X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FFeatureStore.java;h=02ce1c50a5f28eb59603bab4d7b7f7d335c4cfaa;hb=b320470d1ddb95476d3678477b72f6f791a51404;hp=7218b380cc4d07a36ff2d79650974fb341e292e9;hpb=b44349fe3a5f2d70b74a1b110018a753a1036aca;p=jalview.git

diff --git a/src/jalview/datamodel/features/FeatureStore.java b/src/jalview/datamodel/features/FeatureStore.java
index 7218b38..02ce1c5 100644
--- a/src/jalview/datamodel/features/FeatureStore.java
+++ b/src/jalview/datamodel/features/FeatureStore.java
@@ -1,5 +1,26 @@
+/*
+ * 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 java.util.ArrayList;
@@ -32,6 +53,13 @@ public class FeatureStore
      */
     abstract boolean compare(SequenceFeature entry);
 
+    /**
+     * serves a search condition for finding the first feature whose start
+     * position follows a given target location
+     * 
+     * @param target
+     * @return
+     */
     static SearchCriterion byStart(final long target)
     {
       return new SearchCriterion() {
@@ -44,6 +72,13 @@ public class FeatureStore
       };
     }
 
+    /**
+     * serves a search condition for finding the first feature whose end
+     * position is at or follows a given target location
+     * 
+     * @param target
+     * @return
+     */
     static SearchCriterion byEnd(final long target)
     {
       return new SearchCriterion()
@@ -57,6 +92,13 @@ public class FeatureStore
       };
     }
 
+    /**
+     * serves a search condition for finding the first feature which follows the
+     * given range as determined by a supplied comparator
+     * 
+     * @param target
+     * @return
+     */
     static SearchCriterion byFeature(final ContiguousI to,
             final Comparator<ContiguousI> rc)
     {
@@ -158,6 +200,11 @@ public class FeatureStore
    */
   public boolean addFeature(SequenceFeature feature)
   {
+    if (contains(feature))
+    {
+      return false;
+    }
+
     /*
      * keep a record of feature groups
      */
@@ -178,16 +225,13 @@ public class FeatureStore
     }
     else
     {
-      if (!contains(nonNestedFeatures, feature))
+      added = addNonNestedFeature(feature);
+      if (!added)
       {
-        added = addNonNestedFeature(feature);
-        if (!added)
-        {
-          /*
-           * detected a nested feature - put it in the NCList structure
-           */
-          added = addNestedFeature(feature);
-        }
+        /*
+         * detected a nested feature - put it in the NCList structure
+         */
+        added = addNestedFeature(feature);
       }
     }
 
@@ -224,6 +268,36 @@ public class FeatureStore
   }
 
   /**
+   * Answers true if this store contains the given feature (testing by
+   * SequenceFeature.equals), else false
+   * 
+   * @param feature
+   * @return
+   */
+  public boolean contains(SequenceFeature feature)
+  {
+    if (feature.isNonPositional())
+    {
+      return nonPositionalFeatures == null ? false : nonPositionalFeatures
+              .contains(feature);
+    }
+
+    if (feature.isContactFeature())
+    {
+      return contactFeatureStarts == null ? false : listContains(
+              contactFeatureStarts, feature);
+    }
+
+    if (listContains(nonNestedFeatures, feature))
+    {
+      return true;
+    }
+
+    return nestedFeatures == null ? false : nestedFeatures
+            .contains(feature);
+  }
+
+  /**
    * Answers the 'length' of the feature, counting 0 for non-positional features
    * and 1 for contact features
    * 
@@ -245,10 +319,10 @@ public class FeatureStore
 
   /**
    * Adds the feature to the list of non-positional features (with lazy
-   * instantiation of the list if it is null), and returns true. If the
-   * non-positional features already include the new feature (by equality test),
-   * then it is not added, and this method returns false. The feature group is
-   * added to the set of distinct feature groups for non-positional features.
+   * instantiation of the list if it is null), and returns true. The feature
+   * group is added to the set of distinct feature groups for non-positional
+   * features. This method allows duplicate features, so test before calling to
+   * prevent this.
    * 
    * @param feature
    */
@@ -258,10 +332,6 @@ public class FeatureStore
     {
       nonPositionalFeatures = new ArrayList<SequenceFeature>();
     }
-    if (nonPositionalFeatures.contains(feature))
-    {
-      return false;
-    }
 
     nonPositionalFeatures.add(feature);
 
@@ -280,7 +350,7 @@ public class FeatureStore
   {
     if (nestedFeatures == null)
     {
-      nestedFeatures = new NCList<SequenceFeature>(feature);
+      nestedFeatures = new NCList<>(feature);
       return true;
     }
     return nestedFeatures.add(feature, false);
@@ -361,8 +431,8 @@ public class FeatureStore
   /**
    * Add a contact feature to the lists that hold them ordered by start (first
    * contact) and by end (second contact) position, ensuring the lists remain
-   * ordered, and returns true. If the contact feature lists already contain the
-   * given feature (by test for equality), does not add it and returns false.
+   * ordered, and returns true. This method allows duplicate features to be
+   * added, so test before calling to avoid this.
    * 
    * @param feature
    * @return
@@ -378,11 +448,6 @@ public class FeatureStore
       contactFeatureEnds = new ArrayList<SequenceFeature>();
     }
 
-    if (contains(contactFeatureStarts, feature))
-    {
-      return false;
-    }
-
     /*
      * binary search the sorted list to find the insertion point
      */
@@ -411,7 +476,7 @@ public class FeatureStore
    * @param feature
    * @return
    */
-  protected static boolean contains(List<SequenceFeature> features,
+  protected static boolean listContains(List<SequenceFeature> features,
           SequenceFeature feature)
   {
     if (features == null || feature == null)
@@ -454,7 +519,7 @@ public class FeatureStore
    */
   public List<SequenceFeature> findOverlappingFeatures(long start, long end)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
 
     findNonNestedFeatures(start, end, result);
 
@@ -551,28 +616,15 @@ public class FeatureStore
   protected void findNonNestedFeatures(long from, long to,
           List<SequenceFeature> result)
   {
+    /*
+     * find the first feature whose end position is
+     * after the target range start
+     */
     int startIndex = binarySearch(nonNestedFeatures,
             SearchCriterion.byEnd(from));
 
-    findNonNestedFeatures(startIndex, from, to, result);
-  }
-
-  /**
-   * Scans the list of non-nested features, starting from startIndex, to find
-   * those that overlap the from-to range, and adds them to the result list.
-   * Returns the index of the first feature whose start position is after the
-   * target range (or the length of the whole list if none such feature exists).
-   * 
-   * @param startIndex
-   * @param from
-   * @param to
-   * @param result
-   * @return
-   */
-  protected int findNonNestedFeatures(final int startIndex, long from,
-          long to, List<SequenceFeature> result)
-  {
-    int i = startIndex;
+    final int startIndex1 = startIndex;
+    int i = startIndex1;
     while (i < nonNestedFeatures.size())
     {
       SequenceFeature sf = nonNestedFeatures.get(i);
@@ -580,15 +632,12 @@ public class FeatureStore
       {
         break;
       }
-      int start = sf.getBegin();
-      int end = sf.getEnd();
-      if (start <= to && end >= from)
+      if (sf.getBegin() <= to && sf.getEnd() >= from)
       {
         result.add(sf);
       }
       i++;
     }
-    return i;
   }
 
   /**
@@ -632,7 +681,7 @@ public class FeatureStore
     /*
      * add non-nested features (may be all features for many cases)
      */
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
     result.addAll(nonNestedFeatures);
 
     /*
@@ -666,7 +715,7 @@ public class FeatureStore
     {
       return Collections.emptyList();
     }
-    return new ArrayList<SequenceFeature>(contactFeatureStarts);
+    return new ArrayList<>(contactFeatureStarts);
   }
 
   /**
@@ -681,7 +730,7 @@ public class FeatureStore
     {
       return Collections.emptyList();
     }
-    return new ArrayList<SequenceFeature>(nonPositionalFeatures);
+    return new ArrayList<>(nonPositionalFeatures);
   }
 
   /**
@@ -819,27 +868,6 @@ public class FeatureStore
   }
 
   /**
-   * Scans all positional features to check whether the given feature group is
-   * found, and returns true if found, else false
-   * 
-   * @param featureGroup
-   * @return
-   */
-  protected boolean findFeatureGroup(String featureGroup)
-  {
-    for (SequenceFeature sf : getPositionalFeatures())
-    {
-      String group = sf.getFeatureGroup();
-      if (group == featureGroup
-              || (group != null && group.equals(featureGroup)))
-      {
-        return true;
-      }
-    }
-    return false;
-  }
-
-  /**
    * Answers true if this store has no features, else false
    * 
    * @return
@@ -992,7 +1020,7 @@ public class FeatureStore
   public List<SequenceFeature> getFeaturesForGroup(boolean positional,
           String group)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
 
     /*
      * if we know features don't include the target group, no need
@@ -1046,7 +1074,7 @@ public class FeatureStore
       {
         newBegin = Math.max(1, newBegin);
         SequenceFeature sf2 = new SequenceFeature(sf, newBegin, newEnd,
-                sf.getFeatureGroup());
+                sf.getFeatureGroup(), sf.getScore());
         addFeature(sf2);
       }
       delete(sf);