X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=460c2b3eedaf391e1deb1bdbce8cc1dc180aa591;hb=124d129cc007fbfc84039610b364df62efc72707;hp=24fc18194708981efe7c6d1c19162905308e2743;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 24fc181..460c2b3 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -52,14 +52,6 @@ public class AlignViewController implements AlignViewControllerI
    */
   private AlignViewControllerGuiI avcg;
 
-  @Override
-  protected void finalize() throws Throwable
-  {
-    viewport = null;
-    alignPanel = null;
-    avcg = null;
-  };
-
   public AlignViewController(AlignViewControllerGuiI alignFrame,
           AlignViewportI viewport, AlignmentViewPanel alignPanel)
   {
@@ -190,7 +182,7 @@ public class AlignViewController implements AlignViewControllerI
       if (changed)
       {
         viewport.setColumnSelection(cs);
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
         int columnCount = invert
                 ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
                         - bs.cardinality()
@@ -215,7 +207,7 @@ public class AlignViewController implements AlignViewControllerI
       if (!extendCurrent)
       {
         cs.clear();
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
       }
     }
     return false;
@@ -234,91 +226,66 @@ public class AlignViewController implements AlignViewControllerI
   static int findColumnsWithFeature(String featureType,
           SequenceCollectionI sqcol, BitSet bs)
   {
-    final int startPosition = sqcol.getStartRes() + 1; // converted to base 1
-    final int endPosition = sqcol.getEndRes() + 1;
+    final int startColumn = sqcol.getStartRes() + 1; // converted to base 1
+    final int endColumn = sqcol.getEndRes() + 1;
     List<SequenceI> seqs = sqcol.getSequences();
     int nseq = 0;
     for (SequenceI sq : seqs)
     {
-      boolean sequenceHasFeature = false;
       if (sq != null)
       {
-        SequenceFeature[] sfs = sq.getSequenceFeatures();
-        if (sfs != null)
+        // int ist = sq.findPosition(sqcol.getStartRes());
+        List<SequenceFeature> sfs = sq.findFeatures(startColumn,
+                endColumn, featureType);
+
+        if (!sfs.isEmpty())
         {
-          int ist = sq.findIndex(sq.getStart());
-          int iend = sq.findIndex(sq.getEnd());
-          if (iend < startPosition || ist > endPosition)
-          {
-            // sequence not in region
-            continue;
-          }
-          for (SequenceFeature sf : sfs)
+          nseq++;
+        }
+
+        for (SequenceFeature sf : sfs)
+        {
+          int sfStartCol = sq.findIndex(sf.getBegin());
+          int sfEndCol = sq.findIndex(sf.getEnd());
+
+          if (sf.isContactFeature())
           {
-            // future functionality - featureType == null means mark columns
-            // containing all displayed features
-            if (sf != null && (featureType.equals(sf.getType())))
+            /*
+             * 'contact' feature - check for 'start' or 'end'
+             * position within the selected region
+             */
+            if (sfStartCol >= startColumn && sfStartCol <= endColumn)
             {
-              // optimisation - could consider 'spos,apos' like cursor argument
-              // - findIndex wastes time by starting from first character and
-              // counting
-
-              int sfStartCol = sq.findIndex(sf.getBegin());
-              int sfEndCol = sq.findIndex(sf.getEnd());
-
-              if (sf.isContactFeature())
-              {
-                /*
-                 * 'contact' feature - check for 'start' or 'end'
-                 * position within the selected region
-                 */
-                if (sfStartCol >= startPosition
-                        && sfStartCol <= endPosition)
-                {
-                  bs.set(sfStartCol - 1);
-                  sequenceHasFeature = true;
-                }
-                if (sfEndCol >= startPosition && sfEndCol <= endPosition)
-                {
-                  bs.set(sfEndCol - 1);
-                  sequenceHasFeature = true;
-                }
-                continue;
-              }
-
-              /*
-               * contiguous feature - select feature positions (if any) 
-               * within the selected region
-               */
-              if (sfStartCol > endPosition || sfEndCol < startPosition)
-              {
-                // feature is outside selected region
-                continue;
-              }
-              sequenceHasFeature = true;
-              if (sfStartCol < startPosition)
-              {
-                sfStartCol = startPosition;
-              }
-              if (sfStartCol < ist)
-              {
-                sfStartCol = ist;
-              }
-              if (sfEndCol > endPosition)
-              {
-                sfEndCol = endPosition;
-              }
-              for (; sfStartCol <= sfEndCol; sfStartCol++)
-              {
-                bs.set(sfStartCol - 1); // convert to base 0
-              }
+              bs.set(sfStartCol - 1);
             }
+            if (sfEndCol >= startColumn && sfEndCol <= endColumn)
+            {
+              bs.set(sfEndCol - 1);
+            }
+            continue;
           }
-        }
 
-        if (sequenceHasFeature)
-        {
-          nseq++;
+          /*
+           * contiguous feature - select feature positions (if any) 
+           * within the selected region
+           */
+          if (sfStartCol < startColumn)
+          {
+            sfStartCol = startColumn;
+          }
+          // not sure what the point of this is
+          // if (sfStartCol < ist)
+          // {
+          // sfStartCol = ist;
+          // }
+          if (sfEndCol > endColumn)
+          {
+            sfEndCol = endColumn;
+          }
+          for (; sfStartCol <= sfEndCol; sfStartCol++)
+          {
+            bs.set(sfStartCol - 1); // convert to base 0
+          }
         }
       }
     }
@@ -362,7 +329,7 @@ public class AlignViewController implements AlignViewControllerI
     AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
     avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
             viewport.getAlignment()));
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(true, false);
 
   }
 
@@ -400,7 +367,7 @@ public class AlignViewController implements AlignViewControllerI
       {
         avcg.getFeatureSettingsUI().discoverAllFeatureData();
       }
-      alignPanel.paintAlignment(true);
+      alignPanel.paintAlignment(true, true);
     }
 
     return featuresFile;
@@ -439,7 +406,7 @@ public class AlignViewController implements AlignViewControllerI
       if (changed)
       {
         viewport.setColumnSelection(cs);
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
         int columnCount = invert
                 ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
                         - bs.cardinality()
@@ -463,7 +430,7 @@ public class AlignViewController implements AlignViewControllerI
       if (!extendCurrent)
       {
         cs.clear();
-        alignPanel.paintAlignment(true);
+        alignPanel.paintAlignment(false, false);
       }
     }
     return false;