JAL-3253-applet JAL-3397 JAL-3383 fast IntervalStore for JavaScript

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

diff --git a/src/jalview/datamodel/features/FeatureStore.java b/src/jalview/datamodel/features/FeatureStore.java
index d832f4d..1451892 100644 (file)
--- a/src/jalview/datamodel/features/FeatureStore.java
+++ b/src/jalview/datamodel/features/FeatureStore.java
@@ -259,21 +259,26 @@ public abstract class FeatureStore implements FeatureStoreI
   @Override
   public boolean addFeature(SequenceFeature feature)
   {
-    if (contains(feature))
-    {
-      return false;
-    }
-
-    /*
-     * keep a record of feature groups
-     */
-    if (!feature.isNonPositional())
-    {
-      positionalFeatureGroups.add(feature.getFeatureGroup());
-    }
+    // if (contains(feature))
+    // {
+    // return false;
+    // }
+
+    // /*
+    // * keep a record of feature groups
+    // */
+    // if (!feature.isNonPositional())
+    // {
+    // positionalFeatureGroups.add(feature.getFeatureGroup());
+    // }
 
     if (feature.isContactFeature())
     {
+      if (containsContactFeature(feature))
+      {
+        return false;
+      }
+      positionalFeatureGroups.add(feature.getFeatureGroup());
       if (feature.begin > lastContactStart)
       {
         lastContactStart = feature.begin;
@@ -282,11 +287,23 @@ public abstract class FeatureStore implements FeatureStoreI
     }
     else if (feature.isNonPositional())
     {
+      if (containsNonPositional(feature))
+      {
+        return false;
+      }
+
       addNonPositionalFeature(feature);
     }
     else
     {
-      addPositionalFeature(feature);
+      // allow for check with
+      if (checkContainsPositionalFeatureForAdd(feature)
+              || !addPositionalFeature(feature))
+      {
+        return false;
+      }
+      positionalFeatureGroups.add(feature.getFeatureGroup());
+      // addPositionalFeature(feature);
       if (feature.begin > lastStart)
       {
         lastStart = feature.begin;
@@ -343,8 +360,10 @@ public abstract class FeatureStore implements FeatureStoreI
   /**
    * Adds one feature to the IntervalStore that can manage nested features
    * (creating the IntervalStore if necessary)
+   * 
+   * @return true if added -- allowing for late checking during addition
    */
-  abstract protected void addPositionalFeature(SequenceFeature feature);
+  abstract protected boolean addPositionalFeature(SequenceFeature feature);
 
   /**
    * Adds the feature to the list of non-positional features (with lazy
@@ -381,21 +400,50 @@ public abstract class FeatureStore implements FeatureStoreI
   {
     if (feature.isNonPositional())
     {
-      return nonPositionalFeatures == null ? false
-              : nonPositionalFeatures.contains(feature);
+      return containsNonPositional(feature);
+
     }
 
     if (feature.isContactFeature())
     {
-      return contactFeatureStarts != null
-              && feature.begin <= lastContactStart
-              && listContains(contactFeatureStarts, feature);
+      return containsContactFeature(feature);
+
     }
 
+    return containsPositionalFeature(feature);
+
+  }
+
+  /**
+   * A check that can be overridden if the check is being done during the add
+   * operation itself.
+   * 
+   * @param feature
+   * @return
+   */
+  protected boolean checkContainsPositionalFeatureForAdd(
+          SequenceFeature feature)
+  {
+    return containsPositionalFeature(feature);
+  }
+
+  private boolean containsPositionalFeature(SequenceFeature feature)
+  {
     return features == null || feature.begin > lastStart ? false
             : containsFeature(feature);
   }
 
+  private boolean containsContactFeature(SequenceFeature feature)
+  {
+    return contactFeatureStarts != null && feature.begin <= lastContactStart
+            && listContains(contactFeatureStarts, feature);
+  }
+
+  private boolean containsNonPositional(SequenceFeature feature)
+  {
+    return nonPositionalFeatures == null ? false
+            : nonPositionalFeatures.contains(feature);
+  }
 
   abstract protected boolean containsFeature(SequenceFeature feature);