| Package | Description |
|---|---|
| info.bioinfweb.libralign.alignmentarea.tokenpainter |
Contains implementations of
TokenPainter |
| info.bioinfweb.libralign.model |
Contains the
AlignmentModel interface which
is the bridge between LibrAlign and any source of alignment data that is displayed with it as well as
related classes and a set of implementations of this interface provided with LibrAlign. |
| info.bioinfweb.libralign.model.exception |
Contains exceptions thrown by implementations of
AlignmentModel. |
| info.bioinfweb.libralign.model.implementations |
Contains common implementations of
AlignmentModel
which are part of LibrAlign. |
| info.bioinfweb.libralign.model.implementations.decorate | |
| info.bioinfweb.libralign.model.implementations.swingundo |
Contains classes that allow to edit the underlying data source of an implementation of
AlignmentModel using swing edit objects
(implementations of UndoableEdit). |
| info.bioinfweb.libralign.model.io | |
| info.bioinfweb.libralign.model.tokenset | |
| info.bioinfweb.libralign.model.tokenset.continuous |
Contains classes implementing token sets for continuous character states (e.g.
|
| info.bioinfweb.libralign.model.utils |
Contains utility classes to be used with implementations of
AlignmentModel. |
| Modifier and Type | Method and Description |
|---|---|
void |
SingleColorTokenPainter.calculatePreferredWidth(TokenSet<?> tokenSet) |
| Modifier and Type | Method and Description |
|---|---|
TokenSet<T> |
AlignmentModel.getTokenSet()
Returns the token set which is supported by the implementation.
|
| Modifier and Type | Method and Description |
|---|---|
void |
AlignmentModel.setTokenSet(TokenSet<T> set)
Replaces the current token set with the specified one.
|
| Constructor and Description |
|---|
InvalidTokenRepresentationException(TokenSet<?> tokenSet,
java.lang.String invalidRepresentation) |
| Modifier and Type | Method and Description |
|---|---|
TokenSet<T> |
AbstractUndecoratedAlignmentModel.getTokenSet() |
| Modifier and Type | Method and Description |
|---|---|
void |
AbstractUndecoratedAlignmentModel.setTokenSet(TokenSet<T> set) |
void |
PackedAlignmentModel.setTokenSet(TokenSet<T> set)
This method is not supported by this class.
|
| Constructor and Description |
|---|
AbstractListAlignmentModel(TokenSet<T> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs)
Creates a new instance of this class using
AbstractListAlignmentModel.DEFAULT_INITIAL_CAPACITY as the initial capacity
which is only used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array
lists. |
AbstractListAlignmentModel(TokenSet<T> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs,
int initialCapacity,
boolean useMaxLength)
Creates a new instance of this class.
|
AbstractMapBasedAlignmentModel(TokenSet<T> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs)
Creates a new instance of this class relying on a
HashMap. |
AbstractMapBasedAlignmentModel(TokenSet<T> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs,
java.util.Map<java.lang.String,S> sequenceMap)
Creates a new instance of this class with a custom map implementation.
|
AbstractMapBasedAlignmentModel(TokenSet<T> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs,
java.util.Map<java.lang.String,S> sequenceMap,
java.util.List<java.lang.String> sequenceOrder)
Creates a new instance of this class with a custom map and list implementation.
|
AbstractUndecoratedAlignmentModel(TokenSet<T> tokenSet)
Creates a new instance of this class with its own instance of
SequenceIDManager. |
AbstractUndecoratedAlignmentModel(TokenSet<T> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs)
Creates a new instance of this class.
|
AbstractUnmodifyableAlignmentModel(TokenSet<T> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs)
Creates a new instance of this class relying on a
TreeMap. |
AbstractUnmodifyableAlignmentModel(TokenSet<T> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs,
java.util.Map<java.lang.String,S> sequenceMap)
Creates a new instance of this class with a custom map and list implementation.
|
AbstractUnmodifyableAlignmentModel(TokenSet<T> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs,
java.util.Map<java.lang.String,S> sequenceMap,
java.util.List<java.lang.String> sequenceOrder)
Creates a new instance of this class with a custom map and list implementation.
|
ArrayListAlignmentModel(TokenSet<T> tokenSet)
Creates a new instance of this class using
AbstractListAlignmentModel.DEFAULT_INITIAL_CAPACITY as the initial capacity
which is only used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array
lists. |
ArrayListAlignmentModel(TokenSet<T> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs)
Creates a new instance of this class using
AbstractListAlignmentModel.DEFAULT_INITIAL_CAPACITY as the initial capacity
which is only used if it is lower than AbstractUndecoratedAlignmentModel.getMaxSequenceLength() to create new sequence array
lists. |
ArrayListAlignmentModel(TokenSet<T> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs,
int initialCapacity,
boolean useMaxLength)
Creates a new instance of this class.
|
BioJava3SequenceAlignmentModel(TokenSet<C> tokenSet)
Creates a new instance of this class using its own ID manager.
|
BioJava3SequenceAlignmentModel(TokenSet<C> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs)
Creates a new instance of this class using a possibly shared ID manager.
|
CharSequenceAlignmentModel(TokenSet<java.lang.Character> tokenSet)
Creates a new instance of this class using its own ID manager.
|
CharSequenceAlignmentModel(TokenSet<java.lang.Character> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs)
Creates a new instance of this class using a possibly shared ID manager.
|
PackedAlignmentModel(TokenSet<T> tokenSet)
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> tokenSet,
int minTokenCount)
Creates a new instance of this class using its own ID manager.
|
PackedAlignmentModel(TokenSet<T> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs)
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> tokenSet,
SequenceIDManager idManager,
boolean reuseSequenceIDs,
int minTokenCount)
Creates a new instance of this class.
|
| Modifier and Type | Method and Description |
|---|---|
TokenSet<T> |
AbstractAlignmentModelDecorator.getTokenSet() |
TokenSet<T> |
DelegatedAlignmentModelView.getTokenSet() |
| Modifier and Type | Method and Description |
|---|---|
void |
AbstractAlignmentModelDecorator.setTokenSet(TokenSet<T> tokenSet) |
void |
DelegatedAlignmentModelView.setTokenSet(TokenSet<T> set) |
| Constructor and Description |
|---|
AbstractAlignmentModelDecorator(TokenSet<T> tokenSet,
AlignmentModel<U> underlyingModel)
Creates a new instance of this class.
|
AbstractTokenReplacementAlignmentModelDecorator(TokenSet<T> tokenSet,
AlignmentModel<U> underlyingModel)
Creates a new instance of this class.
|
DNAAlignmentModelDecorator(TokenSet<T> tokenSet,
AlignmentModel<U> underlyingModel) |
RNAAlignmentModelDecorator(TokenSet<T> tokenSet,
AlignmentModel<U> underlyingModel) |
| Modifier and Type | Method and Description |
|---|---|
TokenSet<T> |
SwingUndoAlignmentModel.getTokenSet() |
| Modifier and Type | Method and Description |
|---|---|
void |
SwingUndoAlignmentModel.setTokenSet(TokenSet<T> set) |
| Modifier and Type | Method and Description |
|---|---|
TokenSet<T> |
TokenSetAdapter.getTokenSet() |
| Constructor and Description |
|---|
TokenSetAdapter(java.lang.String idPrefix,
TokenSet<T> tokenSet,
long startIndex,
long endIndex) |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractTokenSet<T>
An abstract implementation of
TokenSet that provides a TreeMap used to map key characters
to tokens and inherits from HashSet so also tokens that do not implement Comparable are
supported. |
class |
BioJava3TokenSet<C extends org.biojava3.core.sequence.template.Compound>
Implementation of
TokenSet backed by a BioJava CompoundSet object. |
class |
CharacterTokenSet
A token set consisting of characters.
|
class |
DefaultTokenSet<T>
Basic implementation of a discrete token set.
|
| Modifier and Type | Method and Description |
|---|---|
TokenSet<T> |
TokenSet.clone()
Returns a deep copy of this instance.
|
| Modifier and Type | Method and Description |
|---|---|
static <T> CharacterSymbolMeaning |
TokenSetTools.getMeaning(TokenSet<T> tokenSet,
T token)
Determines the meaning of the specified token as defined by
getMeaning(Object). |
static <T> CharacterSymbolType |
TokenSetTools.getSymbolType(TokenSet<T> tokenSet,
T token)
Returns
CharacterSymbolType.UNCERTAIN for all missing information tokens. |
static <T> boolean |
TokenSetTools.isGapToken(TokenSet<T> tokenSet,
T token)
Tests if the specified token represents a gap in the specified token set.
|
static <T> boolean |
TokenSetTools.isMissingInformationToken(TokenSet<T> tokenSet,
T token)
Tests if the specified token represents missing data in the specified token set.
|
static int |
TokenSetTools.maxRepresentationLength(TokenSet tokenSet)
Calculates the maximal length of a representation returned by
#representationByToken(Object)
of all tokens contained in the specified set. |
static boolean |
TokenSetTools.representationLengthEqual(TokenSet tokenSet)
Checks if all representation strings returned by
#representationByToken(Object)
have the same length. |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractContinuousSet<T extends java.lang.Number & java.lang.Comparable<T>>
Implements type independent functionality for continuous token sets.
|
class |
DoubleTokenSet
Implementation of a token set containing all possible
double values. |
class |
FloatTokenSet
Implementation of a token set containing all possible
float values. |
| Modifier and Type | Method and Description |
|---|---|
static <T> java.util.List<T> |
AlignmentModelUtils.charSequenceToTokenList(java.lang.CharSequence sequence,
TokenSet<T> tokenSet)
Converts a character sequence to a sequence of tokens.
|
static <T> java.util.List<T> |
AlignmentModelUtils.charSequenceToTokenList(java.lang.CharSequence sequence,
TokenSet<T> tokenSet,
boolean allowWhitespace,
T defaultToken)
Convenience method that uses
CharSequenceTokenScanner to parse all tokens contained in the specified
string and returns these as a list. |
| Constructor and Description |
|---|
CharSequenceTokenScanner(java.lang.CharSequence sequence,
TokenSet<T> tokenSet,
boolean allowWhitespace,
T defaultToken)
Creates a new instance of this class.
|