X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=b9ba9f344c7fa4aaebc5af7be02b2d08a0b725bc;hb=9807ea8cc4e867378c52d51b832168d4bc611d29;hp=8486ac1f59f78c5ef76080d5a16f2d3367a36ed6;hpb=ce728f87f1f43be3041ef02f7f2cc2e39314711a;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 8486ac1..b9ba9f3 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -18,8 +18,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.*;
-
 import jalview.datamodel.*;
 
 import jalview.schemes.*;
@@ -91,21 +89,31 @@ public class SeqPanel extends JPanel
 
         ap = p;
 
+
         addMouseMotionListener(new MouseMotionAdapter()
             {
                 public void mouseMoved(MouseEvent evt)
                 {
                     doMouseMoved(evt);
+                    if (editingSeqs)
+                    {
+                      // This is because MacOSX creates a mouseMoved
+                      // If control is down
+                      if(!av.isDataset())
+                        doMouseDragged(evt);
+                    }
                 }
 
                 public void mouseDragged(MouseEvent evt)
                 {
                     if (editingSeqs)
                     {
+                      if(!av.isDataset())
                         doMouseDragged(evt);
                     }
                     else
                     {
+                      if(!av.isDataset())
                         doMouseDraggedDefineMode(evt);
                     }
                 }
@@ -120,7 +128,7 @@ public class SeqPanel extends JPanel
            {
              Font font = av.getFont();
              int fontSize = font.getSize();
-             if (e.getWheelRotation() > 0 && fontSize < 30)
+             if (e.getWheelRotation() > 0 && fontSize < 51)
                fontSize++;
              else if (fontSize > 1)
                fontSize--;
@@ -140,67 +148,71 @@ public class SeqPanel extends JPanel
        });
 
 
-        addMouseListener(new MouseAdapter()
-            {
-                public void mouseReleased(MouseEvent evt)
-                {
-                    mouseWheelPressed = false;
-
-                    if (editingSeqs)
-                    {
-                        doMouseReleased(evt);
-                    }
-                    else
-                    {
-                        doMouseReleasedDefineMode(evt);
-                    }
-                }
-
-                public void mousePressed(MouseEvent evt)
-                {
-                  if( javax.swing.SwingUtilities.isMiddleMouseButton(evt))
-                  {
-                    mouseWheelPressed = true;
-                    return;
-                  }
+       if(!av.isDataset())
+       {
+         addMouseListener(new MouseAdapter()
+         {
+           public void mouseReleased(MouseEvent evt)
+           {
+             mouseWheelPressed = false;
 
-                    if (evt.isShiftDown() || evt.isAltDown() ||
-                            evt.isControlDown())
-                    {
-                        if (evt.isAltDown() || evt.isControlDown())
-                        {
-                            groupEditing = true;
-                        }
+             if (editingSeqs)
+             {
+               doMouseReleased(evt);
+             }
+             else
+             {
+               doMouseReleasedDefineMode(evt);
+             }
+           }
 
-                        editingSeqs = true;
-                        doMousePressed(evt);
-                    }
-                    else
-                    {
-                        doMousePressedDefineMode(evt);
-                    }
-                }
+           public void mousePressed(MouseEvent evt)
+           {
+             if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))
+             {
+               mouseWheelPressed = true;
+               return;
+             }
+
+             if (evt.isShiftDown() || evt.isAltDown() ||
+                 evt.isControlDown())
+             {
+               if (evt.isAltDown() || evt.isControlDown())
+               {
+                 groupEditing = true;
+
+               }
+
+               editingSeqs = true;
+               doMousePressed(evt);
+             }
+             else
+             {
+               doMousePressedDefineMode(evt);
+             }
+           }
 
-                public void mouseExited(MouseEvent evt)
-                {
-                  if (editingSeqs)
-                  {
-                    return;
-                  }
+           public void mouseExited(MouseEvent evt)
+           {
+             if (editingSeqs)
+             {
+               return;
+             }
 
-                  doMouseExitedDefineMode(evt);
-                }
+             doMouseExitedDefineMode(evt);
+           }
 
-                public void mouseEntered(MouseEvent evt)
-                {
-                  if (editingSeqs)
-                  {
-                    return;
-                  }
+           public void mouseEntered(MouseEvent evt)
+           {
+             if (editingSeqs)
+             {
+               return;
+             }
 
-                    doMouseEnteredDefineMode(evt);
-                }
-            });
+             doMouseEnteredDefineMode(evt);
+           }
+         });
+       }
     }
 
     int startWrapBlock=-1;
@@ -238,6 +250,9 @@ public class SeqPanel extends JPanel
         res = (x / av.getCharWidth()) + av.getStartRes();
     }
 
+    if(av.hasHiddenColumns)
+          res = av.getColumnSelection().adjustForHiddenColumns(res);
+
     return res;
 
    }
@@ -342,25 +357,41 @@ public class SeqPanel extends JPanel
 
       if (res > sequence.getLength())
       {
-          return;
-        }
+        return;
+      }
 
-        Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
-                "");
-        String aa = "";
+      if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+      {
+        seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+      }
 
-        if (obj != null)
-        {
-            aa = obj.toString();
-        }
 
         StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
                 sequence.getName());
 
-        if (aa != "")
+        Object obj = null;
+        if (av.alignment.isNucleotide())
+        {
+          obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+              "");
+          if(obj!=null)
+            text.append(" Nucleotide: ");
+        }
+        else
         {
-            text.append("  Residue: " + aa + " (" +
-                av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+          obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+          if(obj!=null)
+            text.append("  Residue: ");
+        }
+
+        if (obj != null)
+        {
+
+          if (obj != "")
+          {
+            text.append( obj + " (" +
+                        av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+          }
         }
 
         ap.alignFrame.statusBar.setText(text.toString());
@@ -368,32 +399,62 @@ public class SeqPanel extends JPanel
         // use aa to see if the mouse pointer is on a
         if (av.showSequenceFeatures)
         {
-            Vector features = sequence.getSequenceFeatures();
-            Enumeration e = features.elements();
-            StringBuffer sbuffer = new StringBuffer();
-
-            while (e.hasMoreElements())
+            SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
+            if(features!=null)
             {
-                SequenceFeature sf = (SequenceFeature) e.nextElement();
+              StringBuffer sbuffer = new StringBuffer("<html>");
 
-                if ((sf.getStart() <= sequence.findPosition(res)) &&
-                        (sf.getEnd() >= sequence.findPosition(res)))
+              for (int i = 0; i < features.length; i++)
+              {
+
+                if ( (features[i].getBegin() <= sequence.findPosition(res)) &&
+                    (features[i].getEnd() >= sequence.findPosition(res)))
                 {
-                    if (sbuffer.length() > 0)
+                  if(!av.featuresDisplayed.containsKey(features[i].getType()))
+                  continue;
+
+
+                  if (features[i].getType().equals("disulfide bond"))
+                  {
+                    if (features[i].getBegin() == sequence.findPosition(res)
+                        || features[i].getEnd() == sequence.findPosition(res))
                     {
-                        sbuffer.append("; ");
+                      if (sbuffer.length() > 6)
+                        sbuffer.append("<br>");
+                      sbuffer.append("disulfide bond " + features[i].getBegin() + ":" +
+                                     features[i].getEnd());
                     }
+                  }
+                  else
+                  {
+                    if (sbuffer.length() > 6)
+                      sbuffer.append("<br>");
+                    if(features[i].featureGroup!=null)
+                      sbuffer.append(features[i].featureGroup+";");
 
-                    sbuffer.append(sf.getType() + " " + sf.getDescription());
+                    sbuffer.append(features[i].getType());
 
-                    if (sf.getStatus().length() > 0)
+                    if (features[i].getDescription() != null
+                        && !features[i].description.equals(features[i].getType()))
+                      sbuffer.append("; " + features[i].getDescription());
+
+                    if (features[i].getStatus() != null && features[i].getStatus().length()>0)
                     {
-                        sbuffer.append(" (" + sf.getStatus() + ")");
+                      sbuffer.append("; (" + features[i].getStatus() + ")");
                     }
+                  }
                 }
-            }
 
-            this.setToolTipText(sbuffer.toString());
+              }
+
+              sbuffer.append("</html>");
+              if(sbuffer.length()==13) // <html></html>
+                setToolTipText("");
+              else
+               setToolTipText(sbuffer.toString());
+            }
+            else
+              setToolTipText("");
         }
     }
 
@@ -549,19 +610,6 @@ public class SeqPanel extends JPanel
         seqCanvas.repaint();
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seqstart DOCUMENT ME!
-     * @param seqend DOCUMENT ME!
-     * @param start DOCUMENT ME!
-     */
-    public void drawChars(int seqstart, int seqend, int start)
-    {
-        seqCanvas.drawPanel(seqCanvas.gg, start, av.getEndRes(), seqstart,
-            seqend, av.getStartRes(), av.getStartSeq(), 0);
-        seqCanvas.repaint();
-    }
 
     /**
      * DOCUMENT ME!
@@ -959,7 +1007,7 @@ public class SeqPanel extends JPanel
 
                 try
                 {
-                    Thread.sleep(75);
+                    Thread.sleep(20);
                 }
                 catch (Exception ex)
                 {