X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeaturesI.java;h=7213cbaf47e5c4117cc61e536883119578f96d35;hb=0b573ed90b14079f7326281f50c0c9cffdace586;hp=43e94480fd96785ef88261f8ccbf15a06d97e0a7;hpb=661f8bc80f969f31d7aeceb9af7d01374c8e1f35;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeaturesI.java b/src/jalview/datamodel/features/SequenceFeaturesI.java
index 43e9448..7213cba 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;
@@ -12,33 +32,65 @@ 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
    */
-  abstract boolean add(SequenceFeature sf);
+  boolean add(SequenceFeature sf);
 
   /**
    * 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
    */
-  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
    */
-  abstract List<SequenceFeature> getAllFeatures(String... type);
+  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
@@ -48,7 +100,7 @@ public interface SequenceFeaturesI
    * @param type
    * @return
    */
-  abstract int getFeatureCount(boolean positional, String... type);
+  int getFeatureCount(boolean positional, String... type);
 
   /**
    * Answers the total length of positional features, optionally restricted to
@@ -57,7 +109,7 @@ public interface SequenceFeaturesI
    * @param type
    * @return
    */
-  abstract int getTotalFeatureLength(String... type);
+  int getTotalFeatureLength(String... type);
 
   /**
    * Answers a list of all positional features, optionally restricted to
@@ -66,7 +118,7 @@ public interface SequenceFeaturesI
    * @param type
    * @return
    */
-  abstract List<SequenceFeature> getPositionalFeatures(
+  List<SequenceFeature> getPositionalFeatures(
           String... type);
 
   /**
@@ -75,7 +127,7 @@ public interface SequenceFeaturesI
    * 
    * @return
    */
-  abstract List<SequenceFeature> getContactFeatures(String... type);
+  List<SequenceFeature> getContactFeatures(String... type);
 
   /**
    * Answers a list of all non-positional features, optionally restricted to
@@ -85,7 +137,7 @@ public interface SequenceFeaturesI
    *          if no type is specified, all are returned
    * @return
    */
-  abstract List<SequenceFeature> getNonPositionalFeatures(
+  List<SequenceFeature> getNonPositionalFeatures(
           String... type);
 
   /**
@@ -96,14 +148,14 @@ public interface SequenceFeaturesI
    * 
    * @param sf
    */
-  abstract boolean delete(SequenceFeature sf);
+  boolean delete(SequenceFeature sf);
 
   /**
    * Answers true if this store contains at least one feature, else false
    * 
    * @return
    */
-  abstract boolean hasFeatures();
+  boolean hasFeatures();
 
   /**
    * Returns a set of the distinct feature groups present in the collection. The
@@ -116,7 +168,7 @@ public interface SequenceFeaturesI
    * @param type
    * @return
    */
-  abstract Set<String> getFeatureGroups(boolean positionalFeatures,
+  Set<String> getFeatureGroups(boolean positionalFeatures,
           String... type);
 
   /**
@@ -129,14 +181,52 @@ public interface SequenceFeaturesI
    * @param groups
    * @return
    */
-  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
    */
-  abstract Set<String> getFeatureTypes();
+  float getMinimumScore(String type, boolean positional);
 
-}
\ No newline at end of file
+  /**
+   * 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);
+
+  /**
+   * Deletes all positional and non-positional features
+   */
+  void deleteAll();
+}