X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcontroller%2FAlignViewController.java;h=24fc18194708981efe7c6d1c19162905308e2743;hb=2467c106c4be8b70f244a160739be63efc6b58ea;hp=7d60dc8d62b2045362190d2409fc9a9ff89b9612;hpb=8b27085fa7fc5f2877e078421284c2636b85b8c6;p=jalview.git

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 7d60dc8..24fc181 100644
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -85,10 +85,11 @@ public class AlignViewController implements AlignViewControllerI
     SequenceGroup[] gps = null;
     if (sg != null && (cs == null || cs.isEmpty()))
     {
-      gps = jalview.analysis.Grouping.makeGroupsFrom(viewport
-              .getSequenceSelection(), viewport.getAlignmentView(true)
-              .getSequenceStrings(viewport.getGapCharacter()), viewport
-              .getAlignment().getGroups());
+      gps = jalview.analysis.Grouping.makeGroupsFrom(
+              viewport.getSequenceSelection(),
+              viewport.getAlignmentView(true)
+                      .getSequenceStrings(viewport.getGapCharacter()),
+              viewport.getAlignment().getGroups());
     }
     else
     {
@@ -96,8 +97,8 @@ public class AlignViewController implements AlignViewControllerI
       {
         gps = jalview.analysis.Grouping.makeGroupsFromCols(
                 (sg == null) ? viewport.getAlignment().getSequencesArray()
-                        : sg.getSequences().toArray(new SequenceI[0]), cs,
-                viewport.getAlignment().getGroups());
+                        : sg.getSequences().toArray(new SequenceI[0]),
+                cs, viewport.getAlignment().getGroups());
       }
     }
     if (gps != null)
@@ -170,8 +171,9 @@ 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();
-    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null || extendCurrent) ? viewport
-            .getAlignment() : viewport.getSelectionGroup();
+    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null
+            || extendCurrent) ? viewport.getAlignment()
+                    : viewport.getSelectionGroup();
 
     int nseq = findColumnsWithFeature(featureType, sqcol, bs);
 
@@ -189,14 +191,14 @@ public class AlignViewController implements AlignViewControllerI
       {
         viewport.setColumnSelection(cs);
         alignPanel.paintAlignment(true);
-        int columnCount = invert ? (sqcol.getEndRes() - sqcol.getStartRes() + 1)
-                - bs.cardinality()
+        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"),
+                "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")
@@ -207,9 +209,9 @@ public class AlignViewController implements AlignViewControllerI
     }
     else
     {
-      avcg.setStatus(MessageManager.formatMessage(
-              "label.no_feature_of_type_found",
-              new String[] { featureType }));
+      avcg.setStatus(MessageManager
+              .formatMessage("label.no_feature_of_type_found", new String[]
+              { featureType }));
       if (!extendCurrent)
       {
         cs.clear();
@@ -244,10 +246,6 @@ 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)
@@ -265,29 +263,54 @@ 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
               }
             }
           }
@@ -337,8 +360,8 @@ public class AlignViewController implements AlignViewControllerI
     }
     SequenceI[] oldOrder = al.getSequencesArray();
     AlignmentSorter.sortByFeature(typ, gps, start, stop, al, method);
-    avcg.addHistoryItem(new OrderCommand(methodText, oldOrder, viewport
-            .getAlignment()));
+    avcg.addHistoryItem(new OrderCommand(methodText, oldOrder,
+            viewport.getAlignment()));
     alignPanel.paintAlignment(true);
 
   }
@@ -356,9 +379,10 @@ public class AlignViewController implements AlignViewControllerI
     boolean featuresFile = false;
     try
     {
-      featuresFile = new FeaturesFile(false, file, protocol).parse(viewport
-              .getAlignment().getDataset(), alignPanel.getFeatureRenderer()
-              .getFeatureColours(), false, relaxedIdMatching);
+      featuresFile = new FeaturesFile(false, file, protocol).parse(
+              viewport.getAlignment().getDataset(),
+              alignPanel.getFeatureRenderer().getFeatureColours(), false,
+              relaxedIdMatching);
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -382,4 +406,67 @@ 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;
+  }
+
 }