X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=d1d61d23bb960d31693ec8aa59e521aca7d51e3c;hb=3f62ab98313f836c9e0cdec277e2ec9a0c194801;hp=806e9a5083bd488f33cd42f0321740cf75a0b27e;hpb=095f0d92cb343875bd0f76f833c1eaa8614c22cd;p=jalview.git

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 806e9a5..d1d61d2 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -33,6 +33,7 @@ import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
 import jalview.io.FeaturesFile;
 import jalview.util.MessageManager;
 
@@ -237,83 +238,65 @@ public class AlignViewController implements AlignViewControllerI
     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());
+        int iend = sq.findPosition(sqcol.getEndRes()); // see JAL-2526
+        List<SequenceFeature> sfs = sq.getFeatures().findFeatures(ist,
+                iend, featureType);
+        boolean overlap = false;
+        for (SequenceFeature sf : sfs)
         {
-          int ist = sq.findIndex(sq.getStart());
-          int iend = sq.findIndex(sq.getEnd());
-          if (iend < startPosition || ist > endPosition)
+          // future functionality - featureType == null means mark columns
+          // containing all displayed features
+          if (sf != null && (featureType.equals(sf.getType())))
           {
-            // sequence not in region
-            continue;
-          }
-          for (SequenceFeature sf : sfs)
-          {
-            // future functionality - featureType == null means mark columns
-            // containing all displayed features
-            if (sf != null && (featureType.equals(sf.getType())))
-            {
-              // 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;
-              }
+            int sfStartCol = sq.findIndex(sf.getBegin());
+            int sfEndCol = sq.findIndex(sf.getEnd()); // inefficient - JAL-2526
 
+            if (sf.isContactFeature())
+            {
               /*
-               * contiguous feature - select feature positions (if any) 
-               * within the selected region
+               * 'contact' feature - check for 'start' or 'end'
+               * position within the selected region
                */
-              if (sfStartCol > endPosition || sfEndCol < startPosition)
-              {
-                // feature is outside selected region
-                continue;
-              }
-              sequenceHasFeature = true;
-              if (sfStartCol < startPosition)
+              if (sfStartCol >= startPosition && sfStartCol <= endPosition)
               {
-                sfStartCol = startPosition;
+                bs.set(sfStartCol - 1);
+                overlap = true;
               }
-              if (sfStartCol < ist)
+              if (sfEndCol >= startPosition && sfEndCol <= endPosition)
               {
-                sfStartCol = ist;
-              }
-              if (sfEndCol > endPosition)
-              {
-                sfEndCol = endPosition;
-              }
-              for (; sfStartCol <= sfEndCol; sfStartCol++)
-              {
-                bs.set(sfStartCol - 1); // convert to base 0
+                bs.set(sfEndCol - 1);
+                overlap = true;
               }
+              continue;
+            }
+
+            /*
+             * contiguous feature - select feature positions (if any) 
+             * within the selected region
+             */
+            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
+              overlap = true;
             }
           }
         }
-
-        if (sequenceHasFeature)
+        if (overlap)
         {
           nseq++;
         }
@@ -370,7 +353,7 @@ public class AlignViewController implements AlignViewControllerI
   }
 
   @Override
-  public boolean parseFeaturesFile(String file, String protocol,
+  public boolean parseFeaturesFile(String file, DataSourceType protocol,
           boolean relaxedIdMatching)
   {
     boolean featuresFile = false;
@@ -402,4 +385,66 @@ public class AlignViewController implements AlignViewControllerI
     return featuresFile;
 
   }
+
+  @Override
+  public boolean markHighlightedColumns(boolean invert,
+          boolean extendCurrent, boolean toggle)
+  {
+    if (!viewport.hasSearchResults())
+    {
+      // do nothing if no selection exists
+      return false;
+    }
+    // JBPNote this routine could also mark rows, not just columns.
+    BitSet bs = new BitSet();
+    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
+            .getAlignment() : viewport.getSelectionGroup();
+
+    // this could be a lambda... - the remains of the method is boilerplate,
+    // except for the different messages for reporting selection.
+    int nseq = viewport.getSearchResults().markColumns(sqcol, bs);
+
+    ColumnSelection cs = viewport.getColumnSelection();
+    if (cs == null)
+    {
+      cs = new ColumnSelection();
+    }
+
+    if (bs.cardinality() > 0 || invert)
+    {
+      boolean changed = cs.markColumns(bs, sqcol.getStartRes(),
+              sqcol.getEndRes(), invert, extendCurrent, toggle);
+      if (changed)
+      {
+        viewport.setColumnSelection(cs);
+        alignPanel.paintAlignment(true);
+        int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
+                - bs.cardinality()
+                : bs.cardinality();
+        avcg.setStatus(MessageManager.formatMessage(
+                "label.view_controller_toggled_marked",
+                new String[] {
+                    toggle ? MessageManager.getString("label.toggled")
+                            : MessageManager.getString("label.marked"),
+                    String.valueOf(columnCount),
+                    invert ? MessageManager
+                            .getString("label.not_containing")
+                            : MessageManager.getString("label.containing"),
+                    "Highlight", Integer.valueOf(nseq).toString() }));
+        return true;
+      }
+    }
+    else
+    {
+      avcg.setStatus(MessageManager
+              .formatMessage("No highlighted regions marked"));
+      if (!extendCurrent)
+      {
+        cs.clear();
+        alignPanel.paintAlignment(true);
+      }
+    }
+    return false;
+  }
+
 }