X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=3209960d6f183e9a9901884df259378a40a9f61a;hb=e21fb8306a9efaf170d7354daa10e7ee42d37c17;hp=db120e1e585db8c434d2fdadf6866500d3d48623;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index db120e1..3209960 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.*;
@@ -69,6 +67,8 @@ public class SeqPanel extends JPanel
     SequenceGroup stretchGroup = null;
     boolean remove = false;
 
+    boolean mouseWheelPressed = false;
+
     /**
      * Creates a new SeqPanel object.
      *
@@ -89,101 +89,199 @@ public class SeqPanel extends JPanel
 
         ap = p;
 
+
         addMouseMotionListener(new MouseMotionAdapter()
             {
                 public void mouseMoved(MouseEvent evt)
                 {
-                    if (av.getWrapAlignment())
+                    doMouseMoved(evt);
+                    if (editingSeqs)
                     {
-                        return;
+                      // This is because MacOSX creates a mouseMoved
+                      // If control is down
+                      if(!av.isDataset())
+                        doMouseDragged(evt);
                     }
-
-                    doMouseMoved(evt);
                 }
 
                 public void mouseDragged(MouseEvent evt)
                 {
-                    if (av.getWrapAlignment())
-                    {
-                        return;
-                    }
-
                     if (editingSeqs)
                     {
+                      if(!av.isDataset())
                         doMouseDragged(evt);
                     }
                     else
                     {
+                      if(!av.isDataset())
                         doMouseDraggedDefineMode(evt);
                     }
                 }
             });
 
-        addMouseListener(new MouseAdapter()
-            {
-                public void mouseReleased(MouseEvent evt)
-                {
-                    if (av.getWrapAlignment())
-                    {
-                        return;
-                    }
+       addMouseWheelListener(new MouseWheelListener()
+       {
+         public void mouseWheelMoved(MouseWheelEvent e)
+         {
+
+           if (mouseWheelPressed)
+           {
+             Font font = av.getFont();
+             int fontSize = font.getSize();
+             if (e.getWheelRotation() > 0 && fontSize < 51)
+               fontSize++;
+             else if (fontSize > 1)
+               fontSize--;
+
+             av.setFont(new Font(font.getName(), font.getStyle(), fontSize));
+             ap.fontChanged();
+           }
+           else
+           {
+             if (e.getWheelRotation() > 0)
+               ap.scrollUp(false);
+             else
+               ap.scrollUp(true);
+           }
+
+         }
+       });
+
+
+       if(!av.isDataset())
+       {
+         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 (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;
+             }
+
+             doMouseExitedDefineMode(evt);
+           }
+
+           public void mouseEntered(MouseEvent evt)
+           {
+             if (editingSeqs)
+             {
+               return;
+             }
+
+             doMouseEnteredDefineMode(evt);
+           }
+         });
+       }
+    }
 
-                    if (editingSeqs)
-                    {
-                        doMouseReleased(evt);
-                    }
-                    else
-                    {
-                        doMouseReleasedDefineMode(evt);
-                    }
-                }
+    int startWrapBlock=-1;
+    int wrappedBlock=-1;
+    int findRes(MouseEvent evt)
+   {
+     int res = 0;
+     int x = evt.getX();
 
-                public void mousePressed(MouseEvent evt)
-                {
-                    if (av.getWrapAlignment())
-                    {
-                        return;
-                    }
+    if (av.wrapAlignment)
+    {
 
-                    if (evt.isShiftDown() || evt.isAltDown() ||
-                            evt.isControlDown())
-                    {
-                        if (evt.isAltDown() || evt.isControlDown())
-                        {
-                            groupEditing = true;
-                        }
+      int hgap = av.charHeight;
+      if (av.scaleAboveWrapped)
+        hgap += av.charHeight;
 
-                        editingSeqs = true;
-                        doMousePressed(evt);
-                    }
-                    else
-                    {
-                        doMousePressedDefineMode(evt);
-                    }
-                }
+      int cHeight = av.getAlignment().getHeight() * av.charHeight
+          + hgap + seqCanvas.getAnnotationHeight();
 
-                public void mouseExited(MouseEvent evt)
-                {
-                    if (av.getWrapAlignment() || editingSeqs)
-                    {
-                        return;
-                    }
+        int y = evt.getY();
+        y -= hgap;
+        x -= seqCanvas.LABEL_WEST;
 
-                    doMouseExitedDefineMode(evt);
-                }
 
-                public void mouseEntered(MouseEvent evt)
-                {
-                    if (av.getWrapAlignment() || editingSeqs)
-                    {
-                        return;
-                    }
+        int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth());
 
-                    doMouseEnteredDefineMode(evt);
-                }
-            });
+        wrappedBlock = y / cHeight;
+        wrappedBlock += av.getStartRes() / cwidth;
+
+        res = wrappedBlock * cwidth + x / av.getCharWidth();
+
+    }
+    else
+    {
+        res = (x / av.getCharWidth()) + av.getStartRes();
     }
 
+    return res;
+
+   }
+
+   int findSeq(MouseEvent evt)
+   {
+
+     int seq = 0;
+     int y = evt.getY();
+
+     if (av.wrapAlignment)
+     {
+       int hgap = av.charHeight;
+       if (av.scaleAboveWrapped)
+         hgap += av.charHeight;
+
+       int cHeight = av.getAlignment().getHeight() * av.charHeight
+           + hgap + seqCanvas.getAnnotationHeight();
+
+         y -= hgap;
+
+       seq = ( (y % cHeight) / av.getCharHeight());
+     }
+     else
+     {
+       seq = (y / av.getCharHeight()) + av.getStartSeq();
+     }
+
+     return seq;
+   }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -212,17 +310,14 @@ public class SeqPanel extends JPanel
      */
     public void doMousePressed(MouseEvent evt)
     {
-        ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
-                av.alignment, HistoryItem.EDIT));
+      ap.alignFrame.addHistoryItem(new HistoryItem("Edit Sequence",
+                                                   av.alignment, HistoryItem.EDIT));
 
-        int seq;
-        int res;
+      int seq = findSeq(evt);
+      int res = findRes(evt);
 
-        int x = evt.getX();
-        int y = evt.getY();
-
-        res = (x / av.getCharWidth()) + av.getStartRes();
-        seq = (y / av.getCharHeight()) + av.getStartSeq();
+      if(seq<0 || res<0)
+        return;
 
         if ((seq < av.getAlignment().getHeight()) &&
                 (res < av.getAlignment().getSequenceAt(seq).getLength()))
@@ -249,57 +344,51 @@ public class SeqPanel extends JPanel
      */
     public void doMouseMoved(MouseEvent evt)
     {
-        int res = 0;
-        int seq = 0;
-        int x = evt.getX();
-        int y = evt.getY();
+      int res = findRes(evt);
+      int seq = findSeq(evt);
 
-        if (av.wrapAlignment)
-        {
-            y -= (2 * av.charHeight);
+      if(res<0 || seq<0 || seq >= av.getAlignment().getHeight())
+            return;
 
-            int chunkHeight = (av.getAlignment().getHeight() + 2) * av.charHeight;
+      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-            res = (int) ((y / chunkHeight) * (getWidth() / av.charWidth)) +
-                (x / av.getCharWidth()) + av.getStartRes();
+      if (res > sequence.getLength())
+      {
+        return;
+      }
 
-            y %= chunkHeight;
-            seq = (y / av.getCharHeight()) + av.getStartSeq();
-        }
-        else
-        {
-            res = (x / av.getCharWidth()) + av.getStartRes();
-            seq = (y / av.getCharHeight()) + av.getStartSeq();
-        }
+      if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)
+      {
+        seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));
+      }
 
-        if (seq >= av.getAlignment().getHeight())
-        {
-            return;
-        }
 
-        SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+        StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
+                sequence.getName());
 
-        if (res > sequence.getLength())
+        Object obj = null;
+        if (av.alignment.isNucleotide())
         {
-            return;
+          obj = ResidueProperties.nucleotideName.get(sequence.getCharAt(res) +
+              "");
+          if(obj!=null)
+            text.append(" Nucleotide: ");
         }
-
-        Object obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) +
-                "");
-        String aa = "";
-
-        if (obj != null)
+        else
         {
-            aa = obj.toString();
+          obj = ResidueProperties.aa2Triplet.get(sequence.getCharAt(res) + "");
+          if(obj!=null)
+            text.append("  Residue: ");
         }
 
-        StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +
-                sequence.getName());
-
-        if (aa != "")
+        if (obj != null)
         {
-            text.append("  Residue: " + aa + " (" +
-                av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+
+          if (obj != "")
+          {
+            text.append( obj + " (" +
+                        av.getAlignment().getSequenceAt(seq).findPosition(res) + ")");
+          }
         }
 
         ap.alignFrame.statusBar.setText(text.toString());
@@ -307,32 +396,54 @@ 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())
+            Vector features = sequence.getDatasetSequence().getSequenceFeatures();
+            if(features!=null)
             {
-                SequenceFeature sf = (SequenceFeature) e.nextElement();
+              StringBuffer sbuffer = new StringBuffer("<html>");
+
+              for (int i = 0; i < features.size(); i++)
+              {
+                SequenceFeature sf = (SequenceFeature) features.elementAt(i);
 
-                if ((sf.getStart() <= sequence.findPosition(res)) &&
-                        (sf.getEnd() >= sequence.findPosition(res)))
+                if ( (sf.getBegin() <= sequence.findPosition(res)) &&
+                    (sf.getEnd() >= sequence.findPosition(res)))
                 {
-                    if (sbuffer.length() > 0)
+                  if (sf.getType().equals("disulfide bond"))
+                  {
+                    if (sf.getBegin() == sequence.findPosition(res)
+                        || sf.getEnd() == sequence.findPosition(res))
                     {
-                        sbuffer.append("; ");
+                      if (sbuffer.length() > 6)
+                        sbuffer.append("<br>");
+                      sbuffer.append("disulfide bond " + sf.getBegin() + ":" +
+                                     sf.getEnd());
                     }
-
-                    sbuffer.append(sf.getType() + " " + sf.getDescription());
-
-                    if (sf.getStatus().length() > 0)
+                  }
+                  else
+                  {
+                    if (sbuffer.length() > 6)
+                      sbuffer.append("<br>");
+                    sbuffer.append(sf.getType());
+                    if (sf.getDescription() != null)
+                      sbuffer.append(" " + sf.getDescription());
+
+                    if (sf.getStatus() != null)
                     {
-                        sbuffer.append(" (" + sf.getStatus() + ")");
+                      sbuffer.append(" (" + sf.getStatus() + ")");
                     }
+                  }
                 }
-            }
 
-            this.setToolTipText(sbuffer.toString());
+              }
+
+              sbuffer.append("</html>");
+              if(sbuffer.length()==13) // <html></html>
+                setToolTipText("");
+              else
+               setToolTipText(sbuffer.toString());
+            }
+            else
+              setToolTipText("");
         }
     }
 
@@ -344,7 +455,7 @@ public class SeqPanel extends JPanel
     public void doMouseDragged(MouseEvent evt)
     {
         // If we're dragging we're editing
-        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
+        int res = findRes(evt);
 
         if (res < 0)
         {
@@ -536,53 +647,14 @@ public class SeqPanel extends JPanel
      */
     void editOccurred(int i)
     {
-        if (endEdit == startEdit)
-        {
-            ap.alignFrame.historyList.pop();
-            ap.alignFrame.updateEditMenuBar();
-        }
-
-        av.updateConservation();
-        av.updateConsensus();
-
-        // Y O Y CLUSTALX
-        ColourSchemeI cs = av.getGlobalColourScheme();
-
-        if (av.getSelectionGroup() != null)
-        {
-            av.getSelectionGroup().recalcConservation();
-        }
+      if (endEdit == startEdit)
+      {
+        ap.alignFrame.historyList.pop();
+        ap.alignFrame.updateEditMenuBar();
+      }
 
-        if (cs instanceof ConservationColourScheme)
-        {
-            ConservationColourScheme ccs = (ConservationColourScheme) cs;
-            Conservation c = new Conservation("All",
-                    ResidueProperties.propHash, 3, av.alignment.getSequences(),
-                    0, av.alignment.getWidth() - 1);
-            c.calculate();
-            c.verdict(false, av.ConsPercGaps);
-
-            if (ccs.cs instanceof ClustalxColourScheme)
-            {
-                ClustalxColourScheme cxs = (ClustalxColourScheme) ccs.cs;
-                cxs.resetClustalX(av.alignment.getSequences(),
-                    av.alignment.getWidth());
-                ccs = new ConservationColourScheme(c, cxs);
-                av.setGlobalColourScheme(ccs);
-            }
-            else
-            {
-                ccs = new ConservationColourScheme(c, ccs.cs);
-                av.setGlobalColourScheme(ccs);
-            }
-        }
+      av.firePropertyChange("alignment", null,av.getAlignment().getSequences());
 
-        if (cs instanceof ClustalxColourScheme)
-        {
-            ((ClustalxColourScheme) cs).resetClustalX(av.alignment.getSequences(),
-                av.alignment.getWidth());
-            av.setGlobalColourScheme(cs);
-        }
     }
 
     /**
@@ -592,9 +664,24 @@ public class SeqPanel extends JPanel
      */
     public void doMousePressedDefineMode(MouseEvent evt)
     {
-        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-        int seq = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
-        oldSeq = seq;
+      int res = findRes(evt);
+      int seq = findSeq(evt);
+      oldSeq = seq;
+
+      startWrapBlock=wrappedBlock;
+
+      if(av.wrapAlignment && seq>av.alignment.getHeight())
+      {
+          JOptionPane.showInternalMessageDialog(Desktop.desktop,
+              "Cannot edit annotations in wrapped view.",
+              "Wrapped view - no edit",
+              JOptionPane.WARNING_MESSAGE);
+        return;
+      }
+
+      if(seq<0 || res<0)
+            return;
+
 
         SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
 
@@ -707,25 +794,26 @@ public class SeqPanel extends JPanel
             return;
         }
 
-        if (stretchGroup.cs instanceof ClustalxColourScheme)
+        if(stretchGroup.cs!=null)
         {
-            ((ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.sequences,
+          if (stretchGroup.cs instanceof ClustalxColourScheme)
+          {
+            ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
+                sequences,
                 stretchGroup.getWidth());
-        }
+          }
 
-        if (stretchGroup.cs instanceof ConservationColourScheme)
-        {
-            ConservationColourScheme ccs = (ConservationColourScheme) stretchGroup.cs;
-            stretchGroup.cs = ccs;
+          if (stretchGroup.cs.conservationApplied())
+          {
             SliderPanel.setConservationSlider(ap, stretchGroup.cs,
-                stretchGroup.getName());
-        }
-        else
-        {
+                                              stretchGroup.getName());
+          }
+          else
+          {
             SliderPanel.setPIDSliderSource(ap, stretchGroup.cs,
-                stretchGroup.getName());
+                                           stretchGroup.getName());
+          }
         }
-
         changeEndRes = false;
         changeStartRes = false;
         stretchGroup = null;
@@ -739,11 +827,14 @@ public class SeqPanel extends JPanel
      */
     public void doMouseDraggedDefineMode(MouseEvent evt)
     {
-        int res = (evt.getX() / av.getCharWidth()) + av.getStartRes();
-        int y = (evt.getY() / av.getCharHeight()) + av.getStartSeq();
+      int res = findRes(evt);
+      int y = findSeq(evt);
 
-        if (stretchGroup == null)
-        {
+      if(wrappedBlock!=startWrapBlock)
+        return;
+
+      if (stretchGroup == null)
+      {
             return;
         }
 
@@ -767,7 +858,7 @@ public class SeqPanel extends JPanel
         {
             res = av.getStartRes();
         }
-        else if (res > av.getEndRes())
+        else if (res > av.getEndRes() && !av.getWrapAlignment())
         {
             res = av.getEndRes();
         }
@@ -918,7 +1009,7 @@ public class SeqPanel extends JPanel
 
                 try
                 {
-                    Thread.sleep(75);
+                    Thread.sleep(20);
                 }
                 catch (Exception ex)
                 {