Merge branch 'develop' into bug/JAL-2255_seq-fetcher-broken-on-linux

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index f508bc3..bc7f212 100644 (file)
--- 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;
 
@@ -243,10 +244,6 @@ public class AlignViewController implements AlignViewControllerI
         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 < startPosition || ist > endPosition)
@@ -264,29 +261,54 @@ public class AlignViewController implements AlignViewControllerI
               // - findIndex wastes time by starting from first character and
               // counting
 
-              int i = sq.findIndex(sf.getBegin());
-              int j = sq.findIndex(sf.getEnd());
-              if (j < startPosition || i > endPosition)
+              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 (i < startPosition)
+              if (sfStartCol < startPosition)
               {
-                i = startPosition;
+                sfStartCol = startPosition;
               }
-              if (i < ist)
+              if (sfStartCol < ist)
               {
-                i = ist;
+                sfStartCol = ist;
               }
-              if (j > endPosition)
+              if (sfEndCol > endPosition)
               {
-                j = endPosition;
+                sfEndCol = endPosition;
               }
-              for (; i <= j; i++)
+              for (; sfStartCol <= sfEndCol; sfStartCol++)
               {
-                bs.set(i - 1); // convert to base 0
+                bs.set(sfStartCol - 1); // convert to base 0
               }
             }
           }
@@ -349,7 +371,7 @@ 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;
@@ -381,4 +403,66 @@ 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;
+  }
+
 }