G-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

G

GAP - Static variable in class info.bioinfweb.libralign.model.utils.indextranslation.IndexRelation: This value returned as an index indicates that there is a gap in the associated sequence.
GapPattern - Class in info.bioinfweb.libralign.pherogram.distortion: Represents gaps displayed in a PherogramArea within the area of one base call.
GapPattern(int) - Constructor for class info.bioinfweb.libralign.pherogram.distortion.GapPattern: Creates a new instance of this class initially containing no gaps.
get(int) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterList: Returns the painter at the specified index.
get(int) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
getAccession() - Method in class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter: This method always returns null since sequences stored in instances of AlignmentModel do not store an associated instance of AccessionID.
getActionMap() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea
getActionProvider() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Tool object that implements business logic methods to manipulate the alignment model.
getAdapter() - Method in exception info.bioinfweb.libralign.model.adapters.InvalidUnderlyingTokenException
getAffectedElement() - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEvent: Returns the first affected element.
getAffectedElements() - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEvent
getAffectedToken() - Method in class info.bioinfweb.libralign.model.events.TokenChangeEvent: Returns the first affected token.
getAffectedTokens() - Method in class info.bioinfweb.libralign.model.events.TokenChangeEvent: Returns a collection of tokens that have been affected by this operation.
getAfter() - Method in class info.bioinfweb.libralign.model.utils.indextranslation.IndexRelation: This value is only needed if IndexRelation.getCorresponding() returns IndexRelation.GAP or IndexRelation.OUT_OF_RANGE.
getAfterValidIndex() - Method in class info.bioinfweb.libralign.model.utils.indextranslation.IndexRelation: Returns any index that is not IndexRelation.GAP or IndexRelation.OUT_OF_RANGE and first tries IndexRelation.getCorresponding() than IndexRelation.getAfter() and finally IndexRelation.getBefore().
getAlignedIndex(String, int) - Method in class info.bioinfweb.libralign.model.utils.indextranslation.AbstractIndexTranslator
getAlignedIndex(String, int) - Method in interface info.bioinfweb.libralign.model.utils.indextranslation.IndexTranslator: Returns the column in the alignment, the specified token is contained in
getAlignedIndex(String, int) - Method in class info.bioinfweb.libralign.model.utils.indextranslation.RandomAccessIndexTranslator
getAlignmentArea() - Method in class info.bioinfweb.libralign.actions.AlignmentActionProvider: Returns the view this instance is associated with.
getAlignmentAreas() - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer: Use the returned instance to change the alignment areas contained in this container.
getAlignmentID() - Method in class info.bioinfweb.libralign.model.io.DataModelKey
getAlignmentModel() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns the alignment model providing the data displayed by this area.
getAlignmentModelReader() - Method in class info.bioinfweb.libralign.model.io.AlignmentDataReader: Returns the alignment event reader used create to and read alignment model instances
getAlignmentRelation(int) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel
getAlignmentRelation(int) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel
getAnnotation(String, int) - Method in class info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider
getAnnotation(String, int) - Method in interface info.bioinfweb.libralign.pherogram.provider.PherogramProvider: Returns the specified annotation (e.g.
getAnnotation(String, int) - Method in class info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider
getAnnotationFont() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Returns the font used to print the base call quality scores and probability values.
getApproxMaxSequenceLength() - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel: Returns the maximum sequence length that is currently known.
getArea() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubAreaInfo
getAreaByPaintY(double) - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea: Returns the child component containing the specified y-coordinate.
getAreaInfoByPaintY(double) - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea: Returns the child component containing the specified y-coordinate and its top most y-coordinate in an instance of AlignmentSubAreaInfo.
getAsList() - Method in class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter
getAvailableHeight() - Method in class info.bioinfweb.libralign.multiplealignments.SwingMultipleAlignmentsContainer
getAvailableHeight() - Method in class info.bioinfweb.libralign.multiplealignments.SWTMultipleAlignmentsContainer
getAvailableHeight() - Method in interface info.bioinfweb.libralign.multiplealignments.ToolkitSpecificMultipleAlignmentsContainer: Returns the height that is currently available to be distributed among all contained alignment areas.
getBackgroundColor() - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
getBackgroundColor() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Returns the background color for displaying the central part of the pherogram (the positions that have not been cut off).
getBackgroundColorMap() - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
getBaseCall(int) - Method in class info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider
getBaseCall(int) - Method in interface info.bioinfweb.libralign.pherogram.provider.PherogramProvider: Returns a base from the DNA sequence associated with the stored trace.
getBaseCall(int) - Method in class info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider
getBaseCallFont() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Returns the font used to print the characters of the base call sequence.
getBaseCallIndex() - Method in class info.bioinfweb.libralign.pherogram.model.ShiftChange
getBaseCallLineColor() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Returns the 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.
getBaseCallPosition(int) - Method in class info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider
getBaseCallPosition(int) - Method in interface info.bioinfweb.libralign.pherogram.provider.PherogramProvider: Returns the position in the trace where the base at the specified index was observed.
getBaseCallPosition(int) - Method in class info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider
getBefore() - Method in class info.bioinfweb.libralign.model.utils.indextranslation.IndexRelation: This value is only needed if IndexRelation.getCorresponding() returns IndexRelation.GAP or IndexRelation.OUT_OF_RANGE.
getBeforeValidIndex() - Method in class info.bioinfweb.libralign.model.utils.indextranslation.IndexRelation: Returns any index that is not IndexRelation.GAP or IndexRelation.OUT_OF_RANGE and first tries IndexRelation.getCorresponding() than IndexRelation.getBefore() and finally IndexRelation.getAfter().
getBeginIndex() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingTokenEdit: Returns the index in the sequence where this token edit is taking place.
getBottomAreas() - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel: Returns a list of data areas to be displayed underneath the alignment.
getByName(String) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataModel
getChangeListeners() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataModel
getChangeListeners() - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Returns all change listeners currently attached to this object.
getChangeListeners() - Method in class info.bioinfweb.libralign.model.implementations.AbstractAlignmentModel
getChangeListeners() - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
getChangeListeners() - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
getCharacterStateSetType() - Method in class info.bioinfweb.libralign.model.factory.NewAlignmentModelParameterMap: Returns the character set type the alignment model to be created shall have.
getCharSet() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetDataModelChangeEvent
getCharSetID() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetDataModelChangeEvent: Returns the ID of the affected character set used by the associated model.
getColor(String) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.AbstractTokenPainter: Default implementation that returns null.
getColor(AlignmentArea, String, int) - Method in interface info.bioinfweb.libralign.alignmentarea.tokenpainter.ColorOverlay: Determines the color to overlay the specified cell of the alignment.
getColor(String) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter: Returns the background color associated with the specified token as stored in SingleColorTokenPainter.getBackgroundColorMap().
getColor(String) - Method in interface info.bioinfweb.libralign.alignmentarea.tokenpainter.TokenPainter: Returns the color associated with the specified token.
getColor() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSet
getColumn() - Method in class info.bioinfweb.libralign.alignmentarea.selection.AlignmentCursor: Returns the column index in front of which the cursor is located.
getColumnCount(ReadWriteParameterMap) - Method in class info.bioinfweb.libralign.model.io.AlignmentModelDataAdapter: Returns the number of columns in the underlying AlignmentModel instance if all sequences have an equal length.
getCompletedModels() - Method in class info.bioinfweb.libralign.model.io.AbstractDataModelEventReader
getCompletedModels() - Method in class info.bioinfweb.libralign.model.io.AlignmentModelEventReader: Returns the list of alignment models that have been completely read from the underlying JPhyloIO event stream until now.
getCompletedModels() - Method in interface info.bioinfweb.libralign.model.io.DataModelEventReader: Returns the model objects that have been read from the underlying JPhyloIO event stream until now.
getCompoundAt(int) - Method in class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter
getCompoundSet() - Method in class info.bioinfweb.libralign.model.adapters.BioJava3SequenceAdapter: Returns the compound set to be used for the translation.
getCompoundSet() - Method in class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter
getCompoundSet() - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet: Returns the BioJava compound set that is viewed by this instance.
getConsensusToken(int) - Method in class info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea: Returns the string representation of the most frequent token at the specified column.
getContainer() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns the container this object is contained in.
getContainer() - Method in class info.bioinfweb.libralign.alignmentarea.SWTScrollableResizeListener
getContentArea() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns the alignment content area used internally by this instance.
getCorresponding() - Method in class info.bioinfweb.libralign.model.utils.indextranslation.IndexRelation: Returns the position corresponding to the one specified to obtain this result object.
getCount(ReadWriteParameterMap) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataAdapter
getCount(ReadWriteParameterMap) - Method in class info.bioinfweb.libralign.model.io.TokenSetAdapter
getCurrentAlignmentID() - Method in class info.bioinfweb.libralign.model.io.AlignmentModelEventReader: Returns the JPhyloIO ID of the alignment model that is currently read and returned by AlignmentModelEventReader.getCurrentModel().
getCurrentConcatenatedModel() - Method in class info.bioinfweb.libralign.model.io.AlignmentModelEventReader: Returns the concatenated model that is currently read by this instance.
getCurrentID() - Method in class info.bioinfweb.libralign.model.implementations.AbstractSequenceIDIterator: The ID that has been returned by this iterator by the last call of AbstractSequenceIDIterator.next().
getCurrentModel() - Method in class info.bioinfweb.libralign.model.io.AlignmentModelEventReader: Returns the alignment model that is currently read.
getCursorColor() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings
getCursorColumn() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Returns the current column position of the alignment cursor.
getCursorHeight() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Returns the current height of the alignment cursor (which is equal to the height of a possible selection).
getCursorLineWidth() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings
getCursorRectangle() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea: Returns the rectangle in the paint coordinate system of scrolled area displaying the sequences, that contains all cells currently occupied by the alignment cursor.
getCursorRow() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Returns the topmost row included in the current alignment cursor.
getCutBackgroundColor() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Returns the background color for displaying the parts of the pherogram on the left and right end that have been cut off by the user.
getCutBaseCallLineColor() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Returns the 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.
getDataAreaList() - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
getDataAreas() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns the data area model used by this instance containing all data areas attached to the displayed alignment.
getDefaultBackgroundColor() - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
getDefaultFactory() - Method in class info.bioinfweb.libralign.model.io.AlignmentModelEventReader: Returns the alignment model factory that is used to create new model instances for character state (token) set types which are not defined in the factory map.
getDefaultToken() - Method in class info.bioinfweb.libralign.model.factory.AbstractAlignmentModelFactory: Returns the default token to be used if invalid token representations are passed to AbstractAlignmentModelFactory.createToken(AlignmentModel, String).
getDefaultTokenMap() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterList: Returns the default token painter map that is used to paint tokens from the alignment model if no respective painter is defined in the list.
getDefinedTokens() - Method in class info.bioinfweb.libralign.model.factory.NewAlignmentModelParameterMap: Returns a list of defined Tokens (e.g.
getDimension() - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection: Determines of this selection represent columns or rows.
getEditableTokenWidth() - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea: Returns the width of the token in the editable sequence at #getFirstSeqPos(), considering the current zoom factor.
getEditFactory() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel: Returns the edit factory used by this instance to create new edit objects, if one was passed to when this instance was created.
getEditSettings() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns the edit setting object used by this instance.
getEditSettings() - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer: Returns the edit settings that are shared among all contained alignment areas.
getFactory() - Method in class info.bioinfweb.libralign.model.io.AbstractDataModelEventReader
getFactory() - Method in interface info.bioinfweb.libralign.model.io.DataModelEventReader: Returns the factory used to create new data models in this instance.
getFactoryMap() - Method in class info.bioinfweb.libralign.model.io.AlignmentModelEventReader: Returns the map of alignment model factories for different character state (token) set types.
getFirstColumn() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentPaintEvent: Returns the index of the left most alignment column in the area to be (at least partly) painted.
getFirstColumn() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Returns the index of the first column that is contained in the selection.
getFirstCompletedModel(DataModelKey) - Method in class info.bioinfweb.libralign.model.io.AbstractDataModelEventReader
getFirstIndex() - Method in class info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea: Returns the index that will be displayed for the first column of the alignment area.
getFirstPos() - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection: Returns the first column (or row) that is contained in the selection.
getFirstPos() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetColumnChangeEvent
getFirstRow() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Returns the index of the the first row that is contained in the selection.
getFirstSeqPos() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel: Returns the position in the sequence this pherogram is attached to where the output of the visible part of the pherogram starts.
getFirstTracePosition(PherogramProvider, int) - Static method in class info.bioinfweb.libralign.pherogram.PherogramUtils: Returns the index of the first trace value in the area of a trace curve belonging the base call with the specified index.
getFocusedAlignmentArea() - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer: Returns the alignment area contained in this component, that currently has the focus.
getFocusedAlignmentArea() - Method in class info.bioinfweb.libralign.multiplealignments.SwingMultipleAlignmentsContainer
getFocusedAlignmentArea() - Method in class info.bioinfweb.libralign.multiplealignments.SWTMultipleAlignmentsContainer
getFocusedAlignmentArea() - Method in interface info.bioinfweb.libralign.multiplealignments.ToolkitSpecificMultipleAlignmentsContainer: Returns the alignment area contained in this component, that currently has the focus.
getFont() - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea: Returns the font used to display the text in this data area.
getFontColor() - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
getFontName() - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
getFontStyle() - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
getFormats() - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea
getFormats() - Method in interface info.bioinfweb.libralign.pherogram.PherogramComponent: Returns the format object that is used to paint the displayed pherogram.
getFormats() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView
getGapCount() - Method in class info.bioinfweb.libralign.pherogram.distortion.GapPattern: Returns the number of gaps contained in this pattern
getGapPattern(int) - Method in interface info.bioinfweb.libralign.pherogram.distortion.PherogramDistortion: A description of gaps in the pherogram in the area surrounding the specified base call.
getGapPattern(int) - Method in class info.bioinfweb.libralign.pherogram.distortion.ScaledPherogramDistortion
getGapPattern(int) - Method in class info.bioinfweb.libralign.pherogram.distortion.UnscaledPherogramDistortion
getGapToken() - Method in class info.bioinfweb.libralign.model.tokenset.AbstractTokenSet
getGapToken() - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet: Returns the compound associated with AbstractTokenSet#DEFAULT_GAP_REPRESENTATION from the underlying BioJava token set using CompoundSet.getCompoundForString(String).
getGapToken() - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
getGapToken() - Method in interface info.bioinfweb.libralign.model.tokenset.TokenSet: Returns the default object that represents a gap in this token set.
getGapTokens() - Method in class info.bioinfweb.libralign.model.utils.indextranslation.AbstractIndexTranslator
getGapTokens() - Method in interface info.bioinfweb.libralign.model.utils.indextranslation.IndexTranslator: Returns the set of gap tokens used by this instance.
getGlobalMaxLengthBeforeStart() - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel: Returns maximum space left of the alignment calculated over all alignment areas in the parent MultipleAlignmentsContainer of the alignment area using this model.
getGlobalMaxNeededWidth() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns the maximum needed width to display all alignment columns with the according token painters and the current zoom factor and the space before and after the alignment possibly occupied by data areas calculated over all alignments contained in the parent MultipleAlignmentsContainer.
getGlobalMaxNeededWidth() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea: Returns the maximum needed width to label the alignment calculated over all alignments contained in the parent MultipleAlignmentsContainer.
getGlobalMaxSequenceLength() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: If this area is part of an alignment area that is contained in a MultipleAlignmentsContainer than this methods calculates the maximum length of all sequences in all alignment areas contained in this container.
getHeadingBackgroundColor() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Returns the background color for the heading of the pherogram (displaying the base call sequence and nucleotide indices).
getHeadingView() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView
getHeadingView() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramView: Returns the contained heading view.
getHeight() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea: Returns the height in pixels considering the current zoom factor this component needs.
getHeight() - Method in class info.bioinfweb.libralign.alignmentarea.content.SequenceArea
getHeight() - Method in class info.bioinfweb.libralign.alignmentarea.selection.AlignmentCursor: Returns the height in rows if the cursor.
getHeight() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea
getHeight() - Method in class info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea
getHeight() - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
getHeight() - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea
getHeight() - Method in class info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea
getHorizontalScale(int) - Method in interface info.bioinfweb.libralign.pherogram.distortion.PherogramDistortion: Returns the scale (pixels per trace value) in the area surrounding the specified base call.
getHorizontalScale(int) - Method in class info.bioinfweb.libralign.pherogram.distortion.ScaledPherogramDistortion
getHorizontalScale(int) - Method in class info.bioinfweb.libralign.pherogram.distortion.UnscaledPherogramDistortion
getHorizontalScale() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView
getHorizontalScrollbarHeight() - Method in class info.bioinfweb.libralign.alignmentarea.AbstractSWTAlignmentArea: Returns the height of the horizontal content scroll bar.
getID() - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Some implementations may specify string identifying an alignment, which is then returned by this method.
getID() - Method in class info.bioinfweb.libralign.model.implementations.AbstractAlignmentModel
getID() - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
getIDIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataAdapter
getIDIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.libralign.model.io.TokenSetAdapter
getIDManager() - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel
getIDPrefix() - Method in class info.bioinfweb.libralign.model.io.AlignmentModelDataAdapter: Returns the ID prefix used by this instance.
getIDPrefix() - Method in class info.bioinfweb.libralign.model.io.TokenSetAdapter
getIndependentComponent() - Method in class info.bioinfweb.libralign.alignmentarea.AbstractSWTAlignmentArea
getIndependentComponent() - Method in class info.bioinfweb.libralign.alignmentarea.content.ScrollContainerSwingAlignmentContentArea
getIndependentComponent() - Method in class info.bioinfweb.libralign.alignmentarea.content.ScrollContainerSWTAlignmentContentArea
getIndependentComponent() - Method in class info.bioinfweb.libralign.alignmentarea.DirectPaintingSWTAlignmentArea
getIndependentComponent() - Method in class info.bioinfweb.libralign.alignmentarea.DirectPaintingSWTAlignmentContentScroller
getIndependentComponent() - Method in class info.bioinfweb.libralign.alignmentarea.label.ScrollContainerSwingAlignmentLabelArea
getIndependentComponent() - Method in class info.bioinfweb.libralign.alignmentarea.label.SWTAlignmentLabelArea
getIndependentComponent() - Method in class info.bioinfweb.libralign.alignmentarea.ScrollContainerSwingAlignmentArea
getIndependentComponent() - Method in class info.bioinfweb.libralign.multiplealignments.SwingMultipleAlignmentsContainer
getIndependentComponent() - Method in class info.bioinfweb.libralign.multiplealignments.SWTMultipleAlignmentsContainer
getIndependentComponent() - Method in class info.bioinfweb.libralign.pherogram.view.SwingPhergramView
getIndependentComponent() - Method in class info.bioinfweb.libralign.pherogram.view.SWTPhergramView
getIndex() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterReplacedEvent: Returns the index in the token painter list where the specified replace happened.
getIndexFont() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Returns the font used to print the nucleotide indices.
getIndexOf(C) - Method in class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter
getInitialCapacity() - Method in class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel: Returns the default initial capacity of new list objects created by #createNewSequence(int, String, int).
getInverse() - Method in class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter
getIterator() - Method in class info.bioinfweb.libralign.model.implementations.AbstractSequenceIDIterator: Returns the underlying iterator object.
getIterator() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAlignmentRelation: Returns an iterator positioned before the next shift change entry.
getKeyMap() - Method in class info.bioinfweb.libralign.model.tokenset.AbstractTokenSet: Returns the mapping from key characters to tokens.
getLabel() - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Returns a string labeling this alignment.
getLabel() - Method in class info.bioinfweb.libralign.model.implementations.AbstractAlignmentModel
getLabel() - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
getLabel() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
getLabelArea() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns the alignment label area used internally by this instance.
getLabeledAlignmentArea() - Method in class info.bioinfweb.libralign.dataarea.DataArea: Returns the alignment area that is labeled by this data area.
getLabeledAlignmentModel() - Method in class info.bioinfweb.libralign.dataarea.DataArea: Convenience method that returns the alignment model of the labeled alignment area.
getLabeledArea() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelSubArea: Returns the alignment sub area that is labeled by this instance.
getLabeledArea() - Method in class info.bioinfweb.libralign.alignmentarea.label.SequenceLabelArea
getLabeledArea() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetNameArea
getLabelSubArea() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea: Returns the GUI component that displays the row label for this part of the alignment.
getLastColumn() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentPaintEvent: Returns the index after the right most alignment alignment column in the area to be (at least partly) painted.
getLastColumn() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Returns the index of the the last column that is contained in the selection.
getLastIndexOf(C) - Method in class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter
getLastPartModel() - Method in interface info.bioinfweb.libralign.model.concatenated.ConcatenatedAlignmentModel: Returns the right most part model contained in this alignment.
getLastPos() - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection: Returns the last column (or row) that is contained in the selection.
getLastPos() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetColumnChangeEvent
getLastRow() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Returns the index of the the last row that is contained in the selection.
getLeftCutPosition() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel: Returns the first base call index of the pherogram which has not been cut off.
getLength() - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection
getLength() - Method in class info.bioinfweb.libralign.model.adapters.AbstractSingleSequenceDataAdapter: Returns the length of this character sequence.
getLength() - Method in interface info.bioinfweb.libralign.model.adapters.SingleSequenceDataAdapter: Returns the number of tokens (sequence elements) that make up this view.
getLengthAfterEnd() - Method in class info.bioinfweb.libralign.dataarea.DataArea: Returns the length in pixels considering the current zoom factor this component needs to display data right of the last alignment column.
getLengthAfterEnd() - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea
getLengthBeforeStart() - Method in class info.bioinfweb.libralign.dataarea.DataArea: Returns the length in pixels considering the current zoom factor this component needs to display data left of the first alignment column.
getLengthBeforeStart() - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea
getLinkedOTUID(String) - Method in class info.bioinfweb.libralign.model.io.AlignmentModelDataAdapter: Returns the ID of the JPhyloIO OTU that shall be linked with the specified sequence.
getList() - Method in class info.bioinfweb.libralign.dataarea.DataArea: Returns the list this data area is contained in.
getListType() - Method in class info.bioinfweb.libralign.dataarea.DataAreaLocation
getLoadingModels() - Method in class info.bioinfweb.libralign.model.io.AbstractDataModelEventReader
getLocalMaximumNeededAlignmentWidth() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Calculates the needed with to label the associated alignment.
getLocalMaximumNeededWidth() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea: Calculates the needed with to label the associated alignment.
getLocalMaxLengthAfterEnd() - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel: Returns maximum space right of the alignment end that is needed by any currently visible data area in any list contained in this model.
getLocalMaxLengthBeforeStart() - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel: Returns maximum space left of the alignment start that is needed by any currently visible data area in any list contained in this model.
getLocalMaxNeededWidth() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea
getLocation() - Method in class info.bioinfweb.libralign.dataarea.DataAreaList: Returns the location the elements in this list have in the containing AlignmentArea.
getLocationInParent() - Method in class info.bioinfweb.libralign.pherogram.view.SwingPhergramView
getMainReader() - Method in class info.bioinfweb.libralign.model.io.AbstractDataModelEventReader
getMainReader() - Method in interface info.bioinfweb.libralign.model.io.DataModelEventReader: Returns the instance of the main reader (for reading alignment and data models) which uses this data model reader.
getMaximumSize() - Method in class info.bioinfweb.libralign.alignmentarea.ScrollContainerSwingAlignmentArea
getMaximumSize() - Method in class info.bioinfweb.libralign.pherogram.view.SwingPhergramView
getMaxLengthAfterEnd() - Method in class info.bioinfweb.libralign.dataarea.DataAreaList: Returns maximum space right of the alignment end that is needed by any currently visible data area in this list.
getMaxLengthBeforeStart() - Method in class info.bioinfweb.libralign.dataarea.DataAreaList: Returns maximum space left of the alignment start that is needed by any currently visible data area in this list.
getMaxSequenceLength() - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Returns the length of the longest sequence in the alignment which is equivalent to the length of the alignment.
getMaxSequenceLength() - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel: Iterates over all sequence IDs and determines the maximum sequence length by calling #getSequenceLength(int) for each ID.
getMaxSequenceLength() - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator: This default implementation delegates to the underlying model.
getMaxSequenceLength() - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
getMaxSequenceLength() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
getMaxTokenCount() - Method in class info.bioinfweb.libralign.model.implementations.PackedAlignmentModel: Returns the maximum number of different tokens that can be modeled by this packed list.
getMaxTraceValue(char) - Method in class info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider
getMaxTraceValue(char) - Method in interface info.bioinfweb.libralign.pherogram.provider.PherogramProvider: Returns the maximum trace value the specified curve contains.
getMaxTraceValue(char) - Method in class info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider
getMeaning() - Method in class info.bioinfweb.libralign.model.factory.TokenDefinition
getMeaning(T) - Method in class info.bioinfweb.libralign.model.tokenset.AbstractTokenSet
getMeaning(C) - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet
getMeaning(ContinuousToken<T>) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
getMeaning() - Method in class info.bioinfweb.libralign.model.tokenset.continuous.ContinuousToken
getMeaning(T) - Method in interface info.bioinfweb.libralign.model.tokenset.TokenSet: Returns the meaning of the specified symbol.
getMeaning(TokenSet<T>, T) - Static method in class info.bioinfweb.libralign.model.tokenset.TokenSetTools: Determines the meaning of the specified token as defined by TokenSet.getMeaning(Object).
getMissingInformationToken() - Method in class info.bioinfweb.libralign.model.tokenset.AbstractTokenSet
getMissingInformationToken() - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet
getMissingInformationToken() - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
getMissingInformationToken() - Method in interface info.bioinfweb.libralign.model.tokenset.TokenSet: Returns the default object that represents an unknown position in this token set.
getModel() - Method in class info.bioinfweb.libralign.actions.AlignmentActionProvider
getModel() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea: Returns the underlying model providing character set data.
getModel() - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea
getModel() - Method in class info.bioinfweb.libralign.model.implementations.AbstractSequenceIDIterator: Returns the sequence data provider that returned this iterator.
getModel() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.LibrAlignSwingAlignmentEdit: Returns the data provider instance that created and uses this object.
getModel() - Method in class info.bioinfweb.libralign.model.utils.indextranslation.AbstractIndexTranslator
getModel() - Method in interface info.bioinfweb.libralign.model.utils.indextranslation.IndexTranslator: Returns the alignment model this instance works on.
getModel() - Method in interface info.bioinfweb.libralign.pherogram.PherogramComponent: Returns the model providing the base call sequence, the trace curves and the cut positions.
getModel() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView
getModelByJPhyloIOID(String) - Method in class info.bioinfweb.libralign.model.io.AlignmentModelEventReader: Returns the alignment model associated with the specified JPhyloIO ID.
getModels() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSet: Returns a set of model classes that contain this character set.
getName() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSet
getNeededHeight(int) - Method in class info.bioinfweb.libralign.multiplealignments.SwingMultipleAlignmentsContainer
getNeededHeight(int) - Method in class info.bioinfweb.libralign.multiplealignments.SWTMultipleAlignmentsContainer
getNeededHeight(int) - Method in interface info.bioinfweb.libralign.multiplealignments.ToolkitSpecificMultipleAlignmentsContainer: Return the height needed for the specified alignment to be displayed without scroll bars.
getNeededWidth() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelSubArea: Returns the width this component needs to display its label information.
getNeededWidth() - Method in class info.bioinfweb.libralign.alignmentarea.label.DefaultLabelSubArea: Always returns 0 since this default implementation does not display anything.
getNeededWidth() - Method in class info.bioinfweb.libralign.alignmentarea.label.TextLabelArea
getNeededWidth() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetNameArea
getNewBaseCallIndex() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramCutPositionChangeEvent: Returns the current cut position.
getNewEditableIndex() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramCutPositionChangeEvent: The relation to the index of the right cut position in the editable sequence associated with the # displaying PherogramArea.
getNewName() - Method in class info.bioinfweb.libralign.model.events.SequenceRenamedEvent
getNewPainter() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterReplacedEvent: Returns the painter that replaced the previous one
getNewPosition() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramFirstSeqPosChangeEvent: Returns the current position in the editable sequence where the pherogram is anchored.
getNewProvider() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramProviderChangeEvent: Returns the pherogram provider after before this event occurred.
getNewSequenceID() - Method in interface info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingAddSequenceEdit: The ID the newly inserted sequence was assigned to.
getNewSequenceID() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingConcreteAddSequenceEdit
getNewZoomX() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.ZoomChangeEvent
getNewZoomY() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.ZoomChangeEvent
getNucleotideColor(char) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Returns the color associated with the specified token representation.
getObjectStartEvent(ReadWriteParameterMap, String) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataAdapter
getObjectStartEvent(ReadWriteParameterMap, String) - Method in class info.bioinfweb.libralign.model.io.TokenSetAdapter
getOffset() - Method in class info.bioinfweb.libralign.model.adapters.AbstractSingleSequenceDataAdapter
getOffset() - Method in interface info.bioinfweb.libralign.model.adapters.SingleSequenceDataAdapter: Returns the index the first character in this sequence corresponds to in the original sequence in the underlying sequence data provider.
getOldBaseCallIndex() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramCutPositionChangeEvent: Returns the previous cut position.
getOldEditableIndex() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramCutPositionChangeEvent: The relation to the index of the left cut position in the editable sequence associated with the displaying PherogramArea.
getOldPosition() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramFirstSeqPosChangeEvent: Returns the previous position in the editable sequence where the pherogram was anchored.
getOldProvider() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramProviderChangeEvent: Returns the pherogram provider used before this event occurred.
getOldTokens() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingSetTokensEdit: Returns a list of the tokens that are replaced when this edit is executed.
getOldZoomX() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.ZoomChangeEvent
getOldZoomY() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.ZoomChangeEvent
getOperationName() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingInsertTokensEdit
getOperationName() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingRemoveTokensEdit
getOperationName() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingSetTokensEdit
getOperationName() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingTokenEdit
getOrderType() - Method in class info.bioinfweb.libralign.alignmentarea.order.SequenceOrder
getOverlays() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns an editable list of color overlays to be used when painting the contents of this area.
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.content.AbstractAlignmentSubAreaComponent: Returns the alignment subarea that is displayed using this component.
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea: Returns the alignment content area that displays this data area.
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.content.CursorSelectionInputListener
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.content.InputEventForwarder
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.content.SequenceAreaMap
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea: Returns the alignment area that uses this instance.
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelSubArea: Returns the owning GUI component displaying all labels.
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.order.SequenceOrder
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings: Returns the alignment area using this instance.
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterList: Returns the paint settings object containing this instance.
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.selection.AlignmentCursor
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection
getOwner() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Returns the alignment content area that uses this selection object.
getOwner() - Method in class info.bioinfweb.libralign.dataarea.DataAreaList
getOwner() - Method in class info.bioinfweb.libralign.dataarea.DataAreaSequenceChangeListener: Returns the the data area model using this instance.
getOwner() - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel: Returns the alignment content area that uses this instance.
getOwner() - Method in class info.bioinfweb.libralign.multiplealignments.AlignmentAreaList
getOwner() - Method in class info.bioinfweb.libralign.multiplealignments.HorizontalScrollingSynchronizer
getOwner() - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsModelEventForwarder
getOwner() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel: The pherogram area associated with this model.
getOwner() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Returns the owning trace curve view or pherogram data area using this instance.
getPaintCenterX(int) - Method in interface info.bioinfweb.libralign.pherogram.distortion.PherogramDistortion: Returns the x coordinate relative to the left border of the pherogram where the base call with the specified index shall be painted.
getPaintCenterX(int) - Method in class info.bioinfweb.libralign.pherogram.distortion.ScaledPherogramDistortion
getPaintCenterX(int) - Method in class info.bioinfweb.libralign.pherogram.distortion.UnscaledPherogramDistortion
getPainter(CharacterStateSetType) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterMap: Returns the best matching painter to specified token type.
getPainter() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView
getPaintHeight() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Calculates the height of all sequences and all visible data areas together.
getPaintSettings() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns the paint settings object associated with this instance.
getPaintSettingsSynchronizer() - Method in class info.bioinfweb.libralign.multiplealignments.AlignmentAreaList
getPaintSettingsToSynchronize() - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer: Returns a set of property names that are synchronized between the paint setting objects of the alignment areas contained in this container.
getPaintStartX(int) - Method in interface info.bioinfweb.libralign.pherogram.distortion.PherogramDistortion: Returns the x coordinate relative to the left border of the pherogram where the first trace position of the area associated with the specified base call index shall be painted.
getPaintStartX(int) - Method in class info.bioinfweb.libralign.pherogram.distortion.ScaledPherogramDistortion
getPaintStartX(int) - Method in class info.bioinfweb.libralign.pherogram.distortion.UnscaledPherogramDistortion
getParentAlignmentArea() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentPaintEvent: Returns the alignment area that contains the component that triggered this event.
getPartModel(int) - Method in interface info.bioinfweb.libralign.model.concatenated.ConcatenatedAlignmentModel: Returns the part model at the specified position.
getPartModelCount() - Method in interface info.bioinfweb.libralign.model.concatenated.ConcatenatedAlignmentModel: Returns the number of part models contained in this alignment.
getPherogramProvider() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel
getPreferredHeight() - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
getPreferredHeight() - Method in interface info.bioinfweb.libralign.alignmentarea.tokenpainter.TokenPainter: Returns the optimal height this painter would need to paint a supported token in original size (100 % zoom).
getPreferredScrollableViewportSize() - Method in class info.bioinfweb.libralign.alignmentarea.rowsarea.SwingAlignmentRowsArea
getPreferredSize() - Method in class info.bioinfweb.libralign.pherogram.view.SwingPhergramView
getPreferredWidth() - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter
getPreferredWidth() - Method in interface info.bioinfweb.libralign.alignmentarea.tokenpainter.TokenPainter: Returns the optimal width this painter would need to paint a supported token in original size (100 % zoom).
getPresentationName() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingConcreteAddSequenceEdit
getPresentationName() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingRemoveSequenceEdit
getPresentationName() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingRenameSequenceEdit
getPresentationName() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingTokenEdit
getPreviousColor() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetColorChangeEvent
getPreviousName() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetRenamedEvent
getPreviousName() - Method in class info.bioinfweb.libralign.model.events.SequenceRenamedEvent
getPreviousPainter() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterReplacedEvent: Returns the painter that has been replaced.
getPreviousWorkingMode() - Method in class info.bioinfweb.libralign.editsettings.EditSettingsChangeEvent: Returns the working mode that the source object had before this event happened.
getProbabilityColor() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Returns the font color for displaying probability values.
getQuality(char, int) - Method in class info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider
getQuality(char, int) - Method in interface info.bioinfweb.libralign.pherogram.provider.PherogramProvider: Returns the quality score associated with the specified nucleotide.
getQuality(char, int) - Method in class info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider
getQualityOutputType() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats: Determines the way quality scores shall be displayed.
getRelatedTokenPainter() - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea
getReplacedCharSet() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetChangeEvent: Returns a reference to the character set that has been replaced by the inserted set.
getRepresentation() - Method in exception info.bioinfweb.libralign.model.adapters.InvalidUnderlyingTokenException
getRepresentation() - Method in class info.bioinfweb.libralign.model.factory.TokenDefinition
getRightCutPosition() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel: Returns the first base call index of the pherogram that has been cut off (so that the length of the visible area of the pherogram can be calculated as getRightCutPosition() - PherogramComponentModel.getLeftCutPosition()).
getRow() - Method in class info.bioinfweb.libralign.alignmentarea.selection.AlignmentCursor: Returns the row index in front of which the cursor is located.
getSashForm() - Method in class info.bioinfweb.libralign.multiplealignments.SWTMultipleAlignmentsContainer
getScrollable() - Method in class info.bioinfweb.libralign.alignmentarea.SWTScrollableResizeListener
getScrollableBlockIncrement(Rectangle, int, int) - Method in class info.bioinfweb.libralign.alignmentarea.rowsarea.SwingAlignmentRowsArea
getScrollableTracksViewportHeight() - Method in class info.bioinfweb.libralign.alignmentarea.rowsarea.SwingAlignmentRowsArea
getScrollableTracksViewportWidth() - Method in class info.bioinfweb.libralign.alignmentarea.rowsarea.SwingAlignmentRowsArea
getScrollableUnitIncrement(Rectangle, int, int) - Method in class info.bioinfweb.libralign.alignmentarea.rowsarea.SwingAlignmentRowsArea
getScrolledComposite() - Method in class info.bioinfweb.libralign.alignmentarea.ScrollContainerSWTAlignmentArea
getScrollPane() - Method in class info.bioinfweb.libralign.alignmentarea.ScrollContainerSwingAlignmentArea
getSelectedIndex() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea
getSelection() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns the selection model used by this instance.
getSelectionColor() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings
getSelectionListeners() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea
getSequence(String) - Method in class info.bioinfweb.libralign.model.adapters.BioJava3SequenceAdapter: Returns an implementation of Sequence that acts as a view to the sequence with the specified ID in the underlying data source.
getSequence(String) - Method in class info.bioinfweb.libralign.model.adapters.CharSequenceAdapter: Returns an implementation of SingleCharSequenceAdapter<T> that acts as a view to the sequence with the specified ID.
getSequence(String) - Method in class info.bioinfweb.libralign.model.adapters.StringAdapter: Returns a string copy of the sequence with the specified ID in the underlying data source.
getSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel
getSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUnmodifyableAlignmentModel
getSequence(String) - Method in interface info.bioinfweb.libralign.model.SequenceAccess: Returns the sequence object with the specified ID.
getSequenceAreaByID(String) - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea: Returns the SequenceArea inside this area that displays the sequence with the specified ID.
getSequenceAreaByRow(int) - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea: Returns the SequenceArea inside this area that displays the sequence in the specified row.
getSequenceAreaMap() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea
getSequenceAreas(String) - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel: Returns a list of data areas to be displayed underneath the specified sequence.
getSequenceAsString() - Method in class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter
getSequenceCount() - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Returns the number of sequences in the underlying data source.
getSequenceCount() - Method in class info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel
getSequenceCount() - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator
getSequenceCount() - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
getSequenceCount() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
getSequenceCount(ReadWriteParameterMap) - Method in class info.bioinfweb.libralign.model.io.AlignmentModelDataAdapter
getSequenceData(String) - Method in class info.bioinfweb.libralign.model.utils.indextranslation.AbstractIndexTranslator
getSequenceDataChangeListener() - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel: Returns the change listener that forwards events from the associated AlignmentModel to all data areas contained in this model.
getSequenceID() - Method in class info.bioinfweb.libralign.alignmentarea.content.SequenceArea: Returns the unique identifier of the the sequence displayed by this area.
getSequenceID() - Method in class info.bioinfweb.libralign.dataarea.DataAreaLocation
getSequenceID() - Method in class info.bioinfweb.libralign.model.adapters.AbstractSingleSequenceDataAdapter
getSequenceID() - Method in interface info.bioinfweb.libralign.model.adapters.SingleSequenceDataAdapter: The ID of the viewed sequence in the underlying sequence data provider.
getSequenceID() - Method in class info.bioinfweb.libralign.model.events.AlignmentModelChangeEvent: Returns the unique ID of the affected sequence
getSequenceID() - Method in exception info.bioinfweb.libralign.model.exception.SequenceNotFoundException: Returns the sequence ID that was not found in the specified model.
getSequenceID() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingSequenceEdit: Returns the sequence ID this edit deals with.
getSequenceID() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingTokenEdit: Returns the sequence ID this edit deals with.
getSequenceID() - Method in class info.bioinfweb.libralign.model.io.DataModelKey
getSequenceIDIterator(ReadWriteParameterMap) - Method in class info.bioinfweb.libralign.model.io.AlignmentModelDataAdapter
getSequenceLength(String) - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Returns the length of the specified sequence.
getSequenceLength(String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel
getSequenceLength(String) - Method in class info.bioinfweb.libralign.model.implementations.BioJava3SequenceAlignmentModel
getSequenceLength(String) - Method in class info.bioinfweb.libralign.model.implementations.CharSequenceAlignmentModel
getSequenceLength(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
getSequenceLength(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
getSequenceLength(String) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
getSequenceLength(ReadWriteParameterMap, String) - Method in class info.bioinfweb.libralign.model.io.AlignmentModelDataAdapter
getSequenceLength() - Method in class info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider
getSequenceLength() - Method in interface info.bioinfweb.libralign.pherogram.provider.PherogramProvider: Returns the length of the sequence associated with the stored trace.
getSequenceLength() - Method in class info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider
getSequenceMap() - Method in class info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel: Returns the underlying map object used to assign sequences to their IDs.
getSequenceOrder() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns the sequence order object the determines the order in which the sequences of the associated alignment model are displayed in this instance.
getSequenceOrder() - Method in class info.bioinfweb.libralign.model.implementations.AbstractMapBasedAlignmentModel: Returns the list object used to determine the order of the sequences.
getSequenceStartEvent(ReadWriteParameterMap, String) - Method in class info.bioinfweb.libralign.model.io.AlignmentModelDataAdapter
getSharedIDManager() - Method in class info.bioinfweb.libralign.model.factory.AbstractAlignmentModelFactory: Returns the sequence ID manager that is shared among all model instances created by this factory.
getShiftChange() - Method in class info.bioinfweb.libralign.pherogram.model.ShiftChange
getShiftChangeCount() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel: Returns the number of shift changes that are currently contained in this model.
getSize() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns the size of the underlying toolkit specific component.
getSize() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea
getSize() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea: Returns the size of the component depending on the return values of #getLength(), AlignmentSubArea.getHeight() and the maximum length before the first alignment position in the associated alignment area.
getSize() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea
getSize() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelSubArea
getSize() - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer
getSize() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramHeadingView
getSize() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView
getSize() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramView
getSource() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettingsEvent
getSource() - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEvent: Returns the model object that contains the list where the change occurred.
getSource() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetDataModelChangeEvent
getSource() - Method in class info.bioinfweb.libralign.editsettings.EditSettingsChangeEvent
getSource() - Method in class info.bioinfweb.libralign.model.events.AlignmentModelChangeEvent: Returns the data provider where the change took place.
getSource() - Method in exception info.bioinfweb.libralign.model.exception.AlignmentModelException: Returns the instance of AlignmentModel that threw this exception.
getSource() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramModelChangeEvent
getStartColumn() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Returns the column where the current selection was started.
getStartEvent(ReadWriteParameterMap) - Method in class info.bioinfweb.libralign.model.io.AlignmentModelDataAdapter
getStartIndex() - Method in class info.bioinfweb.libralign.model.events.TokenChangeEvent: Returns the (former) index of the first affected token.
getStartPos() - Method in class info.bioinfweb.libralign.alignmentarea.selection.OneDimensionalSelection: Returns the position where the current selection process started.
getStartRow() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Returns the row where the current selection was started.
getSubSequence(String, int, int) - Method in class info.bioinfweb.libralign.model.adapters.BioJava3SequenceAdapter: Returns an implementation of Sequence that acts as a view to a subsequence of the sequence with the specified ID in the underlying data source.
getSubSequence(String, int, int) - Method in class info.bioinfweb.libralign.model.adapters.CharSequenceAdapter: Returns an implementation of SingleCharSequenceAdapter<T> that acts as a view to a subsequence of the sequence with the specified ID.
getSubSequence(String, int, int) - Method in interface info.bioinfweb.libralign.model.adapters.SequenceDataAdapter: Returns a view or copy of a subsequence in the underlying data source.
getSubSequence(Integer, Integer) - Method in class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter
getSubSequence(String, int, int) - Method in class info.bioinfweb.libralign.model.adapters.StringAdapter: Returns a string copy of a subsequence of the sequence with the specified ID in the underlying data source.
getSwingComponent() - Method in class info.bioinfweb.libralign.alignmentarea.ScrollContainerSwingAlignmentArea
getSwingComponentClassName(Object...) - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns the name of a toolkit specific Swing component displaying the contents of this instance.
getSwingComponentClassName(Object...) - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea
getSwingComponentClassName(Object...) - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea
getSwingComponentClassName(Object...) - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer
getSwingComponentClassName(Object...) - Method in class info.bioinfweb.libralign.pherogram.view.PherogramView
getSWTComponentClassName(Object...) - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea: Returns the name of a toolkit specific SWT component displaying the contents of this instance.
getSWTComponentClassName(Object...) - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea
getSWTComponentClassName(Object...) - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea
getSWTComponentClassName(Object...) - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer
getSWTComponentClassName(Object...) - Method in class info.bioinfweb.libralign.pherogram.view.PherogramView
getSWTComponentConstructorParameters(Object...) - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer
getSymbolType(T) - Method in class info.bioinfweb.libralign.model.tokenset.AbstractTokenSet: This default implementation returns CharacterSymbolType.UNCERTAIN for all missing information tokens.
getSymbolType(C) - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet
getSymbolType(ContinuousToken<T>) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
getSymbolType(T) - Method in interface info.bioinfweb.libralign.model.tokenset.TokenSet: Returns the type of the specified token (symbol).
getSymbolType(TokenSet<T>, T) - Static method in class info.bioinfweb.libralign.model.tokenset.TokenSetTools: Returns CharacterSymbolType.UNCERTAIN for all missing information tokens.
getTargetToolkit() - Method in class info.bioinfweb.libralign.pherogram.view.SwingPhergramView
getText() - Method in class info.bioinfweb.libralign.alignmentarea.label.SequenceLabelArea
getText() - Method in class info.bioinfweb.libralign.alignmentarea.label.TextLabelArea
getText() - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
getTextColor() - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea
getToken() - Method in exception info.bioinfweb.libralign.model.adapters.InvalidUnderlyingTokenException
getToken() - Method in exception info.bioinfweb.libralign.model.exception.InvalidTokenException: Returns the invalid token that caused this exception.
getTokenAt(String, int) - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Returns the token at the specified position.
getTokenAt(String, int) - Method in class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel
getTokenAt(String, int) - Method in class info.bioinfweb.libralign.model.implementations.BioJava3SequenceAlignmentModel
getTokenAt(String, int) - Method in class info.bioinfweb.libralign.model.implementations.CharSequenceAlignmentModel
getTokenAt(String, int) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
getTokenAt(String, int) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
getTokenAt(String, int) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
getTokenHeight() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings: Returns the height of tokens displayed in this alignment recognizing the current value of PaintSettings.getZoomY().
getTokenHeightFont() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings: Returns a sans serif plain font object with the size according to the token height in the current zoom factor.
getTokenPainterList() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings: Returns the list of token painters to be used for the output of the data from the alignment model.
getTokens() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingTokenEdit: Returns the list of tokens this edit deals with.
getTokenSet() - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Returns the token set which is supported by the implementation.
getTokenSet() - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel
getTokenSet() - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator
getTokenSet() - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
getTokenSet() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
getTokenSet() - Method in class info.bioinfweb.libralign.model.io.TokenSetAdapter
getTokenSets(ReadWriteParameterMap) - Method in class info.bioinfweb.libralign.model.io.AlignmentModelDataAdapter
getTokenWidth(int) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings: Returns the width of the column with the specified index.
getToolkitComponent() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea
getToolkitComponent() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea
getToolkitComponent() - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea
getToolkitComponent() - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer
getToolkitSize() - Method in class info.bioinfweb.libralign.pherogram.view.SwingPhergramView
getTopAreas() - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel: Returns a list of data areas to be displayed on the top of the alignment.
getTraceCurveView() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramHeadingView
getTraceCurveView() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramView: Returns the contained trace curve view.
getTraceLength() - Method in class info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider
getTraceLength() - Method in interface info.bioinfweb.libralign.pherogram.provider.PherogramProvider: Returns the length of the stored trace.
getTraceLength() - Method in class info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider
getTraceValue(char, int) - Method in class info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider
getTraceValue(char, int) - Method in interface info.bioinfweb.libralign.pherogram.provider.PherogramProvider: Returns the y value of the specified trace curve at the specified position.
getTraceValue(char, int) - Method in class info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider
getType() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Returns the currently used selection pattern.
getType() - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEvent: Returns the type of change that happened.
getType() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetChangeEvent
getType() - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.events.CharSetColumnChangeEvent
getType() - Method in class info.bioinfweb.libralign.model.events.SequenceChangeEvent
getType() - Method in class info.bioinfweb.libralign.model.tokenset.AbstractTokenSet
getType() - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet
getType() - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
getType() - Method in interface info.bioinfweb.libralign.model.tokenset.TokenSet: Determines the type of tokens that are defined by this instance.
getUnalignedIndex(String, int) - Method in class info.bioinfweb.libralign.model.utils.indextranslation.AbstractIndexTranslator
getUnalignedIndex(String, int) - Method in interface info.bioinfweb.libralign.model.utils.indextranslation.IndexTranslator: Returns the index of the sequence token at the specified alignment column.
getUnalignedIndex(String, int) - Method in class info.bioinfweb.libralign.model.utils.indextranslation.RandomAccessIndexTranslator
getUnalignedLength(String) - Method in interface info.bioinfweb.libralign.model.utils.indextranslation.IndexTranslator
getUnalignedLength(String) - Method in class info.bioinfweb.libralign.model.utils.indextranslation.RandomAccessIndexTranslator
getUnderlyingList() - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
getUnderlyingModel() - Method in class info.bioinfweb.libralign.model.adapters.AbstractBasicAlignmentModelView
getUnderlyingModel() - Method in interface info.bioinfweb.libralign.model.BasicAlignmentModelView: Returns the underlying sequence data provider that provides the data accessed with this object.
getUnderlyingModel() - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator
getUnderlyingModel() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel: Returns the underlying sequence data provider used to perform the actual manipulation of the data.
getUndoManager() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel: Returns the undo manager used by this instance.
getUnknownCompound() - Method in class info.bioinfweb.libralign.model.adapters.SingleBioJava3SequenceAdapter: Returns the compound that will be inserted into the BioJava sequence if no according compound to the token in the underlying data source can be found in the specified compound set.
getValue() - Method in class info.bioinfweb.libralign.model.tokenset.continuous.ContinuousToken
getVerticalScale() - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea
getVerticalScale() - Method in interface info.bioinfweb.libralign.pherogram.PherogramComponent
getVerticalScale() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView
getVisibleAreaHeight() - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel: Calculates the sum of the heights of all visible data areas contained in this model (above, underneath and attached to any sequence).
getVisibleHeight() - Method in class info.bioinfweb.libralign.dataarea.DataAreaList: Calculates the sum of the heights of all visible data areas contained in this list.
getVisibleRectangle() - Method in class info.bioinfweb.libralign.alignmentarea.DirectPaintingSWTAlignmentArea
getVisibleSequenceAreaHeight() - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel: Calculates the sum of the heights of all visible data areas contained in this model, that are attached to any sequence.
getWidth() - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel: Returns the number of columns that are currently part of the selection.
getWidth() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView
getWorkingMode() - Method in class info.bioinfweb.libralign.editsettings.EditSettings
getWriteType() - Method in interface info.bioinfweb.libralign.model.AlignmentModel: Returns a value that specifies if whole sequences or single tokens can be edited in the underlying data source.
getWriteType() - Method in class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel
getWriteType() - Method in class info.bioinfweb.libralign.model.implementations.AbstractUnmodifyableAlignmentModel
getWriteType() - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator
getWriteType() - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView
getWriteType() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel
getY() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubAreaInfo
getZoomX() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings: Returns the vertical zoom factor in an alignment area, that e.g.
getZoomY() - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings: Returns the horizontal zoom factor in an alignment area, that e.g.
GUITools - Class in info.bioinfweb.libralign.alignmentarea: Provides tool methods for the GUI components of LibrAlign.

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