Class ProjectedFeatureHolder

Method Details

• getContext

  public ProjectionContext getContext()

• 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

• 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

• 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

  Overrides:

  filter in class AbstractFeatureHolder

  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

  Overrides:

  filter in class AbstractFeatureHolder

  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.

• 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

  Overrides:

  createFeature in class AbstractFeatureHolder

  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

• removeFeature

  public void removeFeature(Feature dyingChild) throws ChangeVetoException, BioException

  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

  BioException - if there was an error removing the feature

• 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

• makeProjectionSet

  protected FeatureHolder makeProjectionSet(FeatureHolder fh)

  Called internally to construct a lightweight projected view of a set of features

• forwardChangeEvent

  protected ChangeEvent forwardChangeEvent(ChangeEvent cev)

  Called internally to generate a forwarded version of a ChangeEvent from our underlying FeatureHolder