X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=e11830ccb0c15d1c290c006cc6d6ac4961294584;hb=012fc200ee0d124003524855ac7cd50be4b7456c;hp=3481a3103dd6cecc052a2a7198940f8e55ffe637;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 3481a31..e11830c 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -82,6 +82,7 @@ public class PopupMenu extends JPopupMenu
   JMenuItem enterPDB = new JMenuItem();
   JMenuItem discoverPDB = new JMenuItem();
   JMenu outputMenu = new JMenu();
+  JMenuItem sequenceFeature = new JMenuItem();
 
   /**
      * Creates a new PopupMenu object.
@@ -504,12 +505,22 @@ public class PopupMenu extends JPopupMenu
       }
     });
     outputMenu.setText("Output to Textbox...");
+    sequenceFeature.setText("Create Sequence Feature");
+    sequenceFeature.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        sequenceFeature_actionPerformed(e);
+      }
+    });
     add(groupMenu);
 
     add(sequenceMenu);
     groupMenu.add(editMenu);
     groupMenu.add(outputMenu);
     groupMenu.addSeparator();
+    groupMenu.add(sequenceFeature);
+    groupMenu.addSeparator();
     groupMenu.add(groupName);
     groupMenu.add(unGroupMenuItem);
         groupMenu.add(colourMenu);
@@ -688,7 +699,7 @@ public class PopupMenu extends JPopupMenu
         if (ap.overviewPanel != null)
           ap.overviewPanel.updateOverviewImage();
 
-        ap.seqPanel.repaint();
+        PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
     }
 
     /**
@@ -842,6 +853,7 @@ public class PopupMenu extends JPopupMenu
 
          sg.cs = udc;
        }
+       refresh();
      }
     /**
      * DOCUMENT ME!
@@ -1126,25 +1138,31 @@ public class PopupMenu extends JPopupMenu
       SequenceGroup sg = ap.av.getSelectionGroup();
       if(sg==null || sg.getSize(false)<1)
       {
-        ap.av.hideSequence(sequence);
+        ap.av.hideSequence(new SequenceI[]{sequence});
         return;
       }
 
+      int gsize = sg.getSize(false);
+      SequenceI [] hseqs;
+
+      hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];
+
         int index = 0;
-        while(index < sg.getSize(false))
+        for(int i=0; i<gsize; i++)
         {
-          if(representGroup && sg.getSequenceAt(index)!=sequence)
+          if(representGroup && sg.getSequenceAt(i)!=sequence)
           {
-            sequence.addHiddenSequence(sg.getSequenceAt(index));
-            ap.av.hideSequence(sg.getSequenceAt(index));
+            sequence.addHiddenSequence(sg.getSequenceAt(i));
+            hseqs[index++] = sg.getSequenceAt(i);
           }
           else if(!representGroup)
           {
-            ap.av.hideSequence(sg.getSequenceAt(index));
+            hseqs[index++] = sg.getSequenceAt(i);
           }
-          index ++;
         }
 
+        ap.av.hideSequence(hseqs);
+
         ap.av.setSelectionGroup(null);
     }
 
@@ -1160,45 +1178,58 @@ public class PopupMenu extends JPopupMenu
 
   public void upperCase_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null)
-      return;
-
-    for(int g=0; g<sg.getSize(true); g++)
-    {
-    ( (SequenceI)sg.getSequences(true).elementAt(g))
-        .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);
-    }
-    ap.repaint();
+    changeCase(e.getSource());
   }
 
   public void lowerCase_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if(sg==null)
-      return;
-
-    for(int g=0; g<sg.getSize(true); g++)
-    {
-       ( (SequenceI)sg.getSequences(true).elementAt(g))
-           .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);
-    }
-    ap.repaint();
+    changeCase(e.getSource());
   }
 
   public void toggle_actionPerformed(ActionEvent e)
   {
-    SequenceGroup sg = ap.av.getSelectionGroup();
-    if (sg == null)
-      return;
+    changeCase(e.getSource());
+  }
 
-    for (int g = 0; g < sg.getSize(true); g++)
+  void changeCase(Object source)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if (sg != null)
     {
-      ( (SequenceI)sg.getSequences(true).elementAt(g))
-          .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
-    }
+      for (int g = 0; g < sg.getSize(true); g++)
+      {
+        int start = sg.getStartRes();
+        int end = sg.getEndRes() + 1;
+
+        do
+        {
+          if (ap.av.hasHiddenColumns)
+          {
+            end = ap.av.colSel.getHiddenBoundaryRight(start);
+            if (start == end)
+              end = sg.getEndRes() + 1;
+            if (end > sg.getEndRes())
+              end = sg.getEndRes() + 1;
+          }
+
+          if (source == toggle)
+            ( (SequenceI) sg.getSequences(true).elementAt(g))
+                .toggleCase(start, end);
+          else
+            ( (SequenceI) sg.getSequences(true).elementAt(g))
+                .changeCase(source == upperCase, start, end);
 
-    ap.repaint();
+          if (ap.av.hasHiddenColumns)
+          {
+            start = ap.av.colSel.adjustForHiddenColumns(end);
+            start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
+          }
+
+        }
+        while (end < sg.getEndRes());
+      }
+      PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+    }
   }
 
   public void outputText_actionPerformed(ActionEvent e)
@@ -1290,4 +1321,31 @@ public class PopupMenu extends JPopupMenu
     new jalview.io.DBRefFetcher(
              ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
   }
+
+  public void sequenceFeature_actionPerformed(ActionEvent e)
+  {
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    if(sg==null)
+      return;
+
+    int gSize= sg.getSize(false);
+    SequenceI [] seqs = new SequenceI[gSize];
+    SequenceFeature [] features = new SequenceFeature[gSize];
+
+    for (int i = 0; i < gSize; i++)
+    {
+      seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
+      int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
+      int end = sg.findEndRes(sg.getSequenceAt(i));
+      features[i] = new SequenceFeature(null,null, null,start,end,"Jalview");
+    }
+
+    if (ap.seqPanel.seqCanvas.getFeatureRenderer()
+        .createNewFeatures(seqs, features))
+    {
+      ap.alignFrame.showSeqFeatures.setSelected(true);
+      ap.av.setShowSequenceFeatures(true);
+      ap.highlightSearchResults(null);
+    }
+  }
 }