S-Index

A B C D E F G H I J K L M N O P Q R S T U V W Z

S

ScaledPherogramDistortion - Class in info.bioinfweb.libralign.pherogram.distortion: Stores scale and gap pattern for each base call index of a pherogram.
ScaledPherogramDistortion(int) - Constructor for class info.bioinfweb.libralign.pherogram.distortion.ScaledPherogramDistortion: Creates a new instance of this class.
ScrollContainerSwingAlignmentArea - Class in info.bioinfweb.libralign.alignmentarea: The Swing component rendering the top central or bottom part of an AlignmentArea.
ScrollContainerSwingAlignmentArea(AlignmentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.ScrollContainerSwingAlignmentArea
ScrollContainerSwingAlignmentContentArea - Class in info.bioinfweb.libralign.alignmentarea.content: The Swing component displaying the contents of an AlignmentContentArea.
ScrollContainerSwingAlignmentContentArea(AlignmentContentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.ScrollContainerSwingAlignmentContentArea
ScrollContainerSwingAlignmentLabelArea - Class in info.bioinfweb.libralign.alignmentarea.label: The Swing component displaying the label components for an alignment.
ScrollContainerSwingAlignmentLabelArea(AlignmentLabelArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.label.ScrollContainerSwingAlignmentLabelArea: Creates a new instance of this class.
ScrollContainerSWTAlignmentArea - Class in info.bioinfweb.libralign.alignmentarea: SWT component displaying the head, content, or bottom area of an alignment area.
ScrollContainerSWTAlignmentArea(AlignmentArea, Composite, int) - Constructor for class info.bioinfweb.libralign.alignmentarea.ScrollContainerSWTAlignmentArea: Creates a new instance of this class.
ScrollContainerSWTAlignmentContentArea - Class in info.bioinfweb.libralign.alignmentarea.content: The SWT component displaying a AlignmentContentArea.
ScrollContainerSWTAlignmentContentArea(AlignmentContentArea, Composite, int) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.ScrollContainerSWTAlignmentContentArea
scrollCursorToVisible() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea
selectAll() - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection: Selects all columns or rows (depending on OneDimensionalSelection.getDimension()).
selectAll() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Selects all cells in the alignment.
selectionAsString(AlignmentArea, boolean) - Static method in class info.bioinfweb.libralign.model.utils.AlignmentModelUtils: Converts the current selection to a String.
selectionChanged(GenericEventObject<SelectionModel>) - Method in class info.bioinfweb.libralign.alignmentarea.content.SequenceAreaMap
selectionChanged(E) - Method in interface info.bioinfweb.libralign.alignmentarea.selection.SelectionListener: This method is called every time the selection changes.
SelectionDimension - Enum in info.bioinfweb.libralign.alignmentarea.selection: Used by OneDimensionalSelection to determine if the selection of rows or columns is represented.
SelectionListener<E> - Interface in info.bioinfweb.libralign.alignmentarea.selection: This interface should be implemented by classes that want to track changes of the selection represented by an SelectionModel object.
SelectionModel - Class in info.bioinfweb.libralign.alignmentarea.selection: The selection model of AlignmentArea.
SelectionModel(AlignmentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Creates a new instance of this class.
SelectionSynchronizer - Class in info.bioinfweb.libralign.alignmentarea.selection: Instances of this class allow to synchronize different instances of SelectionModel if possible.
SelectionSynchronizer() - Constructor for class info.bioinfweb.libralign.alignmentarea.selection.SelectionSynchronizer
SelectionType - Enum in info.bioinfweb.libralign.alignmentarea.selection
SequenceAccess<S> - Interface in info.bioinfweb.libralign.model: Implementations of AlignmentModel or SequenceDataAdapter that provide access to a sequence object representing a row in the alignment should implement this interface.
SequenceAccessAlignmentModel<S,T> - Interface in info.bioinfweb.libralign.model: Interface for classes implementing AlignmentModel by using sequence objects.
SequenceArea - Class in info.bioinfweb.libralign.alignmentarea.content: The area inside an AlignmentArea that displays one sequence of the alignment.
SequenceArea(AlignmentContentArea, String) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.SequenceArea: Creates a new instance of this class.
SequenceAreaMap - Class in info.bioinfweb.libralign.alignmentarea.content: Manages the SequenceAreas that are contained in an implementation of ToolkitSpecificMultipleAlignmentsContainer.
SequenceAreaMap(AlignmentContentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.content.SequenceAreaMap
SequenceChangeEvent<T> - Class in info.bioinfweb.libralign.model.events: Event object that indicates that a sequence provided by an instance of AlignmentModel was added or removed.
SequenceChangeEvent(AlignmentModel<T>, String, ListChangeType) - Constructor for class info.bioinfweb.libralign.model.events.SequenceChangeEvent
SequenceDataAdapter<S,T> - Interface in info.bioinfweb.libralign.model.adapters: Classes implementing this interface provide access to the data provided by an implementation of AlignmentModel in a different way (e.g.
sequenceID - Variable in class info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingSequenceEdit
sequenceID - Variable in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingTokenEdit
sequenceIDIterator() - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Returns an iterator over unique IDs of all sequences contained in the underlying data source in the order they are stored in this model.
sequenceIDIterator() - Method in class info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel: Returns an iterator returned the IDs of the stored sequences in the order they were added to this model.
sequenceIDIterator() - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator
sequenceIDIterator() - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
sequenceIDIterator() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
SequenceIDManager - Class in info.bioinfweb.libralign.model.implementations: Manages mappings between sequence IDs and sequence names.
SequenceIDManager() - Constructor for class info.bioinfweb.libralign.model.implementations.SequenceIDManager
SequenceIDManager(String) - Constructor for class info.bioinfweb.libralign.model.implementations.SequenceIDManager
sequenceIDsByName(String) - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Returns the set of unique sequence IDs associated with the specified name.
sequenceIDsByName(String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel
sequenceIDsByName(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator
sequenceIDsByName(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
sequenceIDsByName(String) - Method in class info.bioinfweb.libralign.model.implementations.SequenceIDManager: Returns a set of unique sequence IDs associated with the specified name.
sequenceIDsByName(String) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
SequenceIndexArea - Class in info.bioinfweb.libralign.dataarea.implementations.sequenceindex: A data area displaying the indices of aligned sequences.
SequenceIndexArea(AlignmentContentArea, AlignmentArea) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea: Creates a new instance of this class.
SequenceIndexArea(AlignmentContentArea) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea: Creates a new instance of this class using the parent alignment area of owner as the labeled area.
SequenceLabelArea - Class in info.bioinfweb.libralign.alignmentarea.label: GUI component used to label instances of SequenceArea.
SequenceLabelArea(AlignmentLabelArea, SequenceArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.label.SequenceLabelArea
sequenceNameByID(String) - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Returns the sequence name (that would be visible to the application user) associated with the specified unique ID.
sequenceNameByID(String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel
sequenceNameByID(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator
sequenceNameByID(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
sequenceNameByID(String) - Method in class info.bioinfweb.libralign.model.implementations.SequenceIDManager: Returns the sequence name (that would be visible to the application user) associated with the specified unique ID.
sequenceNameByID(String) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
SequenceNotFoundException - Exception in info.bioinfweb.libralign.model.exception: This exceptions is thrown if a requested sequence provided by an implementation of AlignmentModel was not found in the underlying data source.
SequenceNotFoundException(AlignmentModel<?>, String) - Constructor for exception info.bioinfweb.libralign.model.exception.SequenceNotFoundException: Create a new instance of this class.
SequenceOrder - Class in info.bioinfweb.libralign.alignmentarea.order: Manages the ordering of the sequences displayed by AlignmentArea.
SequenceOrder(AlignmentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.order.SequenceOrder: Crates a new instance of this class and loads the names from the underlying data source of the specified owner, if it has a data source.
SequenceOrderType - Enum in info.bioinfweb.libralign.alignmentarea.order: Enumerates the possible orders of sequences as modeled by SequenceOrder.
SequenceRenamedEvent<T> - Class in info.bioinfweb.libralign.model.events: Event object that indicates that a sequence provided by an instance of AlignmentModel was renamed.
SequenceRenamedEvent(AlignmentModel<T>, String, String, String) - Constructor for class info.bioinfweb.libralign.model.events.SequenceRenamedEvent
set(int, TokenPainter) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterList: Replaces the painter at the specified position in this list with the specified new painter.
set(int, DataArea) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
setAlignmentModel(AlignmentModel<?>, boolean) - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Changes the alignment model providing the data for this instance.
setAlignToFirstColumn(boolean) - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
setAlignToScrollPosition(boolean) - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
setAllowVerticalScrolling(boolean) - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Allows to specify whether this area should be displayed with its whole height insight a MultipleAlignmentsContainer if there is enough space available.
setAllPaintSettingPropertiesToSynchronize() - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer: Sets all properties of PaintSettings to be synchronized between all alignment areas in this container.
setAllVisible(boolean) - Method in class info.bioinfweb.libralign.dataarea.DataAreaList: Fades all elements in this list in or out.
setAlphabeticalSequenceOrder(boolean) - Method in class info.bioinfweb.libralign.alignmentarea.order.SequenceOrder: Sorts the sequences by their name.
setBackgroundColor(Color) - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
setBackgroundColor(Color) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Sets a new background color for displaying the central part of the pherogram (the positions that have not been cut off).
setBaseCallLineColor(Color) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Sets a new color used to paint the vertical lines at each base call position in the background of the trace curve output in the center area that has not been cut off by the user.
setChangeZoomXOnMouseWheel(boolean) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings
setChangeZoomYOnMouseWheel(boolean) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings
setCharacterStateSetType(CharacterStateSetType) - Method in class info.bioinfweb.libralign.model.factory.NewAlignmentModelParameterMap: Sets or replaces the character set type in this map.
setColor(Color) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSet
setColumn(int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.AlignmentCursor
setColumnRowHeight(int, int, int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.AlignmentCursor: Sets a new column, row and height in one step.
setCursorColor(Color) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings: Sets a new color to paint the alignment cursor.
setCursorLineWidth(double) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings
setCutBackgroundColor(Color) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Sets a new background color for displaying the parts of the pherogram on the left and right end that have been cut off by the user.
setCutBaseCallLineColor(Color) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Sets a new color used to paint the vertical lines at each base call position in the background of the trace curve output at the left and right areas that have been cut off by the user.
setDefaultBackgroundColor(Color) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
setDistributeRemainingSpace(boolean) - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer: If the height of this container is higher than the height that is needed to display all alignments without scrolling, you can specify here how the remaining space shall be distributed among the alignments.
setDividerLocations(int[]) - Method in class info.bioinfweb.libralign.multiplealignments.SwingMultipleAlignmentsContainer
setDividerLocations(int[]) - Method in class info.bioinfweb.libralign.multiplealignments.SWTMultipleAlignmentsContainer
setDividerLocations(int[]) - Method in interface info.bioinfweb.libralign.multiplealignments.ToolkitSpecificMultipleAlignmentsContainer: Sets the divider locations to distribute the available height among the contained alignment areas.
setEnabled(boolean) - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionSynchronizer
setFirstIndex(int) - Method in class info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea: Sets a new index that will be displayed for the first column of the alignment area.
setFirstPos(int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection: Sets the first column (or row) of the selection.
setFirstSeqLeftCutPos(int, int) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel: Allows to specify a new first sequence and left cut position at the same time.
setFirstSeqPos(int) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel: Sets the index in the sequence this pherogram is attached to where the displaying of the visible part of the pherogram starts.
setFont(Font) - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
setFontColor(Color) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
setFontName(String) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
setFontStyle(int) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
setGap(int, boolean) - Method in class info.bioinfweb.libralign.pherogram.distortion.GapPattern: This method allows to define whether a gap is located at the specified position or not.
setGapPattern(int, GapPattern) - Method in class info.bioinfweb.libralign.pherogram.distortion.ScaledPherogramDistortion
setHeadingBackgroundColor(Color) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Sets a new background color for the heading of the pherogram (displaying the base call sequence and nucleotide indices).
setHeadingView(PherogramHeadingView) - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView: Use this method to specify the heading component used together with this component.
setHeight(int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.AlignmentCursor
setHideHorizontalBar(boolean) - Method in class info.bioinfweb.libralign.alignmentarea.SWTScrollableResizeListener
setHideHorizontalScrollBar(boolean) - Method in class info.bioinfweb.libralign.alignmentarea.AbstractSWTAlignmentArea
setHideHorizontalScrollBar(boolean) - Method in class info.bioinfweb.libralign.alignmentarea.ScrollContainerSwingAlignmentArea
setHideHorizontalScrollBar(boolean) - Method in interface info.bioinfweb.libralign.alignmentarea.ToolkitSpecificAlignmentArea: Determines whether a horizontal scroll bar should be displayed underneath this element.
setHorizontalScale(int, double) - Method in class info.bioinfweb.libralign.pherogram.distortion.ScaledPherogramDistortion
setHorizontalScale(double) - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView
setID(String) - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Allows to specify a new ID for this alignment.
setID(String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractAlignmentModel
setID(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
setInsert(boolean) - Method in class info.bioinfweb.libralign.editsettings.EditSettings
setInsertLeftInDataArea(boolean) - Method in class info.bioinfweb.libralign.editsettings.EditSettings
setLabel(String) - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Allows to specify a new label for this alignment.
setLabel(String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractAlignmentModel: Allows to specify a new label for this alignment.
setLabel(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
setLabel(String) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
setLastPos(int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection: Sets the last column (or row) of the selection.
setLayout(Layout) - Method in class info.bioinfweb.libralign.multiplealignments.SWTMultipleAlignmentsContainer: Does nothing since this component only uses its own layout.
setLeftCutPosition(int) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel: Sets a new cut position for the left border of the visible part of the pherogram.
setLeftCutPositionBySelection() - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea: Tries to set the left border where the base call sequence is cut off according to the left end of the current selection.
setLength(int) - Method in class info.bioinfweb.libralign.model.adapters.AbstractSingleSequenceDataAdapter
setList(DataAreaList) - Method in class info.bioinfweb.libralign.dataarea.DataArea: Updates the list this element is contained in.
setListType(DataAreaListType) - Method in class info.bioinfweb.libralign.dataarea.DataAreaLocation: Changes the list type.
setLocalMaxLengthBeforeAfterRecalculate() - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel: Flags the properties DataAreasModel.getLocalMaxLengthBeforeStart() and DataAreasModel.getLocalMaxLengthAfterEnd() to be recalculated when they are accessed the next time.
setLocalMaxWidthRecalculate() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea: Flags the needed width to display all labels to be recalculated the next time it is accessed.
setLocalMaxWidthRecalculateToAll() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea
setMaxSequeceLengthRecalculte() - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel
setModel(CharSetDataModel, boolean) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea: Changes the model instance that is displayed by this area.
setModel(PherogramComponentModel) - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView
setName(String) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSet
setNewCursorColumn(int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Moves the cursor to a new column, leaving its row and height unchanged.
setNewCursorPosition(int, int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Specifies a new location of the cursor.
setNewCursorPosition(int, int, int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Specifies a new location and height for the cursor.
setNewCursorRow(int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Specifies a new row position of the cursor.
setNewSelection(int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection: Deletes the current selection and selects the column (or row) at the specified position.
setNucleotideColor(char, Color) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Sets a new color for a nucleotide representation in the internal color map of this instance.
setNucleotideFactories(AlignmentModelFactory<?>) - Method in class info.bioinfweb.libralign.model.io.AlignmentModelEventReader: Sets the specified map for all nucleotide factories (identified with the keys CharacterStateSetType.NUCLEOTIDE, CharacterStateSetType.DNA, CharacterStateSetType.RNA).
setOffset(int) - Method in class info.bioinfweb.libralign.model.adapters.AbstractSingleSequenceDataAdapter
setOwner(PherogramArea) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel: Specifies a new owning pherogram area for this instance.
setPaintCenterX(int, double) - Method in class info.bioinfweb.libralign.pherogram.distortion.ScaledPherogramDistortion
setPaintStartX(int, double) - Method in class info.bioinfweb.libralign.pherogram.distortion.ScaledPherogramDistortion
setProbabilityColor(Color) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Sets a new font font color for displaying probability values.
setProvider(PherogramProvider) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel: Sets a new pherogram provider and fires according events.
setPublishOnAlignmentEnd(boolean) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetEventReader
setQualityOutputType(PherogramFormats.QualityOutputType) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats
setReuseSequenceIDs(boolean) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel: Allows to specify whether unused IDs of the underlying ID manager should be reused by this model.
setRightCutPosition(int) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel: Sets a new cut position for the right border of the visible part of the pherogram.
setRightCutPositionBySelection() - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea: Tries to set the right border where the base call sequence is cut off according to the right end of the current selection.
setRow(int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.AlignmentCursor
setScrollOffset(int, int) - Method in class info.bioinfweb.libralign.alignmentarea.DirectPaintingSWTAlignmentArea
setSelectedIndex(int) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea
setSelectionColor(Color) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings: Sets a new color of the selection in the owning alignment area.
setSelectionEnd(int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection
setSelectionEnd(int, int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Extends the current selection to include the specified cell and positions the cursor there.
setSequenceDataAreasVisible(boolean) - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel: Fades all data areas associated with any sequence in or out.
setSequenceID(String) - Method in class info.bioinfweb.libralign.dataarea.DataAreaLocation: Can be used to update the sequence name, if a sequence was renamed or data area is moved.
setSequenceID(String) - Method in class info.bioinfweb.libralign.model.adapters.AbstractSingleSequenceDataAdapter
setShiftChange(int, int) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel: Adds or replaces a change in the shift between the editable sequence in the alignment and the base call sequence.
setShowBaseCallLines(boolean) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Allows to define if base call lines (vertical lines at each base call position in the background of the trace curve output) shall be painted.
setShowProbabilityValues(boolean) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Allows to specify whether probability values (substitution, overcall and undercall) should be displayed in the pherogram heading.
setSourceSequenceOrder() - Method in class info.bioinfweb.libralign.alignmentarea.order.SequenceOrder: Sorts the sequences by their occurrence in the source data.
setSpaceForGap(boolean) - Method in class info.bioinfweb.libralign.model.tokenset.AbstractTokenSet
setSpaceForGap(boolean) - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet
setSpaceForGap(boolean) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
setSpaceForGap(boolean) - Method in interface info.bioinfweb.libralign.model.tokenset.TokenSet: Allows to specify whether TokenSet.tokenByKeyStroke(KeyStroke) shall return the gap token, if the space bar is pressed, even if that key stroke is not associated with that token.
setStartPos(int) - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection
setText(String) - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
setTextColor(Color) - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
setTokenAt(String, int, T) - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Replaces the token at the specified position by the passed token.
setTokenAt(String, int, T) - Method in class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel
setTokenAt(String, int, T) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUnmodifyableAlignmentModel
setTokenAt(String, int, T) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
setTokenAt(String, int, T) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
setTokenAt(String, int, T) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
setTokensAt(String, int, Collection<? extends T>) - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Replaces a sequence of tokens starting at the specified position.
setTokensAt(String, int, Collection<? extends T>) - Method in class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel
setTokensAt(String, int, Collection<? extends T>) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUnmodifyableAlignmentModel
setTokensAt(String, int, Collection<? extends T>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
setTokensAt(String, int, Collection<? extends T>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
setTokensAt(String, int, Collection<? extends T>) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
setTokenSet(TokenSet<T>) - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Replaces the current token set with the specified one.
setTokenSet(TokenSet<T>) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel
setTokenSet(TokenSet<T>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator
setTokenSet(TokenSet<T>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
setTokenSet(TokenSet<T>) - Method in class info.bioinfweb.libralign.model.implementations.PackedAlignmentModel: This method is not supported by this class.
setTokenSet(TokenSet<T>) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
setType(SelectionType) - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Switches the selection type.
setUnderlyingModel(AlignmentModel<T>) - Method in class info.bioinfweb.libralign.model.adapters.AbstractBasicAlignmentModelView
setUnderlyingModel(AlignmentModel<U>) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator: Replaces the decorated (underlying) model.
setUpdateEditableSequence(boolean) - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea: Specifies whether updated of the editable sequence shall be performed by this class automatically, if the cut positions in the underlying model are changed.
setVerticalScale(double) - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea
setVerticalScale(double) - Method in interface info.bioinfweb.libralign.pherogram.PherogramComponent: Sets the horizontal zoom factor that shall used for displaying the trace curves.
setVerticalScale(double) - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView
setVerticalScrollPosition(int) - Method in class info.bioinfweb.libralign.alignmentarea.label.SWTAlignmentLabelArea: Sets the vertical scroll position of this component.
setVisible(boolean) - Method in class info.bioinfweb.libralign.dataarea.DataArea: Fades this data area in or out and lets the containing alignment area repaint, if necessary.
setWorkingMode(WorkingMode) - Method in class info.bioinfweb.libralign.editsettings.EditSettings
setZoom(double, double) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings: Allows to specify a new horizontal and vertical zoom factor in a single operation.
setZoomX(double) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings: Allows to specify a new horizontal zoom factor.
setZoomY(double) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings: Allows to specify a new vertical zoom factor.
shiftAtBaseCallIndex(int) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel
ShiftChange - Class in info.bioinfweb.libralign.pherogram.model: Used by PherogramAlignmentModel to model which position in the base call sequence corresponds to which position in the editable alignment sequence.
ShiftChange(int, int) - Constructor for class info.bioinfweb.libralign.pherogram.model.ShiftChange
shiftChange - Variable in class info.bioinfweb.libralign.pherogram.model.ShiftChange
shiftChangeIterator(int) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel
shiftChangeIterator() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel
shiftChangeIteratorByBaseCallIndex(int) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel
SingleBioJava3SequenceAdapter<T,C extends org.biojava3.core.sequence.template.Compound> - Class in info.bioinfweb.libralign.model.adapters: Abstract base class for all implementations of SingleSequenceDataAdapter that allow to view one sequence of a AlignmentModel as a BioJava Sequence object.
SingleBioJava3SequenceAdapter(AlignmentModel<T>, String, int, int, CompoundSet<C>) - Constructor for class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter: Creates a new instance of this class that does not allow unknown compounds.
SingleBioJava3SequenceAdapter(AlignmentModel<T>, String, int, int, CompoundSet<C>, C) - Constructor for class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter: Creates a new instance of this class allowing unknown compounds.
SingleBioJava3SequenceAdapter(AlignmentModel<T>, String, CompoundSet<C>) - Constructor for class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter: Creates a new instance of this class that does not allow unknown compounds.
SingleBioJava3SequenceAdapter(AlignmentModel<T>, String, CompoundSet<C>, C) - Constructor for class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter: Creates a new instance of this class allowing unknown compounds.
SingleCharSequenceAdapter<T> - Class in info.bioinfweb.libralign.model.adapters: An adapter class allowing to view a single sequence provided by an implementation of AlignmentModel as a CharSequence.
SingleCharSequenceAdapter(AlignmentModel<T>, String, int, int, boolean) - Constructor for class info.bioinfweb.libralign.model.adapters.SingleCharSequenceAdapter: Creates a new instance of this class specifying a subsequence to be viewed.
SingleCharSequenceAdapter(AlignmentModel<T>, String, boolean) - Constructor for class info.bioinfweb.libralign.model.adapters.SingleCharSequenceAdapter: Creates a new instance of this class specifying a whole sequence to be viewed.
SingleColorTokenPainter - Class in info.bioinfweb.libralign.alignmentarea.tokenpainter: Token painter that paints the string representation of a token centered into a rectangle filled with a specified background color.
SingleColorTokenPainter() - Constructor for class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
SingleSequenceDataAdapter<T> - Interface in info.bioinfweb.libralign.model.adapters: Adapter classes providing views of (sub-) sequences of single rows of an implementation of AlignmentModel should implement this interface.
size() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterList: Returns the number of list elements in this instance.
size() - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
size() - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet
size() - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet: The number of elements in a continuous set is unlimited.
size() - Method in class info.bioinfweb.libralign.pherogram.distortion.GapPattern: Returns the length of this pattern.
startVisibilityUpdate() - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel: After calling this method #fireVisibilityChanged(DataAreaList, Collection) will have no effect until #finishVisibilityUpdate(DataAreaList, Collection) is called.
StringAdapter<T> - Class in info.bioinfweb.libralign.model.adapters: Returns the sequences contained in the underlying data source as strings.
StringAdapter(AlignmentModel<T>, boolean) - Constructor for class info.bioinfweb.libralign.model.adapters.StringAdapter: Creates a new instance of this class.
StringAlignmentModelFactory - Class in info.bioinfweb.libralign.model.factory: Default factory implementation for creating alignment models.
StringAlignmentModelFactory() - Constructor for class info.bioinfweb.libralign.model.factory.StringAlignmentModelFactory
subAreaIterator() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea
subAreaIterator() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea
subList(int, int) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
subSequence(int, int) - Method in class info.bioinfweb.libralign.model.adapters.SingleCharSequenceAdapter
SwingAddSequenceEdit - Interface in info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence: Interface that needs to be implemented by all edits that insert a new sequence into an instance of AlignmentModel.
SwingAlignmentRowsArea<C extends TICComponent> - Class in info.bioinfweb.libralign.alignmentarea.rowsarea: Abstract base class for ScrollContainerSwingAlignmentContentArea and ScrollContainerSwingAlignmentLabelArea.
SwingAlignmentRowsArea(TICComponent) - Constructor for class info.bioinfweb.libralign.alignmentarea.rowsarea.SwingAlignmentRowsArea
SwingConcreteAddSequenceEdit<T> - Class in info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence: Edit object that inserts a new empty sequence into an instance of AlignmentModel.
SwingConcreteAddSequenceEdit(SwingUndoAlignmentModel<T>, String, String) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingConcreteAddSequenceEdit: Creates a new instance of this class.
SwingEditFactory<T> - Interface in info.bioinfweb.libralign.model.implementations.swingundo: Classes providing custom edit objects to an instance of SwingUndoAlignmentModel must implement this interface.
SwingInsertRemoveTokensEdit<T> - Class in info.bioinfweb.libralign.model.implementations.swingundo.edits.token: Implements the insertion and removal of sequence elements in an instance of AlignmentModel.
SwingInsertRemoveTokensEdit(SwingUndoAlignmentModel<T>, String, int, Collection<? extends T>) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingInsertRemoveTokensEdit: Creates a new instance of this class used to insert a new set of tokens into a sequence.
SwingInsertRemoveTokensEdit(SwingUndoAlignmentModel<T>, String, int, T) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingInsertRemoveTokensEdit: Creates a new instance of this class used to insert a new single token into a sequence.
SwingInsertRemoveTokensEdit(SwingUndoAlignmentModel<T>, String, int, int) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingInsertRemoveTokensEdit: Creates a new instance of this class used to remove a set of tokens from a sequence.
SwingInsertRemoveTokensEdit(SwingUndoAlignmentModel<T>, String, int) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingInsertRemoveTokensEdit: Creates a new instance of this class used to remove a single token from a sequence.
SwingInsertTokensEdit<T> - Class in info.bioinfweb.libralign.model.implementations.swingundo.edits.token: Edit object that inserts a set of tokens into a sequence managed by an instance of AlignmentModel.
SwingInsertTokensEdit(SwingUndoAlignmentModel<T>, String, int, Collection<? extends T>) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingInsertTokensEdit
SwingMultipleAlignmentsContainer - Class in info.bioinfweb.libralign.multiplealignments: Swing specific GUI component that contains the three scroll panes that make up an alignment area.
SwingMultipleAlignmentsContainer(MultipleAlignmentsContainer) - Constructor for class info.bioinfweb.libralign.multiplealignments.SwingMultipleAlignmentsContainer: Creates a new instance of this class.
SwingPhergramView - Class in info.bioinfweb.libralign.pherogram.view: The Swing implementation for PherogramView.
SwingPhergramView(PherogramView) - Constructor for class info.bioinfweb.libralign.pherogram.view.SwingPhergramView
SwingRemoveSequenceEdit<T> - Class in info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence: Edit object that removes a sequence from an instance of AlignmentModel.
SwingRemoveSequenceEdit(SwingUndoAlignmentModel<T>, String) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingRemoveSequenceEdit
SwingRemoveTokensEdit<T> - Class in info.bioinfweb.libralign.model.implementations.swingundo.edits.token: Edit object that removes a set of tokens from a sequence managed by an instance of AlignmentModel.
SwingRemoveTokensEdit(SwingUndoAlignmentModel<T>, String, int, int) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingRemoveTokensEdit
SwingRenameSequenceEdit<T> - Class in info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence: Edit object that renames a sequence managed by an instance of AlignmentModel.
SwingRenameSequenceEdit(SwingUndoAlignmentModel<T>, String, String) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingRenameSequenceEdit
SwingSequenceEdit<T> - Class in info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence: Offers basic functionality used by edits that manipulate sequences.
SwingSequenceEdit(SwingUndoAlignmentModel<T>, String) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingSequenceEdit
SwingSetTokensEdit<T> - Class in info.bioinfweb.libralign.model.implementations.swingundo.edits.token: Edit object that replaces a set of tokens in a sequence managed by an instance of AlignmentModel.
SwingSetTokensEdit(SwingUndoAlignmentModel<T>, String, int, Collection<? extends T>) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingSetTokensEdit: Creates a new instance of this class.
SwingSetTokensEdit(SwingUndoAlignmentModel<T>, String, int, T) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingSetTokensEdit: Creates a new instance of this class.
SwingTokenEdit<T> - Class in info.bioinfweb.libralign.model.implementations.swingundo.edits.token: Offers basic functionality used by edits that manipulate sequence elements (tokens).
SwingTokenEdit(SwingUndoAlignmentModel<T>, String, int, Collection<? extends T>) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingTokenEdit
SwingUndoAlignmentModel<T> - Class in info.bioinfweb.libralign.model.implementations.swingundo: An implementation of AlignmentModel that creates an UndoableEdit object for every modification that is made to the underlying data source using any of the methods specified by AlignmentModel.
SwingUndoAlignmentModel(AlignmentModel<T>, UndoManager, SwingEditFactory<T>) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel: Creates a new instance of this class which creates new edit objects using the provided SwingEditFactory.
SwingUndoAlignmentModel(AlignmentModel<T>, UndoManager) - Constructor for class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel: Creates a new instance of this class which creates default LibrAlign edit objects.
SWTAlignmentLabelArea - Class in info.bioinfweb.libralign.alignmentarea.label: The SWT component displaying the label components for an alignment.
SWTAlignmentLabelArea(AlignmentLabelArea, Composite, int) - Constructor for class info.bioinfweb.libralign.alignmentarea.label.SWTAlignmentLabelArea: Creates a new instance of this class.
SWTAlignmentRowsArea<C extends TICComponent> - Class in info.bioinfweb.libralign.alignmentarea.rowsarea: Abstract base class for ScrollContainerSWTAlignmentContentArea and ScrollContainerSWTAlignmentLabelArea.
SWTAlignmentRowsArea(TICComponent, Composite, int) - Constructor for class info.bioinfweb.libralign.alignmentarea.rowsarea.SWTAlignmentRowsArea: Creates a new instance of this class with RowLayout.
SWTMultipleAlignmentsContainer - Class in info.bioinfweb.libralign.multiplealignments: The SWT component rendering all parts of an AlignmentArea.
SWTMultipleAlignmentsContainer(MultipleAlignmentsContainer, Composite, int, boolean) - Constructor for class info.bioinfweb.libralign.multiplealignments.SWTMultipleAlignmentsContainer
SWTPhergramView - Class in info.bioinfweb.libralign.pherogram.view: The SWT implementation for PherogramView.
SWTPhergramView(PherogramView, Composite, int) - Constructor for class info.bioinfweb.libralign.pherogram.view.SWTPhergramView
SWTScrollableResizeListener - Class in info.bioinfweb.libralign.alignmentarea: Helper class that cuts off the horizontal scroll bar from an SWT Scrollable to provide functionality comparable to Swing components.
SWTScrollableResizeListener(Composite, Scrollable, boolean, boolean) - Constructor for class info.bioinfweb.libralign.alignmentarea.SWTScrollableResizeListener

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