public class SimpleGappedSequence extends SimpleGappedSymbolList implements GappedSequence
| Modifier and Type | Class and Description |
|---|---|
class |
SimpleGappedSequence.GappedContext |
SimpleGappedSymbolList.BlockAbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslaterFeatureHolder.EmptyFeatureHolderAnnotatable.AnnotationForwarderEMPTY_FEATURE_HOLDER, FEATURES, SCHEMAANNOTATIONEDIT, EMPTY_LIST| Constructor and Description |
|---|
SimpleGappedSequence(Alphabet alpha) |
SimpleGappedSequence(GappedSequence seq) |
SimpleGappedSequence(Sequence seq) |
| Modifier and Type | Method and Description |
|---|---|
boolean |
containsFeature(Feature f)
Check if the feature is present in this holder.
|
int |
countFeatures()
Count how many features are contained.
|
Feature |
createFeature(Feature.Template templ)
Create a new Feature, and add it to this FeatureHolder.
|
Iterator<Feature> |
features()
Iterate over the features in no well defined order.
|
FeatureHolder |
filter(FeatureFilter ff)
Query this set of features using a supplied
FeatureFilter. |
FeatureHolder |
filter(FeatureFilter ff,
boolean recurse)
Return a new FeatureHolder that contains all of the children of this one
that passed the filter fc.
|
Annotation |
getAnnotation()
Should return the associated annotation object.
|
boolean |
getCreateOnUnderlyingSequence() |
String |
getName()
The name of this sequence.
|
FeatureFilter |
getSchema()
Return a schema-filter for this
FeatureHolder. |
String |
getURN()
A Uniform
Resource Identifier (URI) which identifies the sequence
represented by this object.
|
void |
removeFeature(Feature f)
Remove a feature from this FeatureHolder.
|
void |
setCreateOnUnderlyingSequence(boolean underlying) |
addGapInSource, addGapInView, addGapsInSource, addGapsInView, BlockIterator, dumpBlocks, findSourceBlock, findSourceGap, findViewBlock, findViewGap, firstNonGap, gappedToLocation, getAlphabet, getSourceSymbolList, getUngappedLocation, isSane, lastNonGap, length, locationToGapped, removeGap, removeGaps, renumber, sourceToView, sourceToView, symbolAt, viewToSource, viewToSourceedit, equals, hashCode, iterator, seqString, subList, subStr, toList, toStringaddChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListenerclone, finalize, getClass, notify, notifyAll, wait, wait, waitaddGapInSource, addGapInView, addGapsInSource, addGapsInView, firstNonGap, getSourceSymbolList, getUngappedLocation, lastNonGap, removeGap, removeGaps, sourceToView, viewToSourceedit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toListaddChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListenerpublic SimpleGappedSequence(Alphabet alpha)
public SimpleGappedSequence(Sequence seq)
public SimpleGappedSequence(GappedSequence seq)
public boolean getCreateOnUnderlyingSequence()
public void setCreateOnUnderlyingSequence(boolean underlying)
public Annotation getAnnotation()
AnnotatablegetAnnotation in interface Annotatablepublic String getName()
SequenceThe name may contain spaces or odd characters.
public String getURN()
Sequenceurn:sequence/embl:AL121903It may also be a URL identifying a specific resource, either locally or over the network
file:///home/thomas/myseq.fa|seq22 http://www.mysequences.net/chr22.seq
public Iterator<Feature> features()
FeatureHolderfeatures in interface FeatureHolderpublic FeatureHolder filter(FeatureFilter ff)
FeatureHolderFeatureFilter.filter in interface FeatureHolderff - the FeatureFilter to apply.filter.public FeatureHolder filter(FeatureFilter ff, boolean recurse)
FeatureHolderfilter in interface FeatureHolderff - the FeatureFilter to applyrecurse - true if all features-of-features should be scanned, and a
single flat collection of features returned, or false if
just immediate children should be filtered.public int countFeatures()
FeatureHoldercountFeatures in interface FeatureHolderpublic boolean containsFeature(Feature f)
FeatureHoldercontainsFeature in interface FeatureHolderf - the Feature to checkpublic FeatureFilter getSchema()
FeatureHolderFeatureHolder. This is a filter
which all Features immediately contained by this FeatureHolder
will match. It need not directly match their child features, but it can (and should!) provide
information about them using FeatureFilter.OnlyChildren filters. In cases where there
is no feature hierarchy, this can be indicated by including FeatureFilter.leaf in
the schema filter.
For the truly non-informative case, it is possible to return FeatureFilter.all. However,
it is almost always possible to provide slightly more information that this. For example, Sequence
objects should, at a minimum, return FeatureFilter.top_level. Feature objects
should, as a minimum, return FeatureFilter.ByParent(new FeatureFilter.ByFeature(this)).
getSchema in interface FeatureHolderpublic void removeFeature(Feature f) throws ChangeVetoException, BioException
FeatureHolderremoveFeature in interface FeatureHolderChangeVetoException - if this FeatureHolder does not support
feature removal or if the change was vetoedBioException - if there was an error removing the featurepublic Feature createFeature(Feature.Template templ) throws ChangeVetoException, BioException
FeatureHoldercreateFeature in interface FeatureHolderChangeVetoException - if this FeatureHolder does not support
creation of new features, or if the change was vetoedBioException - if something went wrong during creating the featureCopyright © 2014 BioJava. All rights reserved.