## org.biojava.bio.seq.impl
Class SimpleGappedSequence

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojava.bio.symbol.AbstractSymbolList
              org.biojava.bio.symbol.SimpleGappedSymbolList
                  org.biojava.bio.seq.impl.SimpleGappedSequence

All Implemented Interfaces:
  Serializable, Annotatable, FeatureHolder, GappedSequence, Sequence, GappedSymbolList, SymbolList, Changeable

    public class SimpleGappedSequence

extends SimpleGappedSymbolList
implements GappedSequence

Simple implementation of GappedSequence. Please note that this is a view onto another Sequence. Gaps created and removed are only in the view not the underlying original. This means that any gaps present in the original cannot be manipulated in this view. To manipulate the original you would need to use Edit objects.

Since:
  1.3
Author:
  Thomas Down, Matthew Pocock
See Also:
  Serialized Form

Nested Class Summary
`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.seq.FeatureHolder
`FeatureHolder.EmptyFeatureHolder`

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
`Annotatable.AnnotationForwarder`

Field Summary

Fields inherited from interface org.biojava.bio.symbol.SymbolList
`EDIT, EMPTY_LIST`

Fields inherited from interface org.biojava.bio.seq.FeatureHolder
`EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA`

Fields inherited from interface org.biojava.bio.Annotatable
`ANNOTATION`

Fields inherited from interface org.biojava.bio.symbol.SymbolList
`EDIT, EMPTY_LIST`

Constructor Summary
`SimpleGappedSequence(GappedSequence seq)`
`SimpleGappedSequence(Sequence seq)`

Method Summary
`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` `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.bio.symbol.SymbolList
`edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList`

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

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

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`

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

Constructor Detail

### SimpleGappedSequence

    public SimpleGappedSequence(Sequence seq)

### SimpleGappedSequence

    public SimpleGappedSequence(GappedSequence seq)

Method Detail

### getCreateOnUnderlyingSequence

    public boolean getCreateOnUnderlyingSequence()

### setCreateOnUnderlyingSequence

    public void setCreateOnUnderlyingSequence(boolean underlying)

### getAnnotation

    public Annotation getAnnotation()

  Description copied from interface: `Annotatable`
  Should return the associated annotation object.

  Specified by:
    `getAnnotation` in interface `Annotatable`
  Returns:
    an Annotation object, never null

### getName

    public String getName()

  Description copied from interface: `Sequence`
  The name of this sequence.

  The name may contain spaces or odd characters.

  Specified by:
    `getName` in interface `Sequence`
  Returns:
    the name as a String

### getURN

    public String getURN()

  Description copied from interface: `Sequence`
  A Uniform Resource Identifier (URI) which identifies the sequence represented by this object. For sequences in well-known database, this may be a URN, e.g.

       urn:sequence/embl:AL121903

  It 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

  Specified by:
    `getURN` in interface `Sequence`
  Returns:
    the URI as a String

### features

    public Iterator features()

  Description copied from interface: `FeatureHolder`
  Iterate over the features in no well defined order.

  Specified by:
    `features` in interface `FeatureHolder`
  Returns:
    an Iterator

### filter

    public FeatureHolder filter(FeatureFilter ff)

  Description copied from interface: `FeatureHolder`
  Query this set of features using a supplied `FeatureFilter`.

  Specified by:
    `filter` in interface `FeatureHolder`
  Parameters:
    `ff` - the `FeatureFilter` to apply.
  Returns:
    all features in this container which match `filter`.

### filter

    public FeatureHolder filter(FeatureFilter ff,
                                boolean recurse)

  Description copied from interface: `FeatureHolder`
  Return a new FeatureHolder that contains all of the children of this one that passed the filter fc. This method is scheduled for deprecation. Use the 1-arg filter instead.

  Specified by:
    `filter` in interface `FeatureHolder`
  Parameters:
    `ff` - the FeatureFilter to apply
    `recurse` - 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.

### countFeatures

    public int countFeatures()

  Description copied from interface: `FeatureHolder`
  Count how many features are contained.

  Specified by:
    `countFeatures` in interface `FeatureHolder`
  Returns:
    a positive integer or zero, equal to the number of features contained

### containsFeature

    public boolean containsFeature(Feature f)

  Description copied from interface: `FeatureHolder`
  Check if the feature is present in this holder.

  Specified by:
    `containsFeature` in interface `FeatureHolder`
  Parameters:
    `f` - the Feature to check
  Returns:
    true if f is in this set

### getSchema

    public FeatureFilter getSchema()

  Description copied from interface: `FeatureHolder`
  Return a schema-filter for this `FeatureHolder`. This is a filter which all `Feature`s 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))`.

  Specified by:
    `getSchema` in interface `FeatureHolder`
  Returns:
    the schema filter

### removeFeature

    public void removeFeature(Feature f)
                       throws ChangeVetoException,
                              BioException

  Description copied from interface: `FeatureHolder`
  Remove a feature from this FeatureHolder.

  Specified by:
    `removeFeature` in interface `FeatureHolder`
  Throws:
    `ChangeVetoException` - if this FeatureHolder does not support feature removal or if the change was vetoed
    `BioException` - if there was an error removing the feature

### createFeature

    public Feature createFeature(Feature.Template templ)
                          throws ChangeVetoException,
                                 BioException

  Description copied from interface: `FeatureHolder`
  Create a new Feature, and add it to this FeatureHolder. This method will generally only work on Sequences, and on some Features which have been attached to Sequences.

  Specified by:
    `createFeature` in interface `FeatureHolder`
  Throws:
    `ChangeVetoException` - if this FeatureHolder does not support creation of new features, or if the change was vetoed
    `BioException` - if something went wrong during creating the feature