Package org.biojava.bio.seq

Class SimpleFeatureHolder

java.lang.Object
org.biojava.utils.AbstractChangeable
org.biojava.bio.seq.AbstractFeatureHolder
org.biojava.bio.seq.SimpleFeatureHolder
All Implemented Interfaces:
Serializable, FeatureHolder, Changeable
public class SimpleFeatureHolder extends AbstractFeatureHolder implements Serializable
A no-frills implementation of FeatureHolder.
Author:
Matthew Pocock, Thomas Down
See Also:

  • Constructor Details

  • Method Details

    • getFeatures

      protected List getFeatures()
      Returns the list of features in this featureholder.

    • 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<Feature> features()
      Description copied from interface: FeatureHolder
      Iterate over the features in no well defined order.
      Specified by:
      features in interface FeatureHolder
      Returns:
      an Iterator

    • addFeature

      public void addFeature(Feature f) throws ChangeVetoException
      Add a feature to the featureholder
      Throws:
      ChangeVetoException

    • 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
      Overrides:
      removeFeature in class AbstractFeatureHolder
      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

    • 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