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

R

RandomAccessIndexTranslator<T> - Class in info.bioinfweb.libralign.model.utils.indextranslation

Instance of this tool class allow fast translation between aligned and unaligned indices of tokens in an AlignmentModel.

RandomAccessIndexTranslator(AlignmentModel<T>, Set<T>) - Constructor for class info.bioinfweb.libralign.model.utils.indextranslation.RandomAccessIndexTranslator

RandomAccessIndexTranslator(AlignmentModel<T>) - Constructor for class info.bioinfweb.libralign.model.utils.indextranslation.RandomAccessIndexTranslator

Creates a new instance of this class using a HashSet containing the gap token specified by the token set of model.

RandomAccessIndexTranslator.IndexTranslations - Class in info.bioinfweb.libralign.model.utils.indextranslation

readAlignments(File, ReadWriteParameterMap) - Static method in class info.bioinfweb.libralign.model.io.IOTools

Reads a set of alignments from a file into a list of alignment model instances.

readAlignments(File) - Static method in class info.bioinfweb.libralign.model.io.IOTools

Reads a set of alignments from a file into a list of alignment model instances.

readAll() - Method in class info.bioinfweb.libralign.model.io.AlignmentDataReader

Processes all events from the underlying JPhyloIO event stream.

RECALCULATE_VALUE - Static variable in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea

redistributeHeight() - Method in class info.bioinfweb.libralign.multiplealignments.MultipleAlignmentsContainer

redo() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingConcreteAddSequenceEdit

redo() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingRemoveSequenceEdit

redo() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.sequence.SwingRenameSequenceEdit

redo() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingInsertTokensEdit

redo() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingRemoveTokensEdit

redo() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingSetTokensEdit

refreshFromSource() - Method in class info.bioinfweb.libralign.alignmentarea.order.SequenceOrder

registerDocumentChange() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.LibrAlignSwingAlignmentEdit

Delegates to SwingUndoAlignmentModel.registerDocumentChange() of the associated data provider.

registerDocumentChange() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel

This method is called every time the redo or undo methods of any of the edit objects generated by this class are executed.

reinsertSubelements() - Method in class info.bioinfweb.libralign.alignmentarea.content.ScrollContainerSwingAlignmentContentArea

reinsertSubelements() - Method in class info.bioinfweb.libralign.alignmentarea.content.ScrollContainerSWTAlignmentContentArea

reinsertSubelements() - Method in class info.bioinfweb.libralign.alignmentarea.DirectPaintingSWTAlignmentContentScroller

reinsertSubelements() - Method in class info.bioinfweb.libralign.alignmentarea.label.ScrollContainerSwingAlignmentLabelArea

reinsertSubelements() - Method in class info.bioinfweb.libralign.alignmentarea.label.SWTAlignmentLabelArea

Recreates the components displaying labels for sequences and data areas in the alignment according to the current model information.

reinsertSubelements() - Method in interface info.bioinfweb.libralign.alignmentarea.rowsarea.ToolkitSpecificAlignmentRowsArea

Recreates the subcomponents displaying sequences and data areas in the alignment according to the current model information.

remove() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubAreaIterator

remove(SelectionModel) - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionSynchronizer

remove(int) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList

remove(Object) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList

remove() - Method in class info.bioinfweb.libralign.dataarea.DataAreaVisibleIterator

remove(Object) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSet

remove(int, int) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSet

remove(Object) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataModel

remove() - Method in class info.bioinfweb.libralign.model.implementations.AbstractSequenceIDIterator

Removes the current ID from the underlying iterator and calls AbstractSequenceIDIterator.doRemove().

remove() - Method in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingInsertRemoveTokensEdit

Performs the remove operation.

remove(Object) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet

This method is not supported by this implementation and will always throw an UnsupportedOperationException.

removeAll() - Method in class info.bioinfweb.libralign.alignmentarea.rowsarea.SWTAlignmentRowsArea

removeAll(Collection<?>) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList

removeAll(Collection<?>) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet

This method is not supported by this implementation and will always throw an UnsupportedOperationException.

removeDataModelReader(DataModelEventReader<?>) - Method in class info.bioinfweb.libralign.model.io.AlignmentDataReader

Removes the specified data model reader from this instance.

removeListener(PaintSettingsListener) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings

Removes a paint settings listener from this instance.

removeListener(DataAreasModelListener) - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel

Removes the specified listener from this objects list.

removeListener(EditSettingsListener) - Method in class info.bioinfweb.libralign.editsettings.EditSettings

removeListener(PherogramComponentModelListener) - Method in class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel

removePartModel(int) - Method in interface info.bioinfweb.libralign.model.concatenated.ConcatenatedAlignmentModel

Removes the part model at the specified index from this concatenated alignment model.

removePropertyChangeListener(PropertyChangeListener) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats

removePropertyChangeListener(String, PropertyChangeListener) - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats

removeSelectionListener(SelectionListener<GenericEventObject<SelectionModel>>) - Method in class info.bioinfweb.libralign.alignmentarea.selection.SelectionModel

Removes the specified listener from this objects list.

removeSequence(String) - Method in class info.bioinfweb.libralign.dataarea.DataAreasModel

Removes the list of data areas attached to the specified sequence from this model.

removeSequence(String) - Method in interface info.bioinfweb.libralign.model.AlignmentModel

Removes the specified sequence from the underlying data source.

removeSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel

removeSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator

removeSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView

removeSequence(String) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel

removeTokenAt(String, int) - Method in interface info.bioinfweb.libralign.model.AlignmentModel

Removes the token at the specified position from the underlying data source.

removeTokenAt(String, int) - Method in class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel

removeTokenAt(String, int) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUnmodifyableAlignmentModel

removeTokenAt(String, int) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator

removeTokenAt(String, int) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView

removeTokenAt(String, int) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel

removeTokenPainter(CharacterStateSetType) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterMap

Removes the painter mapping for the specified token type.

removeTokensAt(String, int, int) - Method in interface info.bioinfweb.libralign.model.AlignmentModel

Removes the token inside the specified interval from the underlying data source.

removeTokensAt(String, int, int) - Method in class info.bioinfweb.libralign.model.implementations.AbstractListAlignmentModel

removeTokensAt(String, int, int) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUnmodifyableAlignmentModel

removeTokensAt(String, int, int) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator

removeTokensAt(String, int, int) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView

removeTokensAt(String, int, int) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel

renameSequence(String, String) - Method in interface info.bioinfweb.libralign.model.AlignmentModel

Renames a sequence in the underlying data source.

renameSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUndecoratedAlignmentModel

renameSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator

renameSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.decorate.DelegatedAlignmentModelView

renameSequence(String, String, AlignmentModel<?>) - Method in class info.bioinfweb.libralign.model.implementations.SequenceIDManager

Renames a sequence in the underlying data source.

renameSequence(String, String) - Method in class info.bioinfweb.libralign.model.implementations.swingundo.SwingUndoAlignmentModel

repaint() - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentSubArea

repaint() - Method in class info.bioinfweb.libralign.alignmentarea.rowsarea.SWTAlignmentRowsArea

repaint() - Method in class info.bioinfweb.libralign.multiplealignments.SWTMultipleAlignmentsContainer

repaintAll() - Method in class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView

Repaints this component and the associated heading component.

repaintSequenceAreas() - Method in class info.bioinfweb.libralign.alignmentarea.content.SequenceAreaMap

repaintSequences() - Method in class info.bioinfweb.libralign.alignmentarea.content.ScrollContainerSwingAlignmentContentArea

repaintSequences() - Method in class info.bioinfweb.libralign.alignmentarea.content.ScrollContainerSWTAlignmentContentArea

repaintSequences() - Method in interface info.bioinfweb.libralign.alignmentarea.content.ToolkitSpecificAlignmentContentArea

Forces the repaint of all displayed sequences.

repaintSequences() - Method in class info.bioinfweb.libralign.alignmentarea.DirectPaintingSWTAlignmentContentScroller

replaceSequence(String, S) - Method in class info.bioinfweb.libralign.model.implementations.AbstractUnmodifyableAlignmentModel

Replaces the sequence object with the specified ID by the specified contents.

replaceSequence(String, S) - Method in interface info.bioinfweb.libralign.model.SequenceAccessAlignmentModel

Replaces the sequence object with the specified ID.

representationByToken(C) - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet

representationByToken(Character) - Method in class info.bioinfweb.libralign.model.tokenset.CharacterTokenSet

Returns the character itself.

representationByToken(ContinuousToken<T>) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet

representationByToken(T) - Method in class info.bioinfweb.libralign.model.tokenset.DefaultTokenSet

representationByToken(T) - Method in interface info.bioinfweb.libralign.model.tokenset.TokenSet

Returns the representation string of the specified token that shall be displayed in an AlignmentArea or written into an alignment file.

representationLengthEqual() - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet

representationLengthEqual() - Method in class info.bioinfweb.libralign.model.tokenset.CharacterTokenSet

Always returns true.

representationLengthEqual() - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet

representationLengthEqual() - Method in class info.bioinfweb.libralign.model.tokenset.DefaultTokenSet

representationLengthEqual() - Method in interface info.bioinfweb.libralign.model.tokenset.TokenSet

Checks if all representation strings returned by TokenSet.representationByToken(Object) have the same length.

representationLengthEqual(TokenSet) - Static method in class info.bioinfweb.libralign.model.tokenset.TokenSetTools

Checks if all representation strings returned by #representationByToken(Object) have the same length.

retainAll(Collection<?>) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList

retainAll(Collection<?>) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet

This method is not supported by this implementation and will always throw an UnsupportedOperationException.

returnsCopies() - Method in class info.bioinfweb.libralign.model.adapters.BioJava3SequenceAdapter

Returns false since this class always returns views of the underlying data source.

returnsCopies() - Method in class info.bioinfweb.libralign.model.adapters.CharSequenceAdapter

Returns false since this class always returns views of the underlying data source.

returnsCopies() - Method in interface info.bioinfweb.libralign.model.adapters.SequenceDataAdapter

Specifies if the instances returned by #getSequence(int) are views of the underlying data source or independent copies of the sequences.

returnsCopies() - Method in class info.bioinfweb.libralign.model.adapters.StringAdapter

Returns true since this class always returns copies of the data in the underlying data source.

revalidate() - Method in class info.bioinfweb.libralign.alignmentarea.AlignmentArea

Recalculates the size of this and all subcomponents.

reverseComplement(AlignmentModel<T>, String, int, int) - Static method in class info.bioinfweb.libralign.model.utils.AlignmentModelUtils

Reverse complements a part of a nucleotide sequence.

reverseComplement(AlignmentModel<?>, String) - Static method in class info.bioinfweb.libralign.model.utils.AlignmentModelUtils

Reverse complements a whole nucleotide sequence.

reverseComplement() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel

reverseComplement() - Method in class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel

Reverse complements the pherogram and swaps the left and right cut positions accordingly.

reverseComplement() - Method in class info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider

Returns a new instance of this class which uses the reverse complemented version of the underlying BioJava 1 chromatogram.

reverseComplement() - Method in interface info.bioinfweb.libralign.pherogram.provider.PherogramProvider

Returns a reverse complemented view of this model.

reverseComplement() - Method in class info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider

Returns the source instance.

ReverseComplementPherogramProvider - Class in info.bioinfweb.libralign.pherogram.provider

Pherogram model that allows to view another model instance reverse complemented.

ReverseComplementPherogramProvider(PherogramProvider) - Constructor for class info.bioinfweb.libralign.pherogram.provider.ReverseComplementPherogramProvider

Creates a new instance of this class.

rightCutPositionChange(PherogramCutPositionChangeEvent) - Method in interface info.bioinfweb.libralign.pherogram.model.PherogramComponentModelListener

This method is called, if the right cut position of the pherogram was changed.

RNAAlignmentModelDecorator<T,U> - Class in info.bioinfweb.libralign.model.implementations.decorate

Shows the underlying nucleotide data source as a RNA sequence, i.e.

RNAAlignmentModelDecorator(TokenSet<T>, AlignmentModel<U>) - Constructor for class info.bioinfweb.libralign.model.implementations.decorate.RNAAlignmentModelDecorator

rowByPaintY(double) - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea

Returns the row index of the sequence displayed at the specified y coordinate considering the current order of sequences.

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