X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeaturesI.java;h=40beae367d219f435a214abf450bb7fa97211f8c;hb=1580169b8b5b244d380ec7b99a732dd34b0d454a;hp=5f904da05349c48c470039daac65f0ea8f0d07d6;hpb=6a2fd9a13d79f316acdd4fcff066b8cfaaefa939;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeaturesI.java b/src/jalview/datamodel/features/SequenceFeaturesI.java
index 5f904da..40beae3 100644
--- a/src/jalview/datamodel/features/SequenceFeaturesI.java
+++ b/src/jalview/datamodel/features/SequenceFeaturesI.java
@@ -12,11 +12,12 @@ public interface SequenceFeaturesI
    * Adds one sequence feature to the store, and returns true, unless the
    * feature is already contained in the store, in which case this method
    * returns false. Containment is determined by SequenceFeature.equals()
-   * comparison.
+   * comparison. Answers false, and does not add the feature, if feature type is
+   * null.
    * 
    * @param sf
    */
-  public abstract boolean add(SequenceFeature sf);
+  boolean add(SequenceFeature sf);
 
   /**
    * Returns a (possibly empty) list of features, optionally restricted to
@@ -28,19 +29,66 @@ public interface SequenceFeaturesI
    * @param type
    * @return
    */
-  public abstract List<SequenceFeature> findFeatures(int from, int to,
+  List<SequenceFeature> findFeatures(int from, int to,
           String... type);
 
   /**
-   * Answers a list of all features stored, optionally restricted to specified
-   * types, in no particular guaranteed order
+   * Answers a list of all features stored, in no particular guaranteed order.
+   * Positional features may optionally be restricted to specified types, but
+   * all non-positional features (if any) are always returned.
+   * <p>
+   * To filter non-positional features by type, use
+   * getNonPositionalFeatures(type).
+   * 
+   * @param type
+   * @return
+   */
+  List<SequenceFeature> getAllFeatures(String... type);
+
+  /**
+   * Answers a list of all positional (or non-positional) features which are in
+   * the specified feature group, optionally restricted to features of specified
+   * types.
    * 
+   * @param positional
+   *          if true returns positional features, else non-positional features
+   * @param group
+   *          the feature group to be matched (which may be null)
    * @param type
+   *          optional feature types to filter by
+   * @return
+   */
+  List<SequenceFeature> getFeaturesForGroup(boolean positional,
+          String group, String... type);
+
+  /**
+   * Answers a list of all features stored, whose type either matches one of the
+   * given ontology terms, or is a specialisation of a term in the Sequence
+   * Ontology. Results are returned in no particular guaranteed order.
+   * 
+   * @param ontologyTerm
    * @return
    */
-  public abstract List<SequenceFeature> getAllFeatures(String... type);
+  List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm);
 
-  public abstract int getFeatureCount(boolean positional, String... type);
+  /**
+   * Answers the number of (positional or non-positional) features, optionally
+   * restricted to specified feature types. Contact features are counted as 1.
+   * 
+   * @param positional
+   * @param type
+   * @return
+   */
+  int getFeatureCount(boolean positional, String... type);
+
+  /**
+   * Answers the total length of positional features, optionally restricted to
+   * specified feature types. Contact features are counted as length 1.
+   * 
+   * @param type
+   * @return
+   */
+  int getTotalFeatureLength(String... type);
 
   /**
    * Answers a list of all positional features, optionally restricted to
@@ -49,7 +97,7 @@ public interface SequenceFeaturesI
    * @param type
    * @return
    */
-  public abstract List<SequenceFeature> getPositionalFeatures(
+  List<SequenceFeature> getPositionalFeatures(
           String... type);
 
   /**
@@ -58,7 +106,7 @@ public interface SequenceFeaturesI
    * 
    * @return
    */
-  public abstract List<SequenceFeature> getContactFeatures(String... type);
+  List<SequenceFeature> getContactFeatures(String... type);
 
   /**
    * Answers a list of all non-positional features, optionally restricted to
@@ -68,7 +116,7 @@ public interface SequenceFeaturesI
    *          if no type is specified, all are returned
    * @return
    */
-  public abstract List<SequenceFeature> getNonPositionalFeatures(
+  List<SequenceFeature> getNonPositionalFeatures(
           String... type);
 
   /**
@@ -79,14 +127,14 @@ public interface SequenceFeaturesI
    * 
    * @param sf
    */
-  public abstract boolean delete(SequenceFeature sf);
+  boolean delete(SequenceFeature sf);
 
   /**
    * Answers true if this store contains at least one feature, else false
    * 
    * @return
    */
-  public abstract boolean hasFeatures();
+  boolean hasFeatures();
 
   /**
    * Returns a set of the distinct feature groups present in the collection. The
@@ -99,7 +147,7 @@ public interface SequenceFeaturesI
    * @param type
    * @return
    */
-  public abstract Set<String> getFeatureGroups(boolean positionalFeatures,
+  Set<String> getFeatureGroups(boolean positionalFeatures,
           String... type);
 
   /**
@@ -112,14 +160,47 @@ public interface SequenceFeaturesI
    * @param groups
    * @return
    */
-  public abstract Set<String> getFeatureTypesForGroups(
+  Set<String> getFeatureTypesForGroups(
           boolean positionalFeatures, String... groups);
 
   /**
-   * Answers a set of the distinct feature types for which a feature is stored
+   * Answers a set of the distinct feature types for which a feature is stored.
+   * The types may optionally be restricted to those which match, or are a
+   * subtype of, given sequence ontology terms
+   * 
+   * @return
+   */
+  Set<String> getFeatureTypes(String... soTerm);
+
+  /**
+   * Answers the minimum score held for positional or non-positional features
+   * for the specified type. This may be Float.NaN if there are no features, or
+   * none has a non-NaN score.
    * 
+   * @param type
+   * @param positional
    * @return
    */
-  public abstract Set<String> getFeatureTypes();
+  float getMinimumScore(String type, boolean positional);
 
+  /**
+   * Answers the maximum score held for positional or non-positional features
+   * for the specified type. This may be Float.NaN if there are no features, or
+   * none has a non-NaN score.
+   * 
+   * @param type
+   * @param positional
+   * @return
+   */
+  float getMaximumScore(String type, boolean positional);
+
+  /**
+   * Adds the shift amount to the start and end of all positional features whose
+   * start position is at or after fromPosition. Returns true if at least one
+   * feature was shifted, else false.
+   * 
+   * @param fromPosition
+   * @param shiftBy
+   */
+  boolean shiftFeatures(int fromPosition, int shiftBy);
 }
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