X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeaturesI.java;h=ca142781a3cfe05019dd24d46754e2fdf1afab49;hb=15a605b8a12026b453e252477b416b2c82b6344a;hp=cfcdc761b5426b36ad6c0505a6aa1f266fc631f1;hpb=b5a5b5fa7fe3fb77e55acf930d25d10ddc0e80e2;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeaturesI.java b/src/jalview/datamodel/features/SequenceFeaturesI.java
index cfcdc76..ca14278 100644
--- a/src/jalview/datamodel/features/SequenceFeaturesI.java
+++ b/src/jalview/datamodel/features/SequenceFeaturesI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel.features;
 
 import jalview.datamodel.SequenceFeature;
@@ -22,19 +42,23 @@ public interface SequenceFeaturesI
   /**
    * Returns a (possibly empty) list of features, optionally restricted to
    * specified types, which overlap the given (inclusive) sequence position
-   * range
+   * range. If types are specified, features are returned in the order of the
+   * types given.
    * 
    * @param from
    * @param to
    * @param type
    * @return
    */
-  List<SequenceFeature> findFeatures(int from, int to,
-          String... type);
+  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
@@ -42,6 +66,32 @@ public interface SequenceFeaturesI
   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, or is a
+   * specialisation (in the Sequence Ontology) of, one of the given terms.
+   * Results are returned in no particular order.
+   * 
+   * @param ontologyTerm
+   * @return
+   */
+  List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm);
+
+  /**
    * Answers the number of (positional or non-positional) features, optionally
    * restricted to specified feature types. Contact features are counted as 1.
    * 
@@ -67,8 +117,7 @@ public interface SequenceFeaturesI
    * @param type
    * @return
    */
-  List<SequenceFeature> getPositionalFeatures(
-          String... type);
+  List<SequenceFeature> getPositionalFeatures(String... type);
 
   /**
    * Answers a list of all contact features, optionally restricted to specified
@@ -86,8 +135,7 @@ public interface SequenceFeaturesI
    *          if no type is specified, all are returned
    * @return
    */
-  List<SequenceFeature> getNonPositionalFeatures(
-          String... type);
+  List<SequenceFeature> getNonPositionalFeatures(String... type);
 
   /**
    * Deletes the given feature from the store, returning true if it was found
@@ -117,8 +165,7 @@ public interface SequenceFeaturesI
    * @param type
    * @return
    */
-  Set<String> getFeatureGroups(boolean positionalFeatures,
-          String... type);
+  Set<String> getFeatureGroups(boolean positionalFeatures, String... type);
 
   /**
    * Answers the set of distinct feature types for which there is at least one
@@ -130,15 +177,17 @@ public interface SequenceFeaturesI
    * @param groups
    * @return
    */
-  Set<String> getFeatureTypesForGroups(
-          boolean positionalFeatures, String... groups);
+  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();
+  Set<String> getFeatureTypes(String... soTerm);
 
   /**
    * Answers the minimum score held for positional or non-positional features
@@ -161,4 +210,19 @@ public interface SequenceFeaturesI
    * @return
    */
   float getMaximumScore(String type, boolean positional);
-}
\ No newline at end of file
+
+  /**
+   * 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);
+
+  /**
+   * Deletes all positional and non-positional features
+   */
+  void deleteAll();
+}