JAL-3438 spotless for 2.11.2.0

[jalview.git] / src / jalview / datamodel / features / SequenceFeaturesI.java

diff --git a/src/jalview/datamodel/features/SequenceFeaturesI.java b/src/jalview/datamodel/features/SequenceFeaturesI.java
index 58beca2..ca14278 100644 (file)
--- 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;
@@ -22,15 +42,15 @@ 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, in no particular guaranteed order.
@@ -62,9 +82,9 @@ public interface SequenceFeaturesI
           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.
+   * 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
@@ -97,8 +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
@@ -116,8 +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
@@ -147,8 +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
@@ -160,8 +177,8 @@ 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.
@@ -195,10 +212,17 @@ public interface SequenceFeaturesI
   float getMaximumScore(String type, boolean positional);
 
   /**
-   * Adds the shift amount to the start and end of all positional features,
-   * returning true if at least one feature was shifted, else false
+   * 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 shift
+   * @param fromPosition
+   * @param shiftBy
    */
-  abstract boolean shiftFeatures(int shift);
-}
\ No newline at end of file
+  boolean shiftFeatures(int fromPosition, int shiftBy);
+
+  /**
+   * Deletes all positional and non-positional features
+   */
+  void deleteAll();
+}