X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=6869964d91f826c82e935dea85be8bc32a5d76e1;hb=9c1232ed2d632dd4968e407a6c9aa3e2beb6bacf;hp=987b0b801eabdde8b7657d0e735bf1108e7468b5;hpb=25e0e98d70d32d81c952a5927e847deeee76b810;p=jalview.git

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 987b0b8..6869964 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -25,6 +25,8 @@ import java.awt.event.*;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 
+import java.util.Vector;
+
 public class SeqPanel
     extends Panel implements MouseMotionListener, MouseListener
 {
@@ -55,6 +57,9 @@ public class SeqPanel
   StringBuffer keyboardNo1;
   StringBuffer keyboardNo2;
 
+  boolean mouseWheelPressed = false;
+  Point lastMousePress;
+
   public SeqPanel(AlignViewport avp, AlignmentPanel p)
   {
     this.av = avp;
@@ -182,7 +187,7 @@ public class SeqPanel
        SequenceGroup sg = av.selectionGroup;
        //Find the top and bottom of this group
        int min = av.alignment.getHeight(), max = 0;
-       for(int i=0; i<sg.getSize(); i++)
+       for(int i=0; i<sg.getSize(false); i++)
        {
          int index = av.alignment.findIndex( sg.getSequenceAt(i) );
          if(index > max)
@@ -218,7 +223,7 @@ public class SeqPanel
        else
        {
          // Now add any sequences between min and max
-         sg.sequences.removeAllElements();
+         sg.getSequences(false).removeAllElements();
          for (int i = min; i < max; i++)
          {
            sg.addSequence(av.alignment.getSequenceAt(i), false);
@@ -309,11 +314,21 @@ public class SeqPanel
                      ")");
        }
      }
+
      ap.alignFrame.statusBar.setText(text.toString());
 
     }
      public void mousePressed(MouseEvent evt)
      {
+       lastMousePress = evt.getPoint();
+
+       if ( (evt.getModifiers() & InputEvent.BUTTON2_MASK) ==
+         InputEvent.BUTTON2_MASK)
+       {
+         mouseWheelPressed = true;
+         return;
+       }
+
        if (evt.isShiftDown() || evt.isAltDown() ||
            evt.isControlDown())
        {
@@ -360,6 +375,7 @@ public class SeqPanel
   public void mouseReleased(MouseEvent evt)
   {
     mouseDragging = false;
+    mouseWheelPressed = false;
 
     if (!editingSeqs)
     {
@@ -370,7 +386,7 @@ public class SeqPanel
      editOccurred();
 
      endEditing();
-       ap.repaint();
+     ap.repaint();
   }
 
   int startWrapBlock=-1;
@@ -522,55 +538,133 @@ public class SeqPanel
         && sequence.getSequenceFeatures()!=null
         && av.featuresDisplayed!=null)
     {
+      StringBuffer featureText = new StringBuffer();
+      Vector allFeatures = getAllFeaturesAtRes(sequence, sequence.findPosition(res));
+
       int index = 0;
-      sequence.getSequenceFeatures();
-      boolean first = true;
-      while (index < sequence.getSequenceFeatures().length)
+      while (index < allFeatures.size())
       {
-        SequenceFeature sf = sequence.getSequenceFeatures()[index];
-        if (sf.getBegin() <= sequence.findPosition(res) &&
-            sf.getEnd() >= sequence.findPosition(res))
-        {
-          if(!av.featuresDisplayed.containsKey(sf.getType()))
-           {
-             index++;
-             continue;
-           }
-
-          if(first)
-          {
-            text.append(" Sequence Feature:");
-            first = false;
-          }
+        SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(index);
 
-          text.append(" "+sf.getType());
+        featureText.append(sf.getType()+" "+sf.begin+":"+sf.end);
 
-          if(sf.getDescription()!=null)
-            text.append(" "+sf.getDescription());
+        if (sf.getDescription() != null)
+          featureText.append(" " + sf.getDescription());
 
-          if (sf.getStatus()!=null && sf.getStatus().length() > 0)
-          {
-            text.append(" (" + sf.getStatus() + ")");
-          }
-          text.append("; ");
+        if (sf.getValue("status") != null )
+        {
+          featureText.append(" (" + sf.getValue("status") + ")");
         }
+        featureText.append("\n");
 
         index++;
-
       }
+
+
+        if (tooltip == null)
+          tooltip = new Tooltip(featureText.toString(), seqCanvas);
+        else
+          tooltip.setTip(featureText.toString());
+
+        tooltip.repaint();
+
+     //   text.append(" Sequence Feature:");
+     //   text.append(featureText);
+
     }
 
+
      ap.alignFrame.statusBar.setText(text.toString());
 
   }
 
+  Vector getAllFeaturesAtRes(SequenceI seq, int res)
+  {
+    Vector allFeatures = new Vector();
+    int index = 0;
+    if(seq.getSequenceFeatures()!=null)
+    {
+      while (index < seq.getSequenceFeatures().length)
+      {
+        SequenceFeature sf = seq.getSequenceFeatures()[index];
+        if (sf.getBegin() <= res &&
+            sf.getEnd() >= res)
+        {
+          if (av.featuresDisplayed.containsKey(sf.getType()))
+          {
+            allFeatures.addElement(sf);
+          }
+        }
+        index++;
+      }
+    }
+    return allFeatures;
+  }
+
+  Tooltip tooltip;
+
   public void mouseDragged(MouseEvent evt)
   {
-    if (!editingSeqs)
-{
-  doMouseDraggedDefineMode(evt);
-  return;
-}
+    if (mouseWheelPressed)
+    {
+      int oldWidth = av.charWidth;
+
+      //Which is bigger, left-right or up-down?
+      if (Math.abs(evt.getY() - lastMousePress.y)
+          > Math.abs(evt.getX() - lastMousePress.x))
+      {
+        int fontSize = av.font.getSize();
+
+        if (evt.getY() < lastMousePress.y && av.charHeight > 1)
+        {
+          fontSize--;
+        }
+        else if (evt.getY() > lastMousePress.y)
+        {
+          fontSize++;
+        }
+
+
+        if(fontSize<1)
+          fontSize = 1;
+
+        av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+        av.charWidth = oldWidth;
+      }
+      else
+      {
+        if (evt.getX() < lastMousePress.x && av.charWidth > 1)
+        {
+          av.charWidth--;
+        }
+        else if (evt.getX() > lastMousePress.x)
+        {
+          av.charWidth++;
+        }
+
+        if(av.charWidth<1)
+        {
+          av.charWidth = 1;
+        }
+      }
+
+      ap.fontChanged();
+
+      FontMetrics fm = getFontMetrics(av.getFont());
+      av.validCharWidth = fm.charWidth('M') <= av.charWidth;
+
+      lastMousePress = evt.getPoint();
+
+      ap.repaint();
+      ap.annotationPanel.image = null;
+      return;
+      }
+
+      if (!editingSeqs)
+      {
+        doMouseDraggedDefineMode(evt);
+        return;
+      }
 
   int res = findRes(evt);
 
@@ -626,7 +720,7 @@ public class SeqPanel
 
         //Are we editing within a selection group?
         if (groupEditing
-            || (sg != null && sg.sequences.contains(seq)))
+            || (sg != null && sg.getSequences(false).contains(seq)))
         {
           fixedColumns = true;
 
@@ -677,7 +771,7 @@ public class SeqPanel
                  fixedRight--)
             {
               blank = true;
-              for (int s = 0; s < sg.getSize(); s++)
+              for (int s = 0; s < sg.getSize(false); s++)
               {
                 seq = sg.getSequenceAt(s);
                 for (int j = 0; j < startres - lastres; j++)
@@ -696,7 +790,7 @@ public class SeqPanel
 
             if (!blank)
             {
-              if(sg.getSize() == av.alignment.getHeight())
+              if(sg.getSize(false) == av.alignment.getHeight())
               {
                 //We can still insert gaps if the selectionGroup
                 //contains all the sequences
@@ -718,7 +812,7 @@ public class SeqPanel
             /// Are we able to delete?
             // ie are all columns blank?
 
-            for (int s = 0; s < sg.getSize(); s++)
+            for (int s = 0; s < sg.getSize(false); s++)
             {
               seq = sg.getSequenceAt(s);
 
@@ -741,7 +835,7 @@ public class SeqPanel
           }
 
 
-          for (int i = 0; i < sg.getSize(); i++)
+          for (int i = 0; i < sg.getSize(false); i++)
           {
             seq = sg.getSequenceAt(i);
 
@@ -925,6 +1019,8 @@ public class SeqPanel
 //////////////////////////////////////////
   public void doMousePressedDefineMode(MouseEvent evt)
   {
+
+
     if (scrollThread != null)
     {
       scrollThread.running = false;
@@ -962,7 +1058,7 @@ public class SeqPanel
       }
     }
 
-    else if (!stretchGroup.sequences.contains(sequence)
+    else if (!stretchGroup.getSequences(false).contains(sequence)
              || stretchGroup.getStartRes() > res
              || stretchGroup.getEndRes() < res)
     {
@@ -978,57 +1074,90 @@ public class SeqPanel
               allGroups[i].getEndRes() >= res)
           {
             stretchGroup = allGroups[i];
-            av.setSelectionGroup(stretchGroup);
             break;
           }
         }
       }
+      av.setSelectionGroup(stretchGroup);
     }
 
-    if (stretchGroup == null)
+    if (av.cursorMode)
     {
-      // define a new group here
-      SequenceGroup sg = new SequenceGroup();
-      sg.setStartRes(res);
-      sg.setEndRes(res);
-      sg.addSequence(sequence, false);
-      av.setSelectionGroup(sg);
-      stretchGroup = sg;
-
-      if (av.getConservationSelected())
-      {
-        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
-                                          "Background");
-      }
-      if (av.getAbovePIDThreshold())
-      {
-        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
-                                       "Background");
-      }
-
+      seqCanvas.cursorX = findRes(evt);
+      seqCanvas.cursorY = findSeq(evt);
+      seqCanvas.repaint();
+      return;
     }
 
+
+
     // DETECT RIGHT MOUSE BUTTON IN AWT
-    else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
+    if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
              InputEvent.BUTTON3_MASK)
     {
-      APopupMenu popup = new APopupMenu(ap, null, null);
+      Vector allFeatures = getAllFeaturesAtRes(sequence,
+                                               sequence.findPosition(res));
+
+      Vector links = null;
+      if(allFeatures!=null)
+      {
+        for (int i = 0; i < allFeatures.size(); i++)
+        {
+          SequenceFeature sf = (SequenceFeature) allFeatures.elementAt(i);
+          if (sf.links != null)
+          {
+            links = new Vector();
+            for (int j = 0; j < sf.links.size(); j++)
+            {
+              links.addElement(sf.links.elementAt(j));
+            }
+          }
+        }
+      }
+      APopupMenu popup = new APopupMenu(ap, null, links);
       this.add(popup);
       popup.show(this, evt.getX(), evt.getY());
+      ap.repaint();
     }
-
-    if (stretchGroup != null && stretchGroup.getEndRes() == res)
+    else
     {
-      // Edit end res position of selected group
-      changeEndRes = true;
-    }
+      //Only if left mouse button do we want to change group sizes
 
-    else if (stretchGroup != null && stretchGroup.getStartRes() == res)
-    {
-      // Edit end res position of selected group
-      changeStartRes = true;
-    }
+      if (stretchGroup == null)
+      {
+        // define a new group here
+        SequenceGroup sg = new SequenceGroup();
+        sg.setStartRes(res);
+        sg.setEndRes(res);
+        sg.addSequence(sequence, false);
+        av.setSelectionGroup(sg);
+        stretchGroup = sg;
+
+        if (av.getConservationSelected())
+        {
+          SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(),
+                                            "Background");
+        }
+        if (av.getAbovePIDThreshold())
+        {
+          SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(),
+                                         "Background");
+        }
+
+      }
+
+      if (stretchGroup != null && stretchGroup.getEndRes() == res)
+      {
+        // Edit end res position of selected group
+        changeEndRes = true;
+      }
 
+      else if (stretchGroup != null && stretchGroup.getStartRes() == res)
+      {
+        // Edit end res position of selected group
+        changeStartRes = true;
+      }
+    }
   }
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
@@ -1042,8 +1171,8 @@ public class SeqPanel
     {
       if (stretchGroup.cs instanceof ClustalxColourScheme)
       {
-        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(stretchGroup.
-            sequences,
+        ( (ClustalxColourScheme) stretchGroup.cs).resetClustalX(
+            stretchGroup.getSequences(true),
             stretchGroup.getWidth());
       }
 
@@ -1146,7 +1275,7 @@ public class SeqPanel
 
           Sequence nextSeq = (Sequence) av.getAlignment().getSequenceAt(oldSeq);
 
-          if (stretchGroup.sequences.contains(nextSeq))
+          if (stretchGroup.getSequences(false).contains(nextSeq))
           {
               stretchGroup.deleteSequence(seq, false);
           }