public class CharSequenceAlignmentModel extends AbstractUnmodifyableAlignmentModel<java.lang.CharSequence,java.lang.Character> implements SequenceAccessAlignmentModel<java.lang.CharSequence,java.lang.Character>
AlignmentModel backed by a set of CharSequence implementations
(e.g. String objects).
This class does not allow to write tokens (characters) since this is not supported by the
CharSequence interface. If you use a character sequence implementation that supports writing
you can subclass this class and overwrite the methods that edit tokens.
| Constructor and Description |
|---|
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.
|
| Modifier and Type | Method and Description |
|---|---|
protected java.lang.CharSequence |
createNewSequence(java.lang.String sequenceID,
java.lang.String sequenceName)
Returns an empty string as the new character sequence.
|
int |
getSequenceLength(java.lang.String sequenceID)
Returns the length of the specified sequence.
|
java.lang.Character |
getTokenAt(java.lang.String sequenceID,
int index)
Returns the token at the specified position.
|
addSequence, getSequence, getWriteType, insertTokenAt, insertTokensAt, removeTokenAt, removeTokensAt, replaceSequence, setTokenAt, setTokensAtcontainsSequence, doAddSequence, doRemoveSequence, getSequenceCount, getSequenceMap, getSequenceOrder, sequenceIDIteratoraddSequence, addSequence, appendToken, appendTokens, doRenameSequence, fireAfterSequenceChange, fireAfterTokenChange, getApproxMaxSequenceLength, getIDManager, getMaxSequenceLength, getTokenSet, isReuseSequenceIDs, isSequencesReadOnly, isTokensReadOnly, removeSequence, renameSequence, sequenceIDsByName, sequenceNameByID, setMaxSequeceLengthRecalculte, setReuseSequenceIDs, setTokenSetfireAfterSequenceRenamed, getChangeListeners, getID, getLabel, setID, setLabelclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitaddSequence, replaceSequenceaddSequence, addSequence, appendToken, appendTokens, containsSequence, getChangeListeners, getID, getLabel, getMaxSequenceLength, getSequenceCount, getTokenSet, getWriteType, insertTokenAt, insertTokensAt, isSequencesReadOnly, isTokensReadOnly, removeSequence, removeTokenAt, removeTokensAt, renameSequence, sequenceIDIterator, sequenceIDsByName, sequenceNameByID, setID, setLabel, setTokenAt, setTokensAt, setTokenSetgetSequencepublic CharSequenceAlignmentModel(TokenSet<java.lang.Character> tokenSet, SequenceIDManager idManager, boolean reuseSequenceIDs)
tokenSet - the token set which is supported by the implementationidManager - the ID manager to be used by the new instance (maybe shared among multiple instances)reuseSequenceIDs - Specifies whether unused IDs of the underlying ID manager should be reused by this model.
(See the documentation of AbstractUndecoratedAlignmentModel.isReuseSequenceIDs() for details. Specify false, if you are unsure
what this property does.)public CharSequenceAlignmentModel(TokenSet<java.lang.Character> tokenSet)
tokenSet - the token set which is supported by the implementationprotected java.lang.CharSequence createNewSequence(java.lang.String sequenceID, java.lang.String sequenceName)
createNewSequence in class AbstractMapBasedAlignmentModel<java.lang.CharSequence,java.lang.Character>sequenceID - the ID the new sequence must havesequenceName - the name the new sequence will havepublic int getSequenceLength(java.lang.String sequenceID)
AlignmentModelgetSequenceLength in interface AlignmentModel<java.lang.Character>sequenceID - the identifier the sequence in the alignment-1 if no sequence with the specified name existspublic java.lang.Character getTokenAt(java.lang.String sequenceID, int index)
AlignmentModelgetTokenAt in interface AlignmentModel<java.lang.Character>sequenceID - the identifier the sequence where the token is containedindex - the index of the element contained in the specified sequence (The first element has the index 0.)