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

B

backgroundColorByRepresentation(String, Color) - Method in class info.bioinfweb.libralign.alignmentarea.tokenpainter.AminoAcidTokenPainter

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

Returns the same color as SingleColorTokenPainter.getColor(String) but blends it with a selection color, if one is specified.

BASE_CALL_LINE_COLOR_FACTOR - Static variable in class info.bioinfweb.libralign.pherogram.PherogramFormats

Used to calculate the default base call line color.

baseCallIndex - Variable in class info.bioinfweb.libralign.pherogram.model.ShiftChange

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

BasicAlignmentModelView<T> - Interface in info.bioinfweb.libralign.model

Classes implementing this interface provide access to the data provided by an implementation of AlignmentModel in a modified way.

beforeAdd(int, Collection<? extends AlignmentArea>) - Method in class info.bioinfweb.libralign.multiplealignments.AlignmentAreaList

beginIndex - Variable in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingTokenEdit

BioJava3AminoAcidAligmentModelFactory - Class in info.bioinfweb.libralign.model.factory.biojava

Alignment model factory for models representing amino acids as BioJava AminoAcidCompound objects.

BioJava3AminoAcidAligmentModelFactory() - Constructor for class info.bioinfweb.libralign.model.factory.biojava.BioJava3AminoAcidAligmentModelFactory

BioJava3NucleotideAlignmentModelFactory - Class in info.bioinfweb.libralign.model.factory.biojava

Alignment model factory for models representing nucleotides as BioJava NucleotideCompound objects.

BioJava3NucleotideAlignmentModelFactory() - Constructor for class info.bioinfweb.libralign.model.factory.biojava.BioJava3NucleotideAlignmentModelFactory

BioJava3SequenceAdapter<T,C extends org.biojava3.core.sequence.template.Compound> - Class in info.bioinfweb.libralign.model.adapters

Adapter class that allows to access the contents of an implementation of AlignmentModel as a set of BioJava Sequence objects.

BioJava3SequenceAdapter(AlignmentModel<T>, CompoundSet<C>) - Constructor for class info.bioinfweb.libralign.model.adapters.BioJava3SequenceAdapter

Creates a new instance of this class.

BioJava3SequenceAlignmentModel<S extends org.biojava3.core.sequence.template.Sequence<C>,C extends org.biojava3.core.sequence.template.Compound> - Class in info.bioinfweb.libralign.model.implementations

/** An implementation of AlignmentModel backed by a set of BioJava Sequence implementations.

BioJava3SequenceAlignmentModel(TokenSet<C>, SequenceIDManager, boolean) - Constructor for class info.bioinfweb.libralign.model.implementations.BioJava3SequenceAlignmentModel

Creates a new instance of this class using a possibly shared ID manager.

BioJava3SequenceAlignmentModel(TokenSet<C>) - Constructor for class info.bioinfweb.libralign.model.implementations.BioJava3SequenceAlignmentModel

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

BioJava3SequenceAlignmentModel(LightweightProfile<S, C>, String, CharacterStateSetType, boolean, SequenceIDManager) - Constructor for class info.bioinfweb.libralign.model.implementations.BioJava3SequenceAlignmentModel

Creates a new instance of this class and copies the sequences contained underlyingModel to it.

BioJava3SequenceAlignmentModel(LightweightProfile<S, C>, String, CharacterStateSetType, boolean) - Constructor for class info.bioinfweb.libralign.model.implementations.BioJava3SequenceAlignmentModel

Creates a new instance of this class and copies the sequences contained underlyingModel to it.

BioJava3TokenSet<C extends org.biojava3.core.sequence.template.Compound> - Class in info.bioinfweb.libralign.model.tokenset

Implementation of TokenSet backed by a BioJava CompoundSet object.

BioJava3TokenSet(BioJava3TokenSet<C>) - Constructor for class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet

A constructor used to clone instances of this class.

BioJava3TokenSet(CharacterStateSetType, CompoundSet<C>, boolean) - Constructor for class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet

Creates a new instance of this class.

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

Adapter class that provides the contents of any implementation of Chromatogram from BioJava 1 as a PherogramProvider.

BioJavaPherogramProvider(Chromatogram) - Constructor for class info.bioinfweb.libralign.pherogram.provider.BioJavaPherogramProvider

Creates a new instance of this class.

BioPolymerCharAlignmentModelFactory - Class in info.bioinfweb.libralign.model.factory

Creates instances of PackedAlignmentModel using a CharacterTokenSet for nucleotide or amino acid data.

BioPolymerCharAlignmentModelFactory() - Constructor for class info.bioinfweb.libralign.model.factory.BioPolymerCharAlignmentModelFactory

Creates a new instance of this class without an shared sequence ID manager.

BioPolymerCharAlignmentModelFactory(Character, boolean) - Constructor for class info.bioinfweb.libralign.model.factory.BioPolymerCharAlignmentModelFactory

Creates a new instance of this class without an shared sequence ID manager.

BioPolymerCharAlignmentModelFactory(SequenceIDManager, boolean, Character, boolean) - Constructor for class info.bioinfweb.libralign.model.factory.BioPolymerCharAlignmentModelFactory

Creates a new instance of this class using a shared sequence ID manager.

BORDER_FRACTION - Static variable in class info.bioinfweb.libralign.dataarea.implementations.charset.CharSetArea

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

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