org.biojava.bio.seq.impl
Class SimpleGappedSequence

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by org.biojava.bio.symbol.AbstractSymbolList
          extended by org.biojava.bio.symbol.SimpleGappedSymbolList
              extended by org.biojava.bio.seq.impl.SimpleGappedSequence
All Implemented Interfaces:
java.io.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.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.
 java.util.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()
           
 java.lang.String getName()
          The name of this sequence.
 FeatureFilter getSchema()
          Return a schema-filter for this FeatureHolder.
 java.lang.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.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 java.lang.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 java.lang.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 java.util.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 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)).

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