorithm - Enum in org.processmining.plugins.tracealignmentwithguidetree.enumtypes
 
AlignmentAlgorithmConfigurationStep - Class in org.processmining.plugins.tracealignmentwithguidetree.ui
 
AlignmentAlgorithmConfigurationStep() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.ui.AlignmentAlgorithmConfigurationStep
 
AlignmentFrame - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
AlignmentFrame(AlignmentTree, Map<String, Color>) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
AlignmentFrame(AlignmentTree) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
AlignmentListener - Interface in org.processmining.plugins.tracealignmentwithguidetree.listeners
 
alignmentNameChanged(Alignment) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
alignmentNameChanged(Alignment) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.AlignmentListener
 
alignmentNameChanged(Alignment) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
alignmentNameChanged(Alignment) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
alignmentNameChanged(Alignment) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
alignmentNameChanged(Alignment) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
alignmentNameChanged(Alignment) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
AlignmentNamePanel - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
AlignmentNamePanel(AlignmentFrame, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
AlignmentPanel - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
AlignmentPanel(AlignmentFrame, Alignment, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.AlignmentListener
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
alignmentSeqActivityChanged(Alignment, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.AlignmentListener
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
alignmentSeqDeleted(Alignment, int, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
alignmentSeqSwapped(Alignment, int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
alignmentSeqSwapped(Alignment, int, int) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.AlignmentListener
 
alignmentSeqSwapped(Alignment, int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
alignmentSeqSwapped(Alignment, int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
alignmentSeqSwapped(Alignment, int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
alignmentSeqSwapped(Alignment, int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
alignmentSeqSwapped(Alignment, int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
AlignmentSorter - Class in org.processmining.plugins.tracealignmentwithguidetree.datatypes
 
AlignmentSorter(Alignment, Comparator<Sequence>) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.datatypes.AlignmentSorter
 
AlignmentTree - Class in org.processmining.plugins.tracealignmentwithguidetree.tree
 
AlignmentTree() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
AlignmentTreeNode - Class in org.processmining.plugins.tracealignmentwithguidetree.tree
 
AlignmentTreeNode(int, int, int, String) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
AlignmentTreeVisualization - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
AlignmentTreeVisualization() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentTreeVisualization
 
AlignmentType - Enum in org.processmining.plugins.tracealignmentwithguidetree.enumtypes
 
ArrayMatrixFileIO - Class in org.processmining.plugins.tracealignmentwithguidetree.util
 
ArrayMatrixFileIO() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.util.ArrayMatrixFileIO
 

C

cachedValue - Variable in class org.processmining.plugins.tracealignmentwithguidetree.swingx.LazyBoundedRangeModel
 
calcSortValueBasedOnColumnSorts(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
caretUpdate(CaretEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSeqAnnBaseDialog
 
clearHighlights() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
clearLastActivityIndexSelected() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
clearLastColumnIndexSelected() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
clearLastRulerAnnIndexSelected() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
clearSelections() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
ColorEditor - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
ColorEditor() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColorEditor
 
ColorRenderer - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
ColorRenderer(boolean) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColorRenderer
 
ColorSequenceDialog - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
ColorSequenceDialog(AlignmentFrame, Sequence) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColorSequenceDialog
 
ColumnFilter - Class in org.processmining.plugins.tracealignmentwithguidetree.datatypes
 
ColumnFilter(int, int, String) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
ColumnFilter(int, String) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
ColumnFilterComponent - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
ColumnFilterComponent(AlignmentFrame, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
ColumnFilterDialog - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
ColumnFilterDialog(AlignmentFrame, DisplayProperties, int, ColumnFilter, Point) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterDialog
 
columnFiltering - Variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
ColumnSort - Class in org.processmining.plugins.tracealignmentwithguidetree.datatypes
 
ColumnSort(int, int, String, int) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
ColumnSort(int, String, int) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
ColumnSortComponent - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
ColumnSortComponent(AlignmentFrame, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
ColumnSortDialog - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
ColumnSortDialog(AlignmentFrame, DisplayProperties, int, ColumnSort, Point) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortDialog
 
columnSorting - Variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
compare(Sequence, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
ConsensusComponent - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
ConsensusComponent(ConsensusSequence, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
ConsensusSequence - Class in org.processmining.plugins.tracealignmentwithguidetree.datatypes
 
ConsensusSequence(AlignmentFrame, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ConsensusSequence
 
ConsensusSequence(AlignmentFrame, DisplayProperties, Sequence[]) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ConsensusSequence
 
copy(String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
createDir(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.ArrayMatrixFileIO
 
createDir(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 

D

decrementIndelScore(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.IndelSubstitutionScore
 
deleteActivity(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
deriveScores(int, Map<String, String>, List<String>) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.IndelSubstitutionScore
 
deselectAllColumns(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
deselectAllColumns(DisplayProperties, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
deselectAllRulerSelections() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.DisplayPropertiesListener
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
displayAnnViewChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
displayFontChanged(DisplayProperties) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.DisplayPropertiesListener
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
displayFontChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
displayGroupEditingChanged(DisplayProperties) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.DisplayPropertiesListener
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
displayGroupEditingChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.DisplayPropertiesListener
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.DisplayPropertiesListener
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
displayHighlightsChanged(DisplayProperties, Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
displayHighlightsChanged(DisplayProperties, Sequence[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
displayOverwriteChanged(DisplayProperties) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.DisplayPropertiesListener
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
displayOverwriteChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
DisplayProperties - Class in org.processmining.plugins.tracealignmentwithguidetree.datatypes
 
DisplayProperties(Alignment, Font, FontMetrics, boolean, boolean) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
displayProperties - Variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
displayProperties - Variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
displayProperties - Variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
displayProperties - Variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
displayProperties - Variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSeqAnnBaseDialog
 
DisplayPropertiesListener - Interface in org.processmining.plugins.tracealignmentwithguidetree.listeners
 
displayRenderGapsChanged(DisplayProperties) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.DisplayPropertiesListener
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
displayRenderGapsChanged(DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.DisplayPropertiesListener
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
displaySeqSelectChanged(DisplayProperties, Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
doAlignment0() - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.GuideTreeAlignment
 
doAlignment1() - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.GuideTreeAlignment
 

E

EDIT - Static variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColorEditor
 
edit(Point) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
EditActivityAnnotationDialog - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
EditActivityAnnotationDialog(AlignmentFrame, DisplayProperties, Sequence, int) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditActivityAnnotationDialog
 
EditSeqAnnBaseDialog - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
EditSeqAnnBaseDialog(AlignmentFrame, String, DisplayProperties, Sequence) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSeqAnnBaseDialog
 
EditSequenceDialog - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
EditSequenceDialog(AlignmentFrame, Sequence) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSequenceDialog
 
EditSequenceDialog(AlignmentFrame, Sequence, Alignment, int) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSequenceDialog
Allows user to create and edit a NEW sequence
EditSequenceNameDialog - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
EditSequenceNameDialog(AlignmentFrame, DisplayProperties, Sequence) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSequenceNameDialog
 
enforceDisabledElements() - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.JListX
 
EqualsThisLetter - Static variable in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
EqualsThisLetter - Static variable in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 

F

FileIO - Class in org.processmining.plugins.tracealignmentwithguidetree.util
 
FileIO() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
findColumn(int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
findColumn(int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
findColumn(int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.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.tracealignmentwithguidetree.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;
findMouseColumn(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
findOriginalConcurrentActivitySet(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
findRefinedConcurrentActivitySet(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
fireActivityBackGroundChanged() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
fireActivityBackgroundChanged() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
fireDisplayHighlightsChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
fireDisplayHighlightsChanged(Sequence[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
fireSeqSelect(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
FixedWidthTextField - Class in org.processmining.plugins.tracealignmentwithguidetree.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.tracealignmentwithguidetree.swingx.FixedWidthTextField
 

G

generateLikePreferenceScores(int, Map<String, String>, List<String>) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.IndelSubstitutionScore
 
generateUnitScores(Map<String, String>) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.IndelSubstitutionScore
 
getActivity() - Method in exception org.processmining.plugins.tracealignmentwithguidetree.exceptions.ActivityNotFoundException
 
getActivityCharMap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
getActivityCharMapTable() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ActivityCharEncodingTable
 
getActivityHeight() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getActivityIndex(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
getActivityIndexArray() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
getActivityPosition(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
Get the coordinate location of an activity given the activity column (position) number
getActivityWidth() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getAlignedTraces() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getAlignment() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getAlignmentAlgorithm() - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
getAlignments(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.MSA
 
getAlignmentTree() - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.GuideTreeAlignment
 
getAllSelectedSequences() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getAllSelectedSequences(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getAllSequences() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getArrayFromString(String) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
getArrayFromString(String) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
getBaseFileName(File) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.Utils
 
getCellEditorValue() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColorEditor
 
getCharActivityMap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
getCharActivityMap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
getCharWidth() - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.FixedWidthTextField
 
getClusterItems(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.MSA
 
getClusterNodes(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
getCmdOptionChar() - Static method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.Utils
 
getColor() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment.RulerAnnotation
 
getColumnFilter(Integer) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getColumnFilterColumnIterator() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getColumnFilterCurrentColumn() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getColumnFiltering() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getColumnIndices(String[], Set<String>) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.RefineAlignment
 
getColumnLocationRelativeToOwner(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
getColumnLocationRelativeToOwner(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
getColumnSort(Integer) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getColumnSortColumnIterator() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getColumnSortCurrentColumn() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getColumnsSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getComplexAlphabetTandemRepeatMap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 
getComplexTandemRepeats() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 
getConcurrentActivities(String[], boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.RefineAlignment
 
getConcurrentActivityAcrossAllTracesSet() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
getConcurrentActivitySet() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
getConsensusColorAt(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
getConservationScoreAtColumnIndex(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
getCurrentColumnFilter() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getCurrentColumnSort() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getCursorColumn() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getCursorRow() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getDisplayCustom() - Static method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
getDisplayCustom() - Static method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
getDisplayCustomOpNames() - Static method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
getDisplayCustomOpNames() - Static method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
getDisplayNone() - Static method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
getDisplayNone() - Static method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
getDisplayOpNames() - Static method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
getDisplayOpNames() - Static method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
getDisplayProperties() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
getDisplayText() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
getDisplayText() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
getDuplicateTraceNameList() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
getEncodedActivity(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
getEncodedActivityColorMap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getEncodedActivityColorMap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getEncodedActivityColorMap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ActivityCharEncodingTable
 
getEncodedActivityColorMap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
getEncodedTrace() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
getEncodedTraceIdenticalIndicesMap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
getEncodingLength() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getEncodingLength() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getEncodingLength() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
getEncodingLength() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
getFilterActivitiesString() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
getFilterActivitiesString() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
getFilteredMaximalRepeats() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 
getFilteredNearSuperMaximalRepeats() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 
getFilteredSuperMaximalRepeats() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 
getFirstColumnSelected() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getFont() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getFontMetrics() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getFontXOffset() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getFontYOffset() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getHgap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
getHighlights(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getIncrementLikeSubstitutionScoreValue() - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
getIndelLeftGivenRightScoreMap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.IndelSubstitutionScore
 
getIndelRightGivenLeftScoreMap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.IndelSubstitutionScore
 
getIndelScoreFileName() - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
getIndelScoreScaleValue() - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
getIndex(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getInformationInColumnGapsExcluded() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ConsensusSequence
 
getInformationInColumnGapsIncluded() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ConsensusSequence
 
getInput() - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
getInverseRowIndex(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
getIsHidden() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
getItemElements(int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.MSA
 
getLastActivityIndexSelected() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getLastActivityRowSelected() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getLastColumnIdxSelected() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getLastColumnSelected() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getLastRulerAnnIndexSelected() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getLayoutAlignmentX(Container) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
getLayoutAlignmentY(Container) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
getLeaves(SuffixNode) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 
getLeft() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
getLeftDiverseNodes(SuffixNode) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 
getLengthWithGaps() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
getLengthWithoutGaps() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
getLetter() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment.RulerAnnotation
 
getLevel() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
getLog() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
getMatches(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 
getMaximalRepeats() - Method in class org.processmining.plugins.tracealignmentwithguidetree.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();
getMaximumSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
getMaximumSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
getMaximumSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
getMaximumSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
getMaxLength() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getMinimumSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
getMinimumSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
getMinimumSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
getMinimumSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
getName() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getName() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
getNearSuperMaximalRepeats() - Method in class org.processmining.plugins.tracealignmentwithguidetree.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.tracealignmentwithguidetree.visualization.AlignmentFrame
 
getNoChildren() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
getNoColumnSorts() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
getNoDuplicates() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
getNoSelectedSequences() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getNoSequences() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getNoUniqueTraces() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
getNumberOfColumnsSelected() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getNumVisibleRows() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
getOriginalAlignment() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
getOSDirectoryName() - Static method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.Utils
 
getPairWiseGlobalAlign(String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SeqAlignment
 
getPairWiseGlobalAlignment(String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignment
 
getPairWiseGlobalAlignment(String[], String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignment
 
getPairWiseGlobalAlignment(String[], String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignment
 
getPairWiseGlobalAlignment(String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignmentLeftIndel
 
getPairWiseGlobalAlignment(String[], String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignmentLeftIndel
 
getPairWiseGlobalAlignment(String[], String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignmentLeftIndel
 
getPairWiseSemiGlobalAlign(String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SeqAlignment
 
getPairWiseSemiGlobalAlignment(String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignment
 
getPairWiseSemiGlobalAlignment(String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignmentLeftIndel
 
getPreferredScrollableViewportSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
getPreferredSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
getPrevCursorColumn() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getPrevCursorRow() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getPrimitiveTandemRepeats() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
Simple Cases
getPriority() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
getProfileProfileGlobalAlign(String[], String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SeqAlignment
 
getProfileProfileGlobalAlign(String[], String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignment
 
getProfileProfileGlobalAlign(String[], String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignmentLeftIndel
 
getProfileProfileSemiGlobalAlign(String[], String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SeqAlignment
 
getProfileSequenceGlobalAlign(String[], String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SeqAlignment
 
getProfileSequenceGlobalAlign(String[], String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignment
 
getProfileSequenceGlobalAlign(String[], String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignmentLeftIndel
 
getRealignmentStrategy() - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
getRefinedAlignment() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
getRight() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
getRoot() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
getRowIndex(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.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.tracealignmentwithguidetree.datatypes.Alignment
 
getScoringMatrix() - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
getScrollableBlockIncrement(Rectangle, int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
getScrollableTracksViewportHeight() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
getScrollableTracksViewportWidth() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
getScrollableUnitIncrement(Rectangle, int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
getSelectedOption() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
getSelectedOption() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
getSequence(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getSequence(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getSequence() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
getSequence() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
getSequenceComponent(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
getSequenceComponent(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
getSequenceIndex(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
getSequenceNameColor() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
getSequenceNameColor() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
getSequenceNameComponent(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
getSequencesInAlignment() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getSequenceWithGaps() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
getSequenceWithoutGaps() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
getSequenceWithoutGapsString() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
getSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
getSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
getSortValue() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
getSpacingWidth() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
getStep() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
getSubstitutionScoreFileName() - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
getSubstitutionScoreMap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.IndelSubstitutionScore
 
getSuperMaximalRepeats() - Method in class org.processmining.plugins.tracealignmentwithguidetree.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();
getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColorEditor
 
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColorRenderer
 
getTandemRepeats() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 
getToolTipText(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
getUniqueActivitiesInColumn(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getUniqueActivityCounts(int, String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getUniqueActivityCounts(int, String[], Sequence[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
getVerticalScrollBar() - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableViewport
 
getVgap() - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
getXForColumn(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
GuideTreeAlignment - Class in org.processmining.plugins.tracealignmentwithguidetree.msa
 
GuideTreeAlignment(GuideTree, TraceAlignmentWithGuideTreeInput, IndelSubstitutionScore) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.msa.GuideTreeAlignment
 

H

hasAnyActivities(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
hasAnyActivities(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
hasAnyActivities(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
HasAnyOfTheseLetters - Static variable in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
HasAnyOfTheseLetters - Static variable in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
hasCached - Variable in class org.processmining.plugins.tracealignmentwithguidetree.swingx.LazyBoundedRangeModel
 
hasHiddenRows() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
HasNoneOfTheseLetters - Static variable in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
HasNoneOfTheseLetters - Static variable in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
hours() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.Watch
 

I

incrementColumnSorts() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
incrementLikeSubstitutions(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SeqAlignment
 
incrementLikeSubstitutionScore(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.IndelSubstitutionScore
 
IndelSubstitutionScore - Class in org.processmining.plugins.tracealignmentwithguidetree.util
 
IndelSubstitutionScore() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.util.IndelSubstitutionScore
 
init() - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.JListX
 
initialize(String, String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
IntroductionStep - Class in org.processmining.plugins.tracealignmentwithguidetree.ui
 
IntroductionStep() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.ui.IntroductionStep
 
invalidateLayout(Container) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
inverseRGB(Color) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isActivityBackgroundSquare() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isAlignmentBlockShifted() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isAlignmentChanged() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
isAlignmentConcurrentRefined() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isAlignmentRecentlyEdited() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isColumnSelected() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
isColumnSelected(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
isColumnSorting() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
isDeriveSubstitutionIndelScores() - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
isDisplayConcurrentActivities() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isDisplayConcurrentActivitiesAcrossAllTraces() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isElementEnabled(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.JListX
 
isEncodedActivityRendered() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isGapPenalty() - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
isGapRendered() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isGroupEditing() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isHidden - Variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
isIncrementLikeSubstitutionScores() - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
isLazy - Variable in class org.processmining.plugins.tracealignmentwithguidetree.swingx.LazyBoundedRangeModel
 
isMapping() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isPerformRealignment() - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
isRulerAnnotationSelected() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
isRulerEditing() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isScaleIndelScores() - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
isSelected() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment.RulerAnnotation
 
isSeqAnnEditing() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isSeqHighlight(Sequence, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isSequenceHidden(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isSequenceSelected(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
isValidEncodedActivity(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
isValidRefinement() - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.RefineAlignment
 

J

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

L

layoutContainer(Container) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
LazyBoundedRangeModel - Class in org.processmining.plugins.tracealignmentwithguidetree.swingx
Model for ScrollBar's which do not fire events while adjusting.
LazyBoundedRangeModel(boolean) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.swingx.LazyBoundedRangeModel
 
levelOrderAlignmentTreeTraversal() - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.GuideTreeAlignment
 
levelOrderGuideTreeTraversal() - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.GuideTreeAlignment
 
loadIndelLeftGivenRightScores(String, Map<String, String>) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.IndelSubstitutionScore
 
loadIndelRightGivenLeftScores(String, Map<String, String>) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.IndelSubstitutionScore
 
loadSubstitutionScores(String, Map<String, String>) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.IndelSubstitutionScore
 
log2(double) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ConsensusSequence
 
LZDecomposition() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 

M

main(String[]) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.msa.RefineAlignment
 
main(UIPluginContext, GuideTree, TraceAlignmentWithGuideTreeInput) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreePlugin
 
main(String[]) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.util.Temp
 
main(String[]) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 
maximumLayoutSize(Container) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
MaxPriority - Static variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
mine(GuideTree, TraceAlignmentWithGuideTreeInput) - Method in class org.processmining.plugins.tracealignmentwithguidetree.MineAlignment
 
MineAlignment - Class in org.processmining.plugins.tracealignmentwithguidetree
 
MineAlignment() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.MineAlignment
 
minimumLayoutSize(Container) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
mins() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.Watch
 
mouseClicked(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
mouseClicked(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
mouseClicked(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
mouseClicked(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
mouseClicked(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
mouseDragged(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
mouseEntered(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
mouseEntered(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
mouseEntered(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
mouseEntered(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
mouseEntered(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
mouseExited(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
mouseExited(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
mouseExited(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
mouseExited(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
mouseExited(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
mouseMoved(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
mousePressed(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
mousePressed(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
mousePressed(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
mousePressed(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
mousePressed(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
mouseReleased(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
mouseReleased(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
mouseReleased(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
mouseReleased(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
mouseReleased(MouseEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
mouseWheelMoved(MouseWheelEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
MSA - Class in org.processmining.plugins.tracealignmentwithguidetree.msa
 
MSA(int, List<String>, int[][], Map<String, Integer>, Map<String, Integer>, int, float, int, float) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.msa.MSA
 
msecs() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.Watch
 
myStep - Class in org.processmining.plugins.tracealignmentwithguidetree.ui
 
myStep() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.ui.myStep
 

N

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

O

optionNames - Static variable in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
optionNames - Static variable in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
optionTest(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
optionTest(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
optionTestGetPriorityBit(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
org.processmining.plugins.tracealignmentwithguidetree - package org.processmining.plugins.tracealignmentwithguidetree
 
org.processmining.plugins.tracealignmentwithguidetree.datatypes - package org.processmining.plugins.tracealignmentwithguidetree.datatypes
 
org.processmining.plugins.tracealignmentwithguidetree.enumtypes - package org.processmining.plugins.tracealignmentwithguidetree.enumtypes
 
org.processmining.plugins.tracealignmentwithguidetree.exceptions - package org.processmining.plugins.tracealignmentwithguidetree.exceptions
 
org.processmining.plugins.tracealignmentwithguidetree.listeners - package org.processmining.plugins.tracealignmentwithguidetree.listeners
 
org.processmining.plugins.tracealignmentwithguidetree.msa - package org.processmining.plugins.tracealignmentwithguidetree.msa
 
org.processmining.plugins.tracealignmentwithguidetree.settings - package org.processmining.plugins.tracealignmentwithguidetree.settings
 
org.processmining.plugins.tracealignmentwithguidetree.swingx - package org.processmining.plugins.tracealignmentwithguidetree.swingx
 
org.processmining.plugins.tracealignmentwithguidetree.tree - package org.processmining.plugins.tracealignmentwithguidetree.tree
 
org.processmining.plugins.tracealignmentwithguidetree.ui - package org.processmining.plugins.tracealignmentwithguidetree.ui
 
org.processmining.plugins.tracealignmentwithguidetree.util - package org.processmining.plugins.tracealignmentwithguidetree.util
 
org.processmining.plugins.tracealignmentwithguidetree.visualization - package org.processmining.plugins.tracealignmentwithguidetree.visualization
 
owner - Variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
owner - Variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSeqAnnBaseDialog
 

P

paint(Graphics) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
paint(Graphics) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
paint(Graphics) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
paint(Graphics) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
paintComponent(Graphics) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
paintComponent(Graphics) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 
paintComponent(Graphics) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
pause() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.Watch
 
performBlockShiftLeft(String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.RefineAlignment
 
performBlockShiftRight(String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.RefineAlignment
 
popupMenuCanceled(PopupMenuEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
popupMenuCanceled(PopupMenuEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
popupMenuWillBecomeInvisible(PopupMenuEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
popupMenuWillBecomeInvisible(PopupMenuEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
popupMenuWillBecomeVisible(PopupMenuEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterComponent
 
popupMenuWillBecomeVisible(PopupMenuEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortComponent
 
precondition() - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.AlignmentAlgorithmConfigurationStep
 
precondition() - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.IntroductionStep
 
precondition() - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.myStep
 
precondition() - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.RealignmentConfigurationStep
 
precondition() - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.ScoringMatricesConfigurationStep
 
preferredLayoutSize(Container) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
prepareTable() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ActivityCharEncodingTable
 
prepareTable(Map<String, Color>) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ActivityCharEncodingTable
 
printArray(T[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 
printFScoreMatrix(String[], String[], int[][]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignment
 
printFScoreMatrix(String[], String[], int[][]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignmentLeftIndel
 
printSubstitutionIndelScores() - Method in class org.processmining.plugins.tracealignmentwithguidetree.MineAlignment
 
printTraceBack(String[], String[], TraceBack[][]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignment
 
printTraceBack(String[], String[], TraceBack[][]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignmentLeftIndel
 
printTraceBack(String[], String[], TraceBack[][]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.ArrayMatrixFileIO
 
printTree() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 

R

readEquivalenceClassMapFromFile(String, String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
readFile(String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
readFileAsSet(String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
readFloatMatrixFromFile(String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.ArrayMatrixFileIO
 
readInput() - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
readIntMatrixFromFile(String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.ArrayMatrixFileIO
 
readMapFromFile(String, String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
readMapSetIntegerFromFile(String, String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
readMapStringIntegerFromFile(String, String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
readMapStringSetFromFile(String, String, String, String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
readSetFromFile(String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
readSettings() - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.AlignmentAlgorithmConfigurationStep
 
readSettings() - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.IntroductionStep
 
readSettings() - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.myStep
 
readSettings() - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.RealignmentConfigurationStep
 
readSettings() - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.ScoringMatricesConfigurationStep
 
readStringStream(String, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
RealignmentConfigurationStep - Class in org.processmining.plugins.tracealignmentwithguidetree.ui
 
RealignmentConfigurationStep() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.ui.RealignmentConfigurationStep
 
RealignmentStrategy - Enum in org.processmining.plugins.tracealignmentwithguidetree.enumtypes
 
rebuildGUI() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSeqAnnBaseDialog
 
rebuildGUI() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSequenceNameDialog
 
recalc() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ConsensusSequence
 
RefineAlignment - Class in org.processmining.plugins.tracealignmentwithguidetree.msa
 
RefineAlignment(int) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.msa.RefineAlignment
 
refineConcurrent(String[], boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.RefineAlignment
 
refineConcurrent0(int, String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.RefineAlignment
 
removeAllGapColumns() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
removeColumnFilter(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
removeColumnFilter(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
removeColumnFromEnd() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
removeColumnRange(int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
removeColumnSort(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
removeColumnSort(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
removeConcurrent(String[], String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.RefineAlignment
 
removed(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
removeLayoutComponent(Component) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
removeListener(DisplayPropertiesListener) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
removeListener(SequenceListener) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
removeRulerAnnotationFromEnd() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
removeRulerAnnotationRange(int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
reset() - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
revalidateAndRepaintAll() - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
RulerAnnotation(String, Color, boolean) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment.RulerAnnotation
 
RulerAnnotationComponent - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
RulerAnnotationComponent(DisplayProperties, AlignmentFrame) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
rulerAnnotationsSize() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
RulerComponent - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
RulerComponent(DisplayProperties) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerComponent
 

S

scaleIndelScore(float) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.IndelSubstitutionScore
 
ScoringMatricesConfigurationStep - Class in org.processmining.plugins.tracealignmentwithguidetree.ui
 
ScoringMatricesConfigurationStep() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.ui.ScoringMatricesConfigurationStep
 
ScoringMatrix - Enum in org.processmining.plugins.tracealignmentwithguidetree.enumtypes
 
ScrollableGridLayout - Class in org.processmining.plugins.tracealignmentwithguidetree.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.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
ScrollableViewport - Class in org.processmining.plugins.tracealignmentwithguidetree.swingx
JViewport that can sync (horizontally or vertically) to scrollbars or other viewports.
ScrollableViewport() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableViewport
 
secs() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.Watch
 
SeqAlignment - Class in org.processmining.plugins.tracealignmentwithguidetree.msa
 
SeqAlignment(int, Map<String, Integer>, Map<String, Integer>, float) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.msa.SeqAlignment
 
SeqAlignment.TraceBack - Enum in org.processmining.plugins.tracealignmentwithguidetree.msa
 
Sequence - Class in org.processmining.plugins.tracealignmentwithguidetree.datatypes
 
Sequence() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
Sequence(String, String, List<String>, String[]) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
sequence - Variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSeqAnnBaseDialog
 
sequenceActivityChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
sequenceActivityChanged(Sequence) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.SequenceListener
 
sequenceActivityChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
sequenceActivityChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
sequenceActivityChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
SequenceAlignment - Class in org.processmining.plugins.tracealignmentwithguidetree.msa
 
SequenceAlignment(int, Map<String, Integer>, Map<String, Integer>, Map<String, Integer>) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignment
 
SequenceAlignmentLeftIndel - Class in org.processmining.plugins.tracealignmentwithguidetree.msa
 
SequenceAlignmentLeftIndel(int, Map<String, Integer>, Map<String, Integer>, Map<String, Integer>) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.msa.SequenceAlignmentLeftIndel
 
sequenceAnnotationChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
sequenceAnnotationChanged(Sequence) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.SequenceListener
 
sequenceAnnotationChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
sequenceAnnotationChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
sequenceAnnotationChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
sequenceColorChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
sequenceColorChanged(Sequence) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.SequenceListener
 
sequenceColorChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
sequenceColorChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
sequenceColorChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
sequenceColumnAnnotationsChanged(Sequence, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
SequenceComponent - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
SequenceComponent(Sequence, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
sequenceLineAnnotationsChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
sequenceLineAnnotationsChanged(Sequence) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.SequenceListener
 
sequenceLineAnnotationsChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
sequenceLineAnnotationsChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
sequenceLineAnnotationsChanged(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
SequenceListener - Interface in org.processmining.plugins.tracealignmentwithguidetree.listeners
 
sequenceNameChanged(Sequence, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
sequenceNameChanged(Sequence, String) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.SequenceListener
 
sequenceNameChanged(Sequence, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
sequenceNameChanged(Sequence, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
sequenceNameChanged(Sequence, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
sequenceNameColorChanged(Color) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
sequenceNameColorChanged(Color) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.listeners.SequenceListener
 
sequenceNameColorChanged(Color) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
sequenceNameColorChanged(Color) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
sequenceNameColorChanged(Color) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
SequenceNameComponent - Class in org.processmining.plugins.tracealignmentwithguidetree.visualization
 
SequenceNameComponent(AlignmentFrame, Sequence, DisplayProperties) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
sequenceTextField - Variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.EditSeqAnnBaseDialog
 
setActivity(String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
setActivityBackgroundSquare(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setActivityCharMap(Map<String, String>) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
setAlignmentAlgorithm(AlignmentAlgorithm) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.settings.TraceAlignmentWithGuideTreeSettingsListener
 
setAlignmentAlgorithm(AlignmentAlgorithm) - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
setAlignmentAlgorithm(AlignmentAlgorithm) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
setAlignmentRecentlyEdited(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setAllSequenceCollapsed(boolean, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
setAllSequenceCollapsed(boolean, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
setAllSequenceCollapsed(boolean, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
setAllSequencesHidden(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
setChanged(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
setCharActivityMap(Map<String, String>) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
setCollapsed(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
setColor(Color) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment.RulerAnnotation
 
setColumnFilterCurrColumn(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
setColumnFiltering(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
setColumnFiltering(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
setColumnFiltering(boolean, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
setColumnFixed(int, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
setColumnSelected(int, boolean, DisplayProperties) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
setColumnSortCurrColumn(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
setColumnSorting(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
setColumnSorting(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
setColumnSorting(boolean, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
setConsensus(ConsensusSequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ConsensusComponent
 
setCursorHidden(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setElementEnabled(int, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.JListX
 
setEncodedTrace(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
setEncodedTraceIdenticalIndicesMap(Map<String, TreeSet<Integer>>) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
setEncodingLength(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
setFilterActivities(int, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnFilter
 
setFilterActivities(int, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
setGapPenalty(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SeqAlignment
 
setHgap(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
setHorizontalScrollbar(JScrollBar) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableViewport
 
setHorizontalViewport(ScrollableViewport) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableViewport
 
setIncrementLikeSubstitutionScoreValue(int) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.settings.TraceAlignmentWithGuideTreeSettingsListener
 
setIncrementLikeSubstitutionScoreValue(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
setIncrementLikeSubstitutionScoreValue(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
setIndelRightGivenLeftScoreScaleFactor(Map<String, Integer>, float) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SeqAlignment
 
setIndelScoreFileName(String) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.settings.TraceAlignmentWithGuideTreeSettingsListener
 
setIndelScoreFileName(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
setIndelScoreFileName(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
setIndelScoreScaleValue(float) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.settings.TraceAlignmentWithGuideTreeSettingsListener
 
setIndelScoreScaleValue(float) - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
setIndelScoreScaleValue(float) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
setIsAlignmentBlockShifted(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setIsAlignmentConcurrentRefined(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setIsDeriveSubstitutionIndelScores(boolean) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.settings.TraceAlignmentWithGuideTreeSettingsListener
 
setIsDeriveSubstitutionIndelScores(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
setIsDeriveSubstitutionIndelScores(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
setIsDisplayConcurrentActivities(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setIsDisplayConcurrentActivitiesAcrossAllTraces(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setIsGapPenalty(boolean) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.settings.TraceAlignmentWithGuideTreeSettingsListener
 
setIsGapPenalty(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
setIsGapPenalty(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
setIsHidden(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
setIsIncrementLikeSubstitutionScores(boolean) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.settings.TraceAlignmentWithGuideTreeSettingsListener
 
setIsIncrementLikeSubstitutionScores(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
setIsIncrementLikeSubstitutionScores(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
setIsPerformRealignment(boolean) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.settings.TraceAlignmentWithGuideTreeSettingsListener
 
setIsPerformRealignment(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
setIsPerformRealignment(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
setIsScaleIndelScores(boolean) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.settings.TraceAlignmentWithGuideTreeSettingsListener
 
setIsScaleIndelScores(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
setIsScaleIndelScores(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
setIsSequenceSelected(Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setLastActivityIndexSelected(int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
setLastColumnIdxSelected(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
setLastRulerAnnIdxSelected(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
setLazy(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.LazyBoundedRangeModel
 
setLeft(AlignmentTreeNode) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
setLengthRatioThreshold(float) - Method in class org.processmining.plugins.tracealignmentwithguidetree.msa.SeqAlignment
 
setLetter(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment.RulerAnnotation
 
setListener(TraceAlignmentWithGuideTreeSettingsListener) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.AlignmentAlgorithmConfigurationStep
 
setListener(TraceAlignmentWithGuideTreeSettingsListener) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.IntroductionStep
 
setListener(TraceAlignmentWithGuideTreeSettingsListener) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.myStep
 
setListener(TraceAlignmentWithGuideTreeSettingsListener) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.RealignmentConfigurationStep
 
setListener(TraceAlignmentWithGuideTreeSettingsListener) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.ScoringMatricesConfigurationStep
 
setListener(ActivityColorListener) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ActivityCharEncodingTable
 
setListener(ActivityColorListener) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColorEditor
 
setLog(XLog) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
setName(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
setNoElements(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
setNoUniqueTraces(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
setOriginalAlignment(int, String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
setParent(AlignmentTreeNode) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
setPosition(Component, int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
setPriority(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.ColumnSort
 
setRangeProperties(int, int, int, int, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.LazyBoundedRangeModel
 
setRealignmentStrategy(RealignmentStrategy) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.settings.TraceAlignmentWithGuideTreeSettingsListener
 
setRealignmentStrategy(RealignmentStrategy) - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
setRealignmentStrategy(RealignmentStrategy) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
setRefinedAlignment(int, String[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
setRenderEncodedActivity(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setRenderGaps(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setRight(AlignmentTreeNode) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTreeNode
 
setRoot(AlignmentTreeNode) - Method in class org.processmining.plugins.tracealignmentwithguidetree.tree.AlignmentTree
 
setRowFixed(int, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
setRulerEditing(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setScoringMatrix(ScoringMatrix) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.settings.TraceAlignmentWithGuideTreeSettingsListener
 
setScoringMatrix(ScoringMatrix) - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
setScoringMatrix(ScoringMatrix) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
setSelected(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment.RulerAnnotation
 
setSeqAnnEditing(boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setSeqHidden(Sequence, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setSeqHighlight(Sequence, int, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setSeqHighlight(Sequence, int, boolean, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
setSequence(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceComponent
 
setSequence(Sequence) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
setSequenceCollapsed(int, boolean, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentFrame
 
setSequenceCollapsed(int, boolean, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentNamePanel
 
setSequenceCollapsed(int, boolean, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentPanel
 
setSequenceNameColor(Color) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
setSortValue(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
setSubstitutionScoreFileName(String) - Method in interface org.processmining.plugins.tracealignmentwithguidetree.settings.TraceAlignmentWithGuideTreeSettingsListener
 
setSubstitutionScoreFileName(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
setSubstitutionScoreFileName(String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
setVerticalScrollbar(JScrollBar) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableViewport
 
setVerticalViewport(ScrollableViewport) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableViewport
 
setVgap(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.ScrollableGridLayout
 
shiftActivity(int, int, boolean) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
showDialog(AlignmentFrame, DisplayProperties, int, ColumnFilter, Point) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnFilterDialog
 
showDialog(AlignmentFrame, DisplayProperties, int, ColumnSort, Point) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.ColumnSortDialog
 
showPopup(JPopupMenu, Component, int, int) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.Utils
 
sign(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.DisplayProperties
 
sign(int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.RulerAnnotationComponent
 
singleStringTest() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.UkkonenSuffixTree
 
sort() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.AlignmentSorter
 
sortBasedOnColumnSorts() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
sortBasedOnSortValue() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 
Spacing - Static variable in class org.processmining.plugins.tracealignmentwithguidetree.visualization.SequenceNameComponent
 
start() - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.Watch
 
swapSequence(int, int) - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Alignment
 

T

Temp - Class in org.processmining.plugins.tracealignmentwithguidetree.util
 
Temp() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.util.Temp
 
toString() - Method in class org.processmining.plugins.tracealignmentwithguidetree.datatypes.Sequence
 
traceAlignment(UIPluginContext, GuideTree) - Static method in class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreePlugin
 
TraceAlignmentWithGuideTreeInput - Class in org.processmining.plugins.tracealignmentwithguidetree
 
TraceAlignmentWithGuideTreeInput() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreeInput
 
TraceAlignmentWithGuideTreePlugin - Class in org.processmining.plugins.tracealignmentwithguidetree
 
TraceAlignmentWithGuideTreePlugin() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.TraceAlignmentWithGuideTreePlugin
 
TraceAlignmentWithGuideTreeSettingsListener - Interface in org.processmining.plugins.tracealignmentwithguidetree.settings
 
TraceAlignmentWithGuideTreeUI - Class in org.processmining.plugins.tracealignmentwithguidetree.ui
 
TraceAlignmentWithGuideTreeUI(UIPluginContext) - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.ui.TraceAlignmentWithGuideTreeUI
 
TraceBack - Enum in org.processmining.plugins.tracealignmentwithguidetree.enumtypes
 

U

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

V

valueChanged(ListSelectionEvent) - Method in class org.processmining.plugins.tracealignmentwithguidetree.swingx.JListX
 
valueOf(String) - Static method in enum org.processmining.plugins.tracealignmentwithguidetree.enumtypes.AlignmentAlgorithm
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.processmining.plugins.tracealignmentwithguidetree.enumtypes.AlignmentType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.processmining.plugins.tracealignmentwithguidetree.enumtypes.RealignmentStrategy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.processmining.plugins.tracealignmentwithguidetree.enumtypes.ScoringMatrix
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.processmining.plugins.tracealignmentwithguidetree.enumtypes.TraceBack
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.processmining.plugins.tracealignmentwithguidetree.msa.SeqAlignment.TraceBack
Returns the enum constant of this type with the specified name.
values() - Static method in enum org.processmining.plugins.tracealignmentwithguidetree.enumtypes.AlignmentAlgorithm
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.processmining.plugins.tracealignmentwithguidetree.enumtypes.AlignmentType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.processmining.plugins.tracealignmentwithguidetree.enumtypes.RealignmentStrategy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.processmining.plugins.tracealignmentwithguidetree.enumtypes.ScoringMatrix
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.processmining.plugins.tracealignmentwithguidetree.enumtypes.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.tracealignmentwithguidetree.msa.SeqAlignment.TraceBack
Returns an array containing the constants of this enum type, in the order they are declared.
visualize(PluginContext, AlignmentTree) - Method in class org.processmining.plugins.tracealignmentwithguidetree.visualization.AlignmentTreeVisualization
 

W

Watch - Class in org.processmining.plugins.tracealignmentwithguidetree.util
 
Watch() - Constructor for class org.processmining.plugins.tracealignmentwithguidetree.util.Watch
 
write - Variable in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
writeToFile(String, String, float[][]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.ArrayMatrixFileIO
 
writeToFile(String, String, int[][]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.ArrayMatrixFileIO
 
writeToFile(String, String, Map<T, E>, String) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
writeToFile(String, String, Collection<T>) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
writeToFile(String, String, T[]) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
writeToFile(String, String, T) - Method in class org.processmining.plugins.tracealignmentwithguidetree.util.FileIO
 
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