Package org.biojava.bio.seq

Interface Feature

All Superinterfaces:
Annotatable, Changeable, FeatureHolder
All Known Subinterfaces:
ComponentFeature, FramedFeature, HomologyFeature, RemoteFeature, RestrictionSite, RichFeature, SimilarityPairFeature, StrandedFeature
All Known Implementing Classes:
ProjectedFeature, SimpleFeature, SimpleFramedFeature, SimpleHomologyFeature, SimpleRemoteFeature, SimpleRestrictionSite, SimpleRichFeature, SimpleSimilarityPairFeature, SimpleStrandedFeature
public interface Feature extends FeatureHolder, Annotatable
A feature within a sequence, or nested within another feature.

Common operations

 // loop over all features in a sequence
 for(Iterator fi = mySeq.features(); fi.hasNext(); ) {
   Feature f = (Feature) fi.next();
   System.out.println(f.getType() + "\t" + f.getLocation());
 }

 // loop over all features that are children of this one, such as exons in a
 // gene
 for(Iterator cfi = feature.features(); cfi.hasNext(); ) {
   ...

 // extract all stranded features that are directly on a sequence
 FeatureHolder strandedFeatures = mySeq.filter(
   new FeatureFilter.ByClass(StrandedFeature.class),
   false
  );
 for(fi = strandedFeatures.features(); ...

 // find all features with the type property set to "EXON" no matter how
 // far down the feature hierachy they are
 FeatureHolder repeats = mySeq.filter(
   new FeatureFilter.ByType("EXON"),
   true;
 );

Description

Features contain annotation and a location. The type of the feature is something like 'Repeat' or 'BetaStrand'. Where the feature has been read from an EMBL or Genbank source the type will be the same as the feature key in the feature table e.g. 'gene', 'CDS', 'repeat_unit', 'misc_feature'. The source of the feature is something like 'genscan', 'repeatmasker' or 'made-up'.

Features are always contained by a parent FeatureHolder, which may either be a Sequence or another Feature. Feature instances should never be constructed directly by client code, and the BioJava core does not contain any publicly accessible implementations of the Feature interface. Instead, you should create a suitable Feature.Template, then pass this to the createFeature method of a Sequence or Feature.

We may need some standardisation for what the fields mean. In particular, we should be compliant where sensible with GFF.

Author:
Matthew Pocock, Thomas Down, Keith James
See Also:

  • Field Details

    • PROPERTY_DATA_KEY

      static final String PROPERTY_DATA_KEY
      This is used as a key in the Annotation where it identifies internal data. This is not printed when the Feature is written to a flatfile. E.g. the original feature's EMBL location string (if it has one) is stored here.
      See Also:

    • LOCATION

      static final ChangeType LOCATION
      The location of this feature is being altered.

    • TYPE

      static final ChangeType TYPE
      The type of this feature has altered.

    • SOURCE

      static final ChangeType SOURCE
      The source of this feature has altered

    • TYPETERM

      static final ChangeType TYPETERM
      The ontological type of this feature has altered.

    • SOURCETERM

      static final ChangeType SOURCETERM
      The ontological source of this feature has altered

    • byLocationOrder

      static final Feature.ByLocationComparator byLocationOrder
      byLocationOrder contains a Feature comparator which compares by the minimum base position of their Location.

  • Method Details

    • getLocation

      Location getLocation()
      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.

      Returns:
      a Location anchoring this feature

    • setLocation

      void setLocation(Location loc) throws ChangeVetoException
      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.

      Parameters:
      loc - the new Location for this feature
      Throws:
      ChangeVetoException - if the location can't be altered

    • getType

      String getType()
      The type of the feature.
      Returns:
      the type of this sequence

    • setType

      void setType(String type) throws ChangeVetoException
      Change the type of this feature.
      Parameters:
      type - new type String
      Throws:
      ChangeVetoException - if the type can't be altered

    • getTypeTerm

      Term getTypeTerm()
      An ontology term defining the type of feature. This is optional, and will default to OntoTools.ANY in implementations which aren't ontology aware.
      Since:
      1.4

    • setTypeTerm

      void setTypeTerm(Term t) throws ChangeVetoException, InvalidTermException
      Set the type ontology-term for this feature. If this succeeds, it will generally also change the source name.
      Throws:
      ChangeVetoException - if changes are not allowed
      InvalidTermException - if the specified term is not an acceptable type for this feature.
      Since:
      1.4

    • getSourceTerm

      Term getSourceTerm()
      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.
      Since:
      1.4

    • setSourceTerm

      void setSourceTerm(Term t) throws ChangeVetoException, InvalidTermException
      Set the source ontology-term for this feature. If this succeeds, it will generally also change the source name.
      Throws:
      ChangeVetoException - if changes are not allowed
      InvalidTermException - if the specified term is not an acceptable type for this feature.
      Since:
      1.4

    • getSource

      String getSource()
      The source of the feature. This may be a program or process.
      Returns:
      the source, or generator

    • setSource

      void setSource(String source) throws ChangeVetoException
      Change the source of the Feature.
      Parameters:
      source - the new source String
      Throws:
      ChangeVetoException - if the source can't be altered

    • getSymbols

      SymbolList getSymbols()
      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.

      Returns:
      a SymbolList containing each symbol of the parent sequence contained within this feature in the order they appear in the parent

    • getParent

      FeatureHolder getParent()
      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.

    • getSequence

      Sequence getSequence()
      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.
      Returns:
      the ultimate parent Sequence

    • features

      Iterator features()
      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 FeatureHolder
      Returns:
      an Iterator

    • makeTemplate

      Feature.Template makeTemplate()
      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.
      Returns:
      a new Template that would make a feature like this one