Package org.biojava.bio.seq.impl

Class SimpleFeature

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.impl.SimpleFeature
All Implemented Interfaces:
Serializable, Annotatable, Feature, FeatureHolder, RealizingFeatureHolder, Changeable
Direct Known Subclasses:
SimpleStrandedFeature
public class SimpleFeature extends AbstractChangeable implements Feature, RealizingFeatureHolder, Serializable
A no-frills implementation of a feature.
Author:
Matthew Pocock, Thomas Down, Kalle N�slund, Paul Seed, Len Trigg
See Also:

  • Constructor Details

    • SimpleFeature

      public SimpleFeature(Sequence sourceSeq, FeatureHolder parent, Feature.Template template)
      Create a SimpleFeature on the given sequence. The feature is created underneath the parent FeatureHolder and populated directly from the template fields. However, if the template annotation is the Annotation.EMPTY_ANNOTATION, an empty SimpleAnnotation is attached to the feature instead.
      Parameters:
      sourceSeq - the source sequence
      parent - the parent sequence or feature
      template - the template for the feature

  • Method Details

    • getFeatureHolder

      protected SimpleFeatureHolder getFeatureHolder()
      A utility function to retrieve the feature holder delegate, creating it if necessary.
      Returns:
      the FeatureHolder delegate

    • featureHolderAllocated

      protected boolean featureHolderAllocated()
      A utility function to find out if the feature holder delegate has been instantiated yet. If it has not, we may avoid instantiating it by returning some pre-canned result.
      Returns:
      true if the feature holder delegate has been created and false otherwise

    • getChangeSupport

      protected ChangeSupport getChangeSupport(ChangeType ct)
      Description copied from class: AbstractChangeable
      Called to retrieve the ChangeSupport for this object.

      Your implementation of this method should have the following structure: 

       ChangeSupport cs = super.getChangeSupport(ct);

 if(someForwarder == null && ct.isMatching(SomeInterface.SomeChangeType)) {
   someForwarder = new ChangeForwarder(...

   this.stateVariable.addChangeListener(someForwarder, VariableInterface.AChange);
 }

 return cs;
      It is usual for the forwarding listeners (someForwarder in this example) to be transient and lazily instantiated. Be sure to register & unregister the forwarder in the code that does the ChangeEvent handling in setter methods.
      Overrides:
      getChangeSupport in class AbstractChangeable

    • getLocation

      public Location getLocation()
      Description copied from interface: Feature
      The location of this feature.

      The location may be complicated, or simply a range. The annotation is assumed to apply to all the region contained within the location.

      Specified by:
      getLocation in interface Feature
      Returns:
      a Location anchoring this feature

    • setLocation

      public void setLocation(Location loc) throws ChangeVetoException
      Description copied from interface: Feature
      The new location for this feature.

      The location may be complicated or simply a range. The annotation is assumed to apply to the entire region contained within the location. Any values returned from methods that rely on the old location must not be affected.

      Specified by:
      setLocation in interface Feature
      Parameters:
      loc - the new Location for this feature
      Throws:
      ChangeVetoException - if the location can't be altered

    • getTypeTerm

      public Term getTypeTerm()
      Description copied from interface: Feature
      An ontology term defining the type of feature. This is optional, and will default to OntoTools.ANY in implementations which aren't ontology aware.
      Specified by:
      getTypeTerm in interface Feature

    • getType

      public String getType()
      Description copied from interface: Feature
      The type of the feature.
      Specified by:
      getType in interface Feature
      Returns:
      the type of this sequence

    • setType

      public void setType(String type) throws ChangeVetoException
      Description copied from interface: Feature
      Change the type of this feature.
      Specified by:
      setType in interface Feature
      Parameters:
      type - new type String
      Throws:
      ChangeVetoException - if the type can't be altered

    • setTypeTerm

      public void setTypeTerm(Term t) throws ChangeVetoException
      Description copied from interface: Feature
      Set the type ontology-term for this feature. If this succeeds, it will generally also change the source name.
      Specified by:
      setTypeTerm in interface Feature
      Throws:
      ChangeVetoException - if changes are not allowed

    • getSource

      public String getSource()
      Description copied from interface: Feature
      The source of the feature. This may be a program or process.
      Specified by:
      getSource in interface Feature
      Returns:
      the source, or generator

    • getSourceTerm

      public Term getSourceTerm()
      Description copied from interface: Feature
      An ontology term defining the source of this feature. This is optional, and will default to OntoTools.ANY in implementations which aren't ontology aware.
      Specified by:
      getSourceTerm in interface Feature

    • getParent

      public FeatureHolder getParent()
      Description copied from interface: Feature
      Return the FeatureHolder to which this feature has been attached. This will be a Sequence object for top level features, and a Feature object for features further down the tree.
      Specified by:
      getParent in interface Feature

    • setSource

      public void setSource(String source) throws ChangeVetoException
      Description copied from interface: Feature
      Change the source of the Feature.
      Specified by:
      setSource in interface Feature
      Parameters:
      source - the new source String
      Throws:
      ChangeVetoException - if the source can't be altered

    • setSourceTerm

      public void setSourceTerm(Term t) throws ChangeVetoException
      Description copied from interface: Feature
      Set the source ontology-term for this feature. If this succeeds, it will generally also change the source name.
      Specified by:
      setSourceTerm in interface Feature
      Throws:
      ChangeVetoException - if changes are not allowed

    • getSequence

      public Sequence getSequence()
      Description copied from interface: Feature
      Return the Sequence object to which this feature is (ultimately) attached. For top level features, this will be equal to the FeatureHolder returned by getParent.
      Specified by:
      getSequence in interface Feature
      Returns:
      the ultimate parent Sequence

    • 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

    • getSymbols

      public SymbolList getSymbols()
      Description copied from interface: Feature
      Return a list of symbols that are contained in this feature.

      The symbols may not be contiguous in the original sequence, but they will be concatenated together in the resulting SymbolList.

      The order of the Symbols within the resulting symbol list will be according to the concept of ordering within the location object.

      If the feature location is modified then this does not modify any SymbolList produced by earlier invocations of this method.

      Specified by:
      getSymbols in interface Feature
      Returns:
      a SymbolList containing each symbol of the parent sequence contained within this feature in the order they appear in the parent

    • 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

    • features

      public Iterator features()
      Description copied from interface: Feature
      Iterate over any child features which are held by this feature. The order of iteration MAY be significant for some types of Feature.
      Specified by:
      features in interface Feature
      Specified by:
      features in interface FeatureHolder
      Returns:
      an Iterator

    • removeFeature

      public void removeFeature(Feature f) throws ChangeVetoException
      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

    • 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

    • 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.

    • makeTemplate

      public Feature.Template makeTemplate()
      Description copied from interface: Feature
      Create a new Template that could be used to generate a feature identical to this one. The fields of the template can be edited without changing the feature.
      Specified by:
      makeTemplate in interface Feature
      Returns:
      a new Template that would make a feature like this one

    • fillTemplate

      protected void fillTemplate(Feature.Template ft)

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • realizeFeature

      public Feature realizeFeature(FeatureHolder fh, Feature.Template templ) throws BioException
      Description copied from interface: RealizingFeatureHolder
      Realize a feature template. This will be a template which has been passed to the createFeature method of either this FeatureHolder or one of our child Features.
      Specified by:
      realizeFeature in interface RealizingFeatureHolder
      Throws:
      BioException

    • createFeature

      public Feature createFeature(Feature.Template temp) throws BioException, ChangeVetoException
      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:
      BioException - if something went wrong during creating the feature
      ChangeVetoException - if this FeatureHolder does not support creation of new features, or if the change was vetoed

    • hashCode

      public int hashCode()
      Overrides:
      hashCode in class Object

    • equals

      public boolean equals(Object o)
      Overrides:
      equals in class Object

    • 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