- TextLabelArea - Class in info.bioinfweb.libralign.alignmentarea.label
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- TextLabelArea(AlignmentLabelArea, AlignmentSubArea) - Constructor for class info.bioinfweb.libralign.alignmentarea.label.TextLabelArea
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- THYMINE - Static variable in class info.bioinfweb.libralign.model.utils.AlignmentModelUtils
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- toArray() - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
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- toArray(T[]) - Method in class info.bioinfweb.libralign.dataarea.DataAreaChangeEventList
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- toArray() - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
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Continuous sets cannot be stored in arrays, therefore this method is not supported by this class.
- toArray(E[]) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
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Continuous sets cannot be stored in arrays, therefore this method is not supported by this class.
- toggleInsert() - Method in class info.bioinfweb.libralign.editsettings.EditSettings
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- toggleInsertLeftInDataArea() - Method in class info.bioinfweb.libralign.editsettings.EditSettings
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- toggleShowBaseCallLines() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats
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Toggles whether base call lines (vertical lines at each base call position in the background of the
trace curve output) shall be painted.
- toggleShowProbabilityValues() - Method in class info.bioinfweb.libralign.pherogram.PherogramFormats
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Toggles whether probability values (substitution, overcall and undercall) should be displayed
in the pherogram heading.
- tokenByKeyStroke(KeyStroke) - Method in class info.bioinfweb.libralign.model.tokenset.AbstractTokenSet
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- tokenByKeyStroke(KeyStroke) - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet
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- tokenByKeyStroke(KeyStroke) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
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- tokenByKeyStroke(KeyStroke) - Method in interface info.bioinfweb.libralign.model.tokenset.TokenSet
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Returns the token from this set that is associated with the specified key stroke.
- tokenByRepresentation(String) - Method in class info.bioinfweb.libralign.model.tokenset.BioJava3TokenSet
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- tokenByRepresentation(String) - Method in class info.bioinfweb.libralign.model.tokenset.CharacterTokenSet
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Returns the first character of representation if that character is contained in this set.
- tokenByRepresentation(String) - Method in class info.bioinfweb.libralign.model.tokenset.continuous.AbstractContinuousSet
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- tokenByRepresentation(String) - Method in class info.bioinfweb.libralign.model.tokenset.DefaultTokenSet
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Returns the first token in this set returned by HashSet.iterator() with a string representation equal
to representation.
- tokenByRepresentation(String) - Method in interface info.bioinfweb.libralign.model.tokenset.TokenSet
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Returns the token associated with the specified string representation used to display the token in
an
AlignmentArea or an alignment file.
- TokenChangeEvent<T> - Class in info.bioinfweb.libralign.model.events
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Event object that indicates that tokens in a sequence provided by an instance of
AlignmentModel were inserted, removed or replaced.
- TokenChangeEvent(AlignmentModel<T>, String, ListChangeType, int, Collection<? extends T>) - Constructor for class info.bioinfweb.libralign.model.events.TokenChangeEvent
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Creates a new instance of this class.
- TokenDefinition - Class in info.bioinfweb.libralign.model.factory
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Models the definition of a token.
- TokenDefinition(String, CharacterSymbolMeaning) - Constructor for class info.bioinfweb.libralign.model.factory.TokenDefinition
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- TokenPainter - Interface in info.bioinfweb.libralign.alignmentarea.tokenpainter
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- TokenPainterList - Class in info.bioinfweb.libralign.alignmentarea.paintsettings
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- TokenPainterList(PaintSettings) - Constructor for class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterList
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Creates a new instance of this class.
- tokenPainterListChange(PaintSettingsEvent) - Method in interface info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettingsListener
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- TokenPainterMap - Class in info.bioinfweb.libralign.alignmentarea.paintsettings
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Provides best matching token painters depending on the specified token set type.
- TokenPainterMap() - Constructor for class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterMap
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Creates a new instance of this class.
- tokenPainterReplaced(TokenPainterReplacedEvent) - Method in interface info.bioinfweb.libralign.alignmentarea.paintsettings.PaintSettingsListener
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Indicating that a token painter at a certain position in the token painter list was replaced.
- TokenPainterReplacedEvent - Class in info.bioinfweb.libralign.alignmentarea.paintsettings
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Event object indicating that a token painter in an instance of
TokenPainterList has been replaced.
- TokenPainterReplacedEvent(PaintSettings, TokenPainter, TokenPainter, int) - Constructor for class info.bioinfweb.libralign.alignmentarea.paintsettings.TokenPainterReplacedEvent
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Creates a new instance of this class.
- tokens - Variable in class info.bioinfweb.libralign.model.implementations.swingundo.edits.token.SwingTokenEdit
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- TokenSet<T> - Interface in info.bioinfweb.libralign.model.tokenset
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This interface should be implemented by all classes specifying a set of tokens (sequence elements, e.g.
- TokenSetAdapter<T> - Class in info.bioinfweb.libralign.model.io
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- TokenSetAdapter(String, TokenSet<T>, long, long) - Constructor for class info.bioinfweb.libralign.model.io.TokenSetAdapter
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- TokenSetTools - Class in info.bioinfweb.libralign.model.tokenset
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Provides tool methods useful for implementing
TokenSet.
- TokenSetTools() - Constructor for class info.bioinfweb.libralign.model.tokenset.TokenSetTools
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- toLightweightProfile() - Method in class info.bioinfweb.libralign.model.adapters.BioJava3SequenceAdapter
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Returns a BioJava alignment that contains the views of all sequences contained in the underlying data
source in the order they are stored there.
- toLightweightProfile(SequenceOrder) - Method in class info.bioinfweb.libralign.model.adapters.BioJava3SequenceAdapter
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Returns a BioJava alignment that contains the views of all sequences contained in the underlying data
source in the order specified in the order object.
- ToolkitIndependentPhergramView - Interface in info.bioinfweb.libralign.pherogram.view
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- ToolkitSpecificAlignmentArea - Interface in info.bioinfweb.libralign.alignmentarea
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Interface implemented by all toolkit specific components displaying the contents of an
AlignmentArea.
- ToolkitSpecificAlignmentContentArea - Interface in info.bioinfweb.libralign.alignmentarea.content
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Interface for all toolkit specific components displaying the contents of an alignment area (not including
the parent scroll container which is part of implementations of
ToolkitSpecificAlignmentArea).
- ToolkitSpecificAlignmentLabelArea - Interface in info.bioinfweb.libralign.alignmentarea.label
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Interface that defines common methods by toolkit specific implementations of an
AlignmentLabelArea.
- ToolkitSpecificAlignmentRowsArea<C extends TICComponent> - Interface in info.bioinfweb.libralign.alignmentarea.rowsarea
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Interface to be implemented by all classes displaying alignment associated components in rows.
- ToolkitSpecificMultipleAlignmentsContainer - Interface in info.bioinfweb.libralign.multiplealignments
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- toString() - Method in class info.bioinfweb.libralign.model.adapters.SingleCharSequenceAdapter
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Returns a copy of this character sequence as a string.
- toString() - Method in class info.bioinfweb.libralign.model.tokenset.continuous.ContinuousToken
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- toString() - Method in class info.bioinfweb.libralign.model.utils.indextranslation.IndexRelation
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- TRACE_CURVE_NUCLEOTIDES - Static variable in interface info.bioinfweb.libralign.pherogram.provider.PherogramProvider
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A list of the nucleotides A, T, C and G to which trace curves exist in a trace file from Sanger sequencing.
