X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=0d29184ea135d66ce8ffebd7406a843c33e363ce;hb=3d4ead4880755ec949de0300c232544ba965e60d;hp=8d5ba58c57ceee4d566424597dca01339d66dd24;hpb=12ba8429c72ec9428f88adb6ae5338a5df63552e;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index 8d5ba58..0d29184 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -1,14 +1,31 @@
+/*
+ * 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.ContiguousI;
 import jalview.datamodel.SequenceFeature;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
 
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -16,6 +33,8 @@ import java.util.Map.Entry;
 import java.util.Set;
 import java.util.TreeMap;
 
+import intervalstore.api.IntervalI;
+
 /**
  * A class that stores sequence features in a way that supports efficient
  * querying by type and location (overlap). Intended for (but not limited to)
@@ -26,29 +45,6 @@ import java.util.TreeMap;
  */
 public class SequenceFeatures implements SequenceFeaturesI
 {
-  /**
-   * a comparator for sorting features by start position ascending
-   */
-  private static Comparator<ContiguousI> FORWARD_STRAND = new Comparator<ContiguousI>()
-  {
-    @Override
-    public int compare(ContiguousI o1, ContiguousI o2)
-    {
-      return Integer.compare(o1.getBegin(), o2.getBegin());
-    }
-  };
-
-  /**
-   * a comparator for sorting features by end position descending
-   */
-  private static Comparator<ContiguousI> REVERSE_STRAND = new Comparator<ContiguousI>()
-  {
-    @Override
-    public int compare(ContiguousI o1, ContiguousI o2)
-    {
-      return Integer.compare(o2.getEnd(), o1.getEnd());
-    }
-  };
 
   /*
    * map from feature type to structured store of features for that type
@@ -67,7 +63,7 @@ public class SequenceFeatures implements SequenceFeaturesI
      */
     // featureStore = Collections
     // .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
-    featureStore = new TreeMap<String, FeatureStore>();
+    featureStore = new TreeMap<>();
   }
 
   /**
@@ -113,12 +109,10 @@ public class SequenceFeatures implements SequenceFeaturesI
           String... type)
   {
     List<SequenceFeature> result = new ArrayList<>();
-
     for (FeatureStore featureSet : varargToTypes(type))
     {
       result.addAll(featureSet.findOverlappingFeatures(from, to));
     }
-
     return result;
   }
 
@@ -223,6 +217,7 @@ public class SequenceFeatures implements SequenceFeaturesI
       return featureStore.values();
     }
 
+
     List<FeatureStore> types = new ArrayList<>();
     List<String> args = Arrays.asList(type);
     for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
@@ -362,9 +357,10 @@ public class SequenceFeatures implements SequenceFeaturesI
   }
 
   /**
-   * Answers true if the given type is one of the specified sequence ontology
-   * terms (or a sub-type of one), or if no terms are supplied. Answers false if
-   * filter terms are specified and the given term does not match any of them.
+   * Answers true if the given type matches one of the specified terms (or is a
+   * sub-type of one in the Sequence Ontology), or if no terms are supplied.
+   * Answers false if filter terms are specified and the given term does not
+   * match any of them.
    * 
    * @param type
    * @param soTerm
@@ -376,10 +372,10 @@ public class SequenceFeatures implements SequenceFeaturesI
     {
       return true;
     }
-    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
     for (String term : soTerm)
     {
-      if (so.isA(type, term))
+      if (type.equals(term) || so.isA(type, term))
       {
         return true;
       }
@@ -414,11 +410,10 @@ public class SequenceFeatures implements SequenceFeaturesI
    * @param features
    * @param forwardStrand
    */
-  public static void sortFeatures(List<SequenceFeature> features,
+  public static void sortFeatures(List<? extends IntervalI> features,
           final boolean forwardStrand)
   {
-    Collections.sort(features, forwardStrand ? FORWARD_STRAND
-            : REVERSE_STRAND);
+    IntervalI.sortIntervals(features, forwardStrand);
   }
 
   /**
@@ -451,13 +446,88 @@ public class SequenceFeatures implements SequenceFeaturesI
    * {@inheritDoc}
    */
   @Override
-  public boolean shiftFeatures(int shift)
+  public boolean shiftFeatures(int fromPosition, int shiftBy)
   {
     boolean modified = false;
     for (FeatureStore fs : featureStore.values())
     {
-      modified |= fs.shiftFeatures(shift);
+      modified |= fs.shiftFeatures(fromPosition, shiftBy);
     }
     return modified;
   }
-}
\ No newline at end of file
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public void deleteAll()
+  {
+    featureStore.clear();
+  }
+
+  /**
+   * Simplified find for features associated with a given position.
+   * 
+   * JavaScript set to not use IntervalI, but easily testable by setting false
+   * to true in javadoc
+   * 
+   * FeatureRenderer has checked already that featureStore does contain type.
+   * 
+   * @author Bob Hanson 2019.07.30
+   */
+  @Override
+  public List<SequenceFeature> findFeatures(int pos, String type,
+          List<SequenceFeature> list)
+  {
+    FeatureStore fs = featureStore.get(type);
+    boolean useIntervalStore = /**
+                                * @j2sNative false &&
+                                */
+            true;
+    return (useIntervalStore ? fs.findOverlappingFeatures(pos, pos)
+            : fs.findOverlappingFeatures(pos, list));
+  }
+
+  // Chrome; developer console closed
+
+  // BH 2019.08.01 useIntervalStore true, redraw false:
+  // Platform: timer mark 13.848 0.367 overviewrender 16000 pixels row:14
+  // Platform: timer mark 15.391 0.39 overviewrender 16000 pixels row:14
+  // Platform: timer mark 16.498 0.39 overviewrender 16000 pixels row:14
+  // Platform: timer mark 17.596 0.401 overviewrender 16000 pixels row:14
+  // Platform: timer mark 18.738 0.363 overviewrender 16000 pixels row:14
+  // Platform: timer mark 19.659 0.358 overviewrender 16000 pixels row:14
+  // Platform: timer mark 20.737 0.359 overviewrender 16000 pixels row:14
+  // Platform: timer mark 21.797 0.391 overviewrender 16000 pixels row:14
+  // Platform: timer mark 22.851 0.361 overviewrender 16000 pixels row:14
+  // Platform: timer mark 24.019 0.395 overviewrender 16000 pixels row:14
+
+  // BH 2019.08.01 useIntervalStore false, redraw false:
+  // Platform: timer mark 19.011 0.181 overviewrender 16000 pixels row:14
+  // Platform: timer mark 20.311 0.183 overviewrender 16000 pixels row:14
+  // Platform: timer mark 21.368 0.175 overviewrender 16000 pixels row:14
+  // Platform: timer mark 22.347 0.178 overviewrender 16000 pixels row:14
+  // Platform: timer mark 23.605 0.216 overviewrender 16000 pixels row:14
+  // Platform: timer mark 24.836 0.191 overviewrender 16000 pixels row:14
+  // Platform: timer mark 26.016 0.181 overviewrender 16000 pixels row:14
+  // Platform: timer mark 27.278 0.178 overviewrender 16000 pixels row:14
+  // Platform: timer mark 28.158 0.181 overviewrender 16000 pixels row:14
+  // Platform: timer mark 29.227 0.196 overviewrender 16000 pixels row:14
+  // Platform: timer mark 30.1 0.171 overviewrender 16000 pixels row:14
+  // Platform: timer mark 31.684 0.196 overviewrender 16000 pixels row:14
+  // Platform: timer mark 32.779 0.18 overviewrender 16000 pixels row:14
+  // Platform: timer mark 52.355 0.185 overviewrender 16000 pixels row:14
+  // Platform: timer mark 53.829 0.186 overviewrender 16000 pixels row:14
+
+
+
+  /**
+   * @author Bob Hanson 2019.08.01
+   */
+  @Override
+  public boolean hasFeatures(String type)
+  {
+    return featureStore.containsKey(type);
+  }
+
+}