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PackedAlignmentModel<T> - Class in info.bioinfweb.libralign.model.implementations

An alignment model using a PackedObjectArrayList as the underlying data source.

PackedAlignmentModel(TokenSet<T>, SequenceIDManager, boolean, int) - Constructor for class info.bioinfweb.libralign.model.implementations.PackedAlignmentModel

Creates a new instance of this class.

PackedAlignmentModel(TokenSet<T>, int) - Constructor for class info.bioinfweb.libralign.model.implementations.PackedAlignmentModel

Creates a new instance of this class using its own ID manager.

PackedAlignmentModel(TokenSet<T>, SequenceIDManager, boolean) - Constructor for class info.bioinfweb.libralign.model.implementations.PackedAlignmentModel

Creates a new instance of this class with the maximum number of different tokens that is equal to the number of tokens in the specified set.

PackedAlignmentModel(TokenSet<T>) - Constructor for class info.bioinfweb.libralign.model.implementations.PackedAlignmentModel

Creates a new instance of this class with the maximum number of different tokens that is equal to the number of tokens in the specified set.

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

paint(TICPaintEvent) - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea

Paints the contents (sequences and data areas) of an alignment, if this instance is set to use direct painting.

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

This method delegates to AlignmentSubArea.paintPart(AlignmentPaintEvent).

paint(TICPaintEvent) - Method in class info.bioinfweb.libralign.alignmentarea.label.AlignmentLabelArea

paint(TICPaintEvent) - Method in class info.bioinfweb.libralign.alignmentarea.label.DefaultLabelSubArea

paint(TICPaintEvent) - Method in class info.bioinfweb.libralign.alignmentarea.label.SequenceLabelArea

paint(TICPaintEvent) - Method in class info.bioinfweb.libralign.alignmentarea.label.TextLabelArea

paint(TICPaintEvent) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetNameArea

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

paint(TICPaintEvent) - Method in class info.bioinfweb.libralign.pherogram.view.PherogramHeadingView

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

paint(TICPaintEvent) - Method in class info.bioinfweb.libralign.pherogram.view.PherogramView

paintBaseCallIndices(Graphics2D, int, int, double, double, PherogramDistortion, double) - Method in class info.bioinfweb.libralign.pherogram.PherogramPainter

paintBaseCallLines(Graphics2D, int, int, double, double, double, PherogramDistortion) - Method in class info.bioinfweb.libralign.pherogram.PherogramPainter

paintBaseCalls(Graphics2D, int, int, double, double, PherogramDistortion) - Method in class info.bioinfweb.libralign.pherogram.PherogramPainter

painterByColumn(int) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterList

Returns the according painter to the specified column index.

paintGaps(Graphics2D, int, int, double, double, double, PherogramDistortion, double) - Method in class info.bioinfweb.libralign.pherogram.PherogramPainter

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

Implementations of this method perform the painting of a part of the component.

paintPart(AlignmentPaintEvent) - Method in class info.bioinfweb.libralign.alignmentarea.content.SequenceArea

paintPart(AlignmentPaintEvent) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea

paintPart(AlignmentPaintEvent) - Method in class info.bioinfweb.libralign.dataarea.implementations.ConsensusSequenceArea

paintPart(AlignmentPaintEvent) - Method in class info.bioinfweb.libralign.dataarea.implementations.LabelDataArea

paintPart(AlignmentPaintEvent) - Method in class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea

paintPart(AlignmentPaintEvent) - Method in class info.bioinfweb.libralign.dataarea.implementations.sequenceindex.SequenceIndexArea

PaintSettings - Class in info.bioinfweb.libralign.alignmentarea.paintsettings

Object that manages properties related to painting the contents of an AlignmentArea.

PaintSettings(AlignmentArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettings

Creates a new instance of this class using default values for the properties.

PaintSettingsEvent - Class in info.bioinfweb.libralign.alignmentarea.paintsettings

Event object indicating a change in an instance of PaintSettings.

PaintSettingsEvent(PaintSettings) - Constructor for class info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettingsEvent

Creates a new instance of this class.

PaintSettingsListener - Interface in info.bioinfweb.libralign.alignmentarea.paintsettings

Listener interface to be implemented by classes that want to be informed on changes happening in an instance of PaintSettings.

paintText(Graphics2D, Rectangle2D, String, Color) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.SingleColorTokenPainter

paintToken(AlignmentArea, String, int, Graphics2D, Rectangle2D, Color) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.AbstractTokenPainter

Default implementation that delegates to #doPaintToken(AlignmentModel, Object, String, Graphics2D, Rectangle2D) and determines the string representation of the specified token from the token set of the specified alignment model.

paintToken(AlignmentArea, String, int, Graphics2D, Rectangle2D, Color) - Method in interface info.bioinfweb.libralign.alignmentarea.tokenpainter.TokenPainter

Paints a representation of the specified token filling up the specified area.

paintTraceCurves(Graphics2D, int, int, double, double, PherogramDistortion, double) - Method in class info.bioinfweb.libralign.pherogram.PherogramPainter

paintUnscaledBackground(Graphics2D, Rectangle2D, double) - Method in class info.bioinfweb.libralign.pherogram.PherogramPainter

paintUnscaledBaseCallIndices(int, int, Graphics2D, double, double, double) - Method in class info.bioinfweb.libralign.pherogram.PherogramPainter

paintUnscaledBaseCallLines(int, int, Graphics2D, double, double, double, double) - Method in class info.bioinfweb.libralign.pherogram.PherogramPainter

paintUnscaledBaseCalls(int, int, Graphics2D, double, double, double) - Method in class info.bioinfweb.libralign.pherogram.PherogramPainter

Paints the nucleotide characters of the base call sequence at the x-positions stored in the underlying pherogram model.

paintUnscaledTraceCurves(int, int, Graphics2D, double, double, double) - Method in class info.bioinfweb.libralign.pherogram.PherogramPainter

Paints parts the four trace curves stored in the specified provider with a constant scale on x.

paintXByColumn(int) - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea

Returns the left most x-coordinate of the area the specified column is painted in relative to the component on which the sequences are painted.

paintYByRow(int) - Method in class info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea

Returns the top most y-coordinate of the area the specified row is painted in relative to the component on which the sequences are painted.

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

Translates the sequence ID used in an underlying part model to the according sequence ID in this concatenated model.

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

parseValue(String) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.DoubleTokenSet

parseValue(String) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.FloatTokenSet

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

Translates the sequence ID used in this concatenated model to the according sequence ID in an underlying part model.

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

Returns the part model currently responsible for providing the contents of the specified column.

partModelIndex(AlignmentModel<?>) - Method in interface info.bioinfweb.libralign.model.concatenated.ConcatenatedAlignmentModel

Returns the index of the specified part model in this concatenated alignment model.

PherogramAlignmentRelation - Class in info.bioinfweb.libralign.pherogram.model

A bean class storing the base call sequence position corresponding to editable sequence position or the other way around in an alignment between the base call sequence from Sanger sequencing and the corresponding editable sequence in an AlignmentArea.

PherogramAlignmentRelation(int, int, int, ListIterator<ShiftChange>) - Constructor for class info.bioinfweb.libralign.pherogram.model.PherogramAlignmentRelation

PherogramArea - Class in info.bioinfweb.libralign.dataarea.implementations.pherogram

A data area displaying a trace file resulting from Sanger sequencing.

PherogramArea(AlignmentContentArea, PherogramAreaModel) - Constructor for class info.bioinfweb.libralign.dataarea.implementations.pherogram.PherogramArea

Creates a new instance of this class.

PherogramAreaModel - Class in info.bioinfweb.libralign.pherogram.model

The data area model of a PherogramArea containing the pherogram source, as well as cut positions, the column where the pherogram is attached to the editable sequence and pherogram distortion information.

PherogramAreaModel(PherogramProvider) - Constructor for class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel

Creates a new instance of this class.

PherogramAreaModel(PherogramComponentModel) - Constructor for class info.bioinfweb.libralign.pherogram.model.PherogramAreaModel

Creates a new instance based on the specified pherogram component model instance.

PherogramComponent - Interface in info.bioinfweb.libralign.pherogram

This interface should be implemented by all GUI classes displaying a pherogram (trace file from Sanger sequencing).

PherogramComponentModel - Class in info.bioinfweb.libralign.pherogram.model

The model used by all views displaying pherograms.

PherogramComponentModel(PherogramProvider) - Constructor for class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel

Creates a new instance of this class without any cut off pherogram ends.

PherogramComponentModel(PherogramComponentModel) - Constructor for class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel

Creates a copy from the specified instance.

PherogramComponentModel(PherogramProvider, int, int) - Constructor for class info.bioinfweb.libralign.pherogram.model.PherogramComponentModel

Creates a new instance of this class.

PherogramComponentModelListener - Interface in info.bioinfweb.libralign.pherogram.model

Interface to be implemented by all classes that need to be informed on changes in instances of PherogramComponentModel.

PherogramCutPositionChangeEvent - Class in info.bioinfweb.libralign.pherogram.model

Event indicating that a cut position of an instance of PherogramComponentModel was changed.

PherogramCutPositionChangeEvent(PherogramComponentModel, boolean, int, int, PherogramAlignmentRelation, PherogramAlignmentRelation) - Constructor for class info.bioinfweb.libralign.pherogram.model.PherogramCutPositionChangeEvent

Creates a new instance of this class.

PherogramDistortion - Interface in info.bioinfweb.libralign.pherogram.distortion

Classes to be used with PherogramPainter the define the distortion of the pherogram at each base call index should implement this interface.

PherogramFirstSeqPosChangeEvent - Class in info.bioinfweb.libralign.pherogram.model

Event that indicates that PherogramAreaModel.getFirstSeqPos() was changed.

PherogramFirstSeqPosChangeEvent(PherogramComponentModel, boolean, int, int) - Constructor for class info.bioinfweb.libralign.pherogram.model.PherogramFirstSeqPosChangeEvent

Creates a new instance of this class.

PherogramFormats - Class in info.bioinfweb.libralign.pherogram

Class that stores colors and fonts and settings used to display a pherogram from Sanger sequencing.

PherogramFormats(PherogramComponent) - Constructor for class info.bioinfweb.libralign.pherogram.PherogramFormats

Creates a new instance of this class with default values.

PherogramFormats.QualityOutputType - Enum in info.bioinfweb.libralign.pherogram

Enumeration that determines the way quality scores are displays in an

PherogramHeadingView - Class in info.bioinfweb.libralign.pherogram.view

The GUI component that displays the heading information (base call sequence and the nucleotide index) above the trace curves of a pherogram from Sanger sequencing.

PherogramHeadingView(PherogramTraceCurveView) - Constructor for class info.bioinfweb.libralign.pherogram.view.PherogramHeadingView

PherogramModelChangeEvent - Class in info.bioinfweb.libralign.pherogram.model

All events indicating changes in an instance of PherogramComponentModel should be inherited from this class.

PherogramModelChangeEvent(PherogramComponentModel, boolean) - Constructor for class info.bioinfweb.libralign.pherogram.model.PherogramModelChangeEvent

Creates a new instance of this class.

PherogramPainter - Class in info.bioinfweb.libralign.pherogram

Utility class used by GUI components that display a pherogram (e.g.

PherogramPainter(PherogramComponent) - Constructor for class info.bioinfweb.libralign.pherogram.PherogramPainter

PherogramProvider - Interface in info.bioinfweb.libralign.pherogram.provider

Interface that should be implemented by all classes providing pherogram data.

pherogramProviderChange(PherogramProviderChangeEvent) - Method in interface info.bioinfweb.libralign.pherogram.model.PherogramComponentModelListener

This method is called, if the pherogram provider of a pherogram component model was replaced or its contents changed.

PherogramProviderChangeEvent - Class in info.bioinfweb.libralign.pherogram.model

Change event that indicates the the pherogram provider of an instance of PherogramComponentModel was replaced or its contents changed.

PherogramProviderChangeEvent(PherogramComponentModel, boolean, PherogramProvider, PherogramProvider, boolean) - Constructor for class info.bioinfweb.libralign.pherogram.model.PherogramProviderChangeEvent

Creates a new instance of this class.

PherogramTraceCurveView - Class in info.bioinfweb.libralign.pherogram.view

GUI component that allows displaying a pherogram (trace file from Sanger sequencing) which is not attached to a sequence in an AlignmentArea.

PherogramTraceCurveView() - Constructor for class info.bioinfweb.libralign.pherogram.view.PherogramTraceCurveView

PherogramUtils - Class in info.bioinfweb.libralign.pherogram

provides values for constants of PherogramProvider and general tool methods to deal with pherogram data.

PherogramUtils() - Constructor for class info.bioinfweb.libralign.pherogram.PherogramUtils

PherogramView - Class in info.bioinfweb.libralign.pherogram.view

GUI component that displays a scrollable pherogram with undistorted trace curves, its base call sequence and nucleotide probabilities.

PherogramView() - Constructor for class info.bioinfweb.libralign.pherogram.view.PherogramView

Creates a new instance of this class.

PROBABILITY_LABELS - Static variable in interface info.bioinfweb.libralign.pherogram.provider.PherogramProvider

A list that allows to iterate over all probability labels.

processEvent(JPhyloIOEventReader, JPhyloIOEvent) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetEventReader

processEvent(JPhyloIOEventReader, JPhyloIOEvent) - Method in class info.bioinfweb.libralign.model.io.AlignmentModelEventReader

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

put(String, CharSet) - Method in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetDataModel

putAminoAcidColors() - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.AminoAcidTokenPainter

putNucleotideColors(Map<String, Color>) - Static method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.NucleotideTokenPainter

putTokenPainter(CharacterStateSetType, TokenPainter) - Method in class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterMap

Specifies a new painter for a certain token type.

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