JavaDoc comments; minor code clean-up

diff --git a/src/jalview/datamodel/features/FeatureStore.java b/src/jalview/datamodel/features/FeatureStore.java
index e60aec5..716eb04 100644 (file)
--- a/src/jalview/datamodel/features/FeatureStore.java
+++ b/src/jalview/datamodel/features/FeatureStore.java
@@ -965,6 +965,10 @@ public class FeatureStore
   }
 
   /**
+   * Run through the sorted sequence array once, building the containedBy linked
+   * list references. Does a check first to make sure there is actually
+   * something out there that is overlapping. A null for sf.containedBy means
+   * there are no overlaps for this feature.
    * 
    * @param intervals
    */
@@ -977,24 +981,25 @@ public class FeatureStore
     int maxEnd = intervals[0].end;
     for (int i = 1, n = intervals.length; i < n; i++)
     {
-      SequenceFeature ithis = intervals[i];
-      if (ithis.begin <= maxEnd)
+      SequenceFeature sf = intervals[i];
+      if (sf.begin <= maxEnd)
       {
-        ithis.containedBy = getContainedBy(intervals[i - 1], ithis);
+        sf.containedBy = getContainedBy(intervals[i - 1], sf);
       }
-      if (ithis.end > maxEnd)
+      if (sf.end > maxEnd)
       {
-        maxEnd = ithis.end;
+        maxEnd = sf.end;
       }
     }
   }
 
   /**
-   * Since we are traversing the sorted feature array, all elements prior to the
-   * one we are working on have been fully linked. All we are doing is following
-   * those links until we find the first array feature with a containedBy
-   * element that has an end &gt;= our begin point. It is generally a very short
-   * list -- maybe one or two depths. But it might be more than that.
+   * Since we are traversing the sorted feature array in a forward direction,
+   * all elements prior to the one we are working on have been fully linked. All
+   * we are doing is following those links until we find the first array feature
+   * with a containedBy element that has an end &gt;= our begin point. It is
+   * generally a very short list -- maybe one or two depths. But it might be
+   * more than that.
    * 
    * @param sf
    * @param sf0
@@ -1017,7 +1022,7 @@ public class FeatureStore
     return null;
   }
 
-  // Searching for overlapping features at a given position:
+  // search-stage methods
 
   /**
    * Binary search for contact start or end at a given (Overview) position.
@@ -1122,7 +1127,10 @@ public class FeatureStore
 
   /**
    * A binary search identical to the one used for contact start/end, but here
-   * we return the feature itself.
+   * we return the feature itself. Unlike Collection.BinarySearch, all we have
+   * to be is close, not exact, and we make sure if there is a string of
+   * identical starts, then we slide to the end so that we can check all of
+   * them.
    * 
    * @param l
    * @param pos
@@ -1150,8 +1158,7 @@ public class FeatureStore
         {
           ;
         }
-        mid--;
-        return l[mid];
+        return l[--mid];
       }
     }
     // -1 here?