X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=f508bc360dcdb96707fa2354a1484ec9eb27708d;hb=d63bbc2d56c86d7dca68e76104a8682b5e38c763;hp=74a5235e32fecd4a40a4985aed25b8ed1586d7f4;hpb=96ae263e8b15bdba1d53a17fd60ee7109729052f;p=jalview.git

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 74a5235..f508bc3 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -169,159 +169,136 @@ public class AlignViewController implements AlignViewControllerI
     // JBPNote this routine could also mark rows, not just columns.
     // need a decent query structure to allow all types of feature searches
     BitSet bs = new BitSet();
-    int alw, alStart;
-    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
-            .getAlignment() : viewport.getSelectionGroup());
-    alStart = sqcol.getStartRes();
-    alw = sqcol.getEndRes() + 1;
+    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
+            .getAlignment() : viewport.getSelectionGroup();
+
+    int nseq = findColumnsWithFeature(featureType, 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"),
+                    featureType, Integer.valueOf(nseq).toString() }));
+        return true;
+      }
+    }
+    else
+    {
+      avcg.setStatus(MessageManager.formatMessage(
+              "label.no_feature_of_type_found",
+              new String[] { featureType }));
+      if (!extendCurrent)
+      {
+        cs.clear();
+        alignPanel.paintAlignment(true);
+      }
+    }
+    return false;
+  }
+
+  /**
+   * Sets a bit in the BitSet for each column (base 0) in the sequence
+   * collection which includes the specified feature type. Returns the number of
+   * sequences which have the feature in the selected range.
+   * 
+   * @param featureType
+   * @param sqcol
+   * @param bs
+   * @return
+   */
+  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;
     List<SequenceI> seqs = sqcol.getSequences();
     int nseq = 0;
     for (SequenceI sq : seqs)
     {
-      int tfeat = 0;
+      boolean sequenceHasFeature = false;
       if (sq != null)
       {
-        SequenceFeature[] sf = sq.getSequenceFeatures();
-        if (sf != null)
+        SequenceFeature[] sfs = sq.getSequenceFeatures();
+        if (sfs != null)
         {
+          /*
+           * check whether the feature start/end (base 1) 
+           * overlaps the selection start/end
+           */
           int ist = sq.findIndex(sq.getStart());
           int iend = sq.findIndex(sq.getEnd());
-          if (iend < alStart || ist > alw)
+          if (iend < startPosition || ist > endPosition)
           {
             // sequence not in region
             continue;
           }
-          for (SequenceFeature sfpos : sf)
+          for (SequenceFeature sf : sfs)
           {
-            // future functionalty - featureType == null means mark columns
+            // future functionality - featureType == null means mark columns
             // containing all displayed features
-            if (sfpos != null && (featureType.equals(sfpos.getType())))
+            if (sf != null && (featureType.equals(sf.getType())))
             {
-              tfeat++;
               // optimisation - could consider 'spos,apos' like cursor argument
               // - findIndex wastes time by starting from first character and
               // counting
 
-              int i = sq.findIndex(sfpos.getBegin());
-              int j = sq.findIndex(sfpos.getEnd());
-              if (j < alStart || i > alw)
+              int i = sq.findIndex(sf.getBegin());
+              int j = sq.findIndex(sf.getEnd());
+              if (j < startPosition || i > endPosition)
               {
                 // feature is outside selected region
                 continue;
               }
-              if (i < alStart)
+              sequenceHasFeature = true;
+              if (i < startPosition)
               {
-                i = alStart;
+                i = startPosition;
               }
               if (i < ist)
               {
                 i = ist;
               }
-              if (j > alw)
+              if (j > endPosition)
               {
-                j = alw;
+                j = endPosition;
               }
               for (; i <= j; i++)
               {
-                bs.set(i - 1);
+                bs.set(i - 1); // convert to base 0
               }
             }
           }
         }
 
-        if (tfeat > 0)
+        if (sequenceHasFeature)
         {
           nseq++;
         }
       }
     }
-    ColumnSelection cs = viewport.getColumnSelection();
-    if (bs.cardinality() > 0 || invert)
-    {
-      boolean changed = false;
-      if (cs == null)
-      {
-        cs = new ColumnSelection();
-      }
-      else
-      {
-        if (!extendCurrent)
-        {
-          changed = !cs.isEmpty();
-          cs.clear();
-        }
-      }
-      if (invert)
-      {
-        // invert only in the currently selected sequence region
-        for (int i = bs.nextClearBit(alStart), ibs = bs.nextSetBit(alStart); i >= alStart
-                && i < (alw);)
-        {
-          if (ibs < 0 || i < ibs)
-          {
-            changed = true;
-            if (toggle && cs.contains(i))
-            {
-              cs.removeElement(i++);
-            }
-            else
-            {
-              cs.addElement(i++);
-            }
-          }
-          else
-          {
-            i = bs.nextClearBit(ibs);
-            ibs = bs.nextSetBit(i);
-          }
-        }
-      }
-      else
-      {
-        for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
-                .nextSetBit(i + 1))
-        {
-          changed = true;
-          if (toggle && cs.contains(i))
-          {
-            cs.removeElement(i);
-          }
-          else
-          {
-            cs.addElement(i);
-          }
-        }
-      }
-      if (changed)
-      {
-        viewport.setColumnSelection(cs);
-        alignPanel.paintAlignment(true);
-        avcg.setStatus(MessageManager.formatMessage(
-                "label.view_controller_toggled_marked",
-                new String[] {
-                    MessageManager.getString(toggle ? "label.toggled"
-                            : "label.marked"),
-                    String.valueOf(invert ? alw - alStart
-                            - bs.cardinality() : bs.cardinality()),
-                    MessageManager
-                            .getString(invert ? "label.not_containing"
-                                    : "label.containing"),
-                    featureType, Integer.valueOf(nseq).toString() }));
-        return true;
-      }
-    }
-    else
-    {
-      avcg.setStatus(MessageManager.formatMessage(
-              "label.no_feature_of_type_found",
-              new String[] { featureType }));
-      if (!extendCurrent && cs != null)
-      {
-        cs.clear();
-        alignPanel.paintAlignment(true);
-      }
-    }
-    return false;
+    return nseq;
   }
 
   @Override