SimpleGappedSequence (biojava-legacy 1.9.5 API)

SimpleGappedSequence (biojava-legacy 1.9.5 API)

Nested Class Summary

Nested Classes
Modifier and Type Class Description

class SimpleGappedSequence.GappedContext
- Nested classes/interfaces inherited from class org.biojava.bio.symbol.SimpleGappedSymbolList
  SimpleGappedSymbolList.Block
- Nested classes/interfaces inherited from class org.biojava.bio.symbol.AbstractSymbolList
  AbstractSymbolList.EditScreener, AbstractSymbolList.EditTranslater
- Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
  Annotatable.AnnotationForwarder
- Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
  FeatureHolder.EmptyFeatureHolder

Field Summary
- Fields inherited from interface org.biojava.bio.Annotatable
  ANNOTATION
- Fields inherited from interface org.biojava.bio.seq.FeatureHolder
  EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA
- Fields inherited from interface org.biojava.bio.symbol.SymbolList
  EDIT, EMPTY_LIST

Constructor Summary

Constructors
Constructor Description

SimpleGappedSequence(GappedSequence seq)

SimpleGappedSequence(Sequence seq)

SimpleGappedSequence(Alphabet alpha)

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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)`

Methods inherited from class org.biojava.bio.symbol.SimpleGappedSymbolList
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, viewToSource

Methods inherited from class org.biojava.bio.symbol.AbstractSymbolList
edit, equals, hashCode, iterator, seqString, subList, subStr, toList, toString

Methods inherited from class org.biojava.utils.AbstractChangeable
addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.symbol.GappedSymbolList
addGapInSource, addGapInView, addGapsInSource, addGapsInView, firstNonGap, getSourceSymbolList, getUngappedLocation, lastNonGap, removeGap, removeGaps, sourceToView, viewToSource

Methods inherited from interface org.biojava.bio.symbol.SymbolList
edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList