public class SimpleRichSequence extends ThinRichSequence
RichSequence.IOTools, RichSequence.Terms, RichSequence.ToolsAnnotatable.AnnotationForwarderFeatureHolder.EmptyFeatureHolderCIRCULAR, SYMLISTVERSIONCOMMENT, DESCRIPTION, DIVISION, IDENTIFIER, RANKEDCROSSREF, RANKEDDOCREF, RELATIONS, SEQVERSION, TAXONANNOTATIONEDIT, EMPTY_LISTEMPTY_FEATURE_HOLDER, FEATURES, SCHEMA| Modifier | Constructor and Description |
|---|---|
protected |
SimpleRichSequence() |
|
SimpleRichSequence(Namespace ns,
String name,
String accession,
int version,
SymbolList symList,
Double seqversion)
Creates a new instance of SimpleRichSequence.
|
| Modifier and Type | Method and Description |
|---|---|
SymbolList |
getInternalSymbolList()
A special function that returns the SymbolList that this RichSequence is
based around.
|
protected int |
getSequenceLength() |
protected String |
getStringSequence() |
int |
length()
The number of symbols in this SymbolList.
|
protected void |
setAlphabetName(String alphaname) |
protected void |
setSequenceLength(int length) |
protected void |
setStringSequence(String seq) |
containsFeature, countFeatures, createFeature, edit, features, filter, filter, getAlphabet, getAlphabetName, getCircular, getFeatureSet, getSchema, getSeqVersion, getURN, iterator, removeFeature, seqString, setCircular, setFeatureSet, setSeqVersion, subList, subStr, symbolAt, toListaddComment, addRankedCrossRef, addRankedDocRef, addRelationship, compareTo, equals, getAccession, getAnnotation, getComments, getDescription, getDivision, getId, getIdentifier, getName, getNamespace, getNoteSet, getRankedCrossRefs, getRankedDocRefs, getRelationships, getRichAnnotation, getTaxon, getVersion, hashCode, removeComment, removeRankedCrossRef, removeRankedDocRef, removeRelationship, setDescription, setDivision, setId, setIdentifier, setNoteSet, setRankedCrossRefs, setTaxon, toStringaddChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListenerclone, finalize, getClass, notify, notifyAll, wait, wait, waitaddComment, addRankedDocRef, addRelationship, getAccession, getComments, getDescription, getDivision, getIdentifier, getName, getNamespace, getRankedDocRefs, getRelationships, getTaxon, getVersion, removeComment, removeRankedDocRef, removeRelationship, setDescription, setDivision, setIdentifier, setTaxongetNoteSet, getRichAnnotation, setNoteSetgetAnnotationaddChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListeneraddRankedCrossRef, getRankedCrossRefs, removeRankedCrossRef, setRankedCrossRefscompareTopublic SimpleRichSequence(Namespace ns, String name, String accession, int version, SymbolList symList, Double seqversion)
ns - the namespace for this sequence.name - the name of the sequence.accession - the accession of the sequence.version - the version of the sequence.symList - the symbols for the sequence.seqversion - the version of the symbols for the sequence.protected SimpleRichSequence()
protected void setAlphabetName(String alphaname) throws IllegalSymbolException, BioException
setAlphabetName in class ThinRichSequenceIllegalSymbolExceptionBioExceptionprotected void setStringSequence(String seq) throws IllegalSymbolException, BioException
IllegalSymbolExceptionBioExceptionprotected String getStringSequence()
public int length()
length in interface SymbolListlength in class ThinRichSequenceprotected void setSequenceLength(int length)
setSequenceLength in class ThinRichSequenceprotected int getSequenceLength()
getSequenceLength in class ThinRichSequencepublic SymbolList getInternalSymbolList()
getInternalSymbolList in interface RichSequencegetInternalSymbolList in class ThinRichSequenceCopyright © 2014 BioJava. All rights reserved.