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AbstractFeatureHolder (biojava-legacy 1.9.5 API)

  • java.lang.Object
    • org.biojava.utils.AbstractChangeable
      • org.biojava.bio.seq.AbstractFeatureHolder
  • All Implemented Interfaces:
    FeatureHolder, Changeable
    Direct Known Subclasses:
    MergeFeatureHolder, ProjectedFeatureHolder, SimpleFeatureHolder
    public abstract class AbstractFeatureHolder
extends AbstractChangeable
implements FeatureHolder

    An abstract implementation of FeatureHolder. This provides the filter method, but who wants to code that more than once? It also has support for the ChangeEvents.

    Author:
    Matthew Pocock, Thomas Down

    • Nested Class Summary

      • Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder

        FeatureHolder.EmptyFeatureHolder

    • Field Summary

      • Fields inherited from interface org.biojava.bio.seq.FeatureHolder

        EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

    • Constructor Summary

      Constructors 
      Constructor Description
      AbstractFeatureHolder()  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      Feature createFeature​(Feature.Template temp)

      Create a new Feature, and add it to this FeatureHolder.
      FeatureHolder filter​(FeatureFilter filter)

      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.
      void removeFeature​(Feature f)

      Remove a feature from this FeatureHolder.

      • 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, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

      • Methods inherited from interface org.biojava.utils.Changeable

        addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

      • Methods inherited from interface org.biojava.bio.seq.FeatureHolder

        containsFeature, countFeatures, features, getSchema

    • Constructor Detail

      • AbstractFeatureHolder

        public AbstractFeatureHolder()

    • Method Detail

      • filter

        public FeatureHolder filter​(FeatureFilter filter)

        Query this set of features using a supplied FeatureFilter.

        Specified by:
        filter in interface FeatureHolder
        Parameters:
        filter - the FeatureFilter to apply.
        Returns:
        all features in this container which match filter.

      • filter

        public FeatureHolder filter​(FeatureFilter ff,
                            boolean recurse)

        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.

      • createFeature

        public Feature createFeature​(Feature.Template temp)
                      throws BioException,
                             ChangeVetoException

        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

      • removeFeature

        public void removeFeature​(Feature f)
                   throws ChangeVetoException,
                          BioException

        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