X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=162f978ab4adec11a87e246a6f35f6a8a2df3687;hb=e542a2b9968ee6a7def19e79e84c27684ee686e3;hp=9dcebd2159718af8b3ce2adeeb98e0fef0f13582;hpb=4b9d13acc586d87c53ce21078fb380405164e19b;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 9dcebd2..162f978 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -4,15 +4,14 @@ import java.awt.*;
 import java.awt.event.*;
 import jalview.datamodel.*;
 import javax.swing.*;
+import java.util.*;
 import jalview.schemes.*;
-import jalview.analysis.*;
-
 
 public class SeqPanel extends JPanel
 {
 
   public    SeqCanvas         seqCanvas;
-  public    AlignmentPanel    parent;
+  public    AlignmentPanel    ap;
 
   protected int startres;
   protected int lastres;
@@ -26,6 +25,10 @@ public class SeqPanel extends JPanel
   // if character is inserted or deleted, we will need to recalculate the conservation
   int seqEditOccurred = -1;
 
+  ScrollThread scrollThread = null;
+  boolean mouseDragging = false;
+
+
   public SeqPanel(AlignViewport avp, AlignmentPanel p) {
     this.av         = avp;
 
@@ -33,15 +36,20 @@ public class SeqPanel extends JPanel
     setLayout(new BorderLayout());
     add(seqCanvas, BorderLayout.CENTER);
 
-    parent = p;
+    ap = p;
 
     addMouseMotionListener( new MouseMotionAdapter()
     {
       public void mouseMoved(MouseEvent evt)
-      {   doMouseMoved(evt);    }
+      {
+       if(av.getWrapAlignment())
+         return;
+        doMouseMoved(evt);    }
 
       public void mouseDragged(MouseEvent evt)
       {
+        if(av.getWrapAlignment())
+         return;
         if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
           doMouseDragged(evt);
         else
@@ -53,6 +61,8 @@ public class SeqPanel extends JPanel
     {
       public void mouseReleased(MouseEvent evt)
       {
+        if(av.getWrapAlignment())
+         return;
         if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
           doMouseReleased(evt);
         else
@@ -60,11 +70,28 @@ public class SeqPanel extends JPanel
       }
       public void mousePressed(MouseEvent evt)
       {
+        if(av.getWrapAlignment())
+         return;
         if(evt.isShiftDown() || evt.isAltDown() || evt.isControlDown())
           doMousePressed(evt);
         else
           doMousePressedDefineMode(evt);
       }
+      public void mouseExited(MouseEvent evt)
+      {
+        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
+                  evt.isControlDown())
+                return;
+              doMouseExitedDefineMode(evt);
+
+      }
+      public void mouseEntered(MouseEvent evt)
+      {
+        if (av.getWrapAlignment() || evt.isShiftDown() || evt.isAltDown() ||
+            evt.isControlDown())
+          return;
+        doMouseEnteredDefineMode(evt);
+      }
 
     });
     repaint();
@@ -86,13 +113,12 @@ public class SeqPanel extends JPanel
 
     seqEditOccurred = -1;
 
-    parent.RefreshPanels();
-    repaint();
+    ap.repaint();
 
   }
 
   public void doMousePressed(MouseEvent evt) {
-    parent.alignFrame.addHistoryItem("sequence edit");
+    ap.alignFrame.addHistoryItem("sequence edit");
     int seq;
     int res;
 
@@ -146,8 +172,6 @@ public class SeqPanel extends JPanel
       y %= chunkHeight;
       seq =     y / av.getCharHeight() + av.getStartSeq();
 
-      //   chunkHeight =  (da.getHeight() + 2)*charHeight;
-      //  startx += chunkWidth;
     }
     else
     {
@@ -159,22 +183,57 @@ public class SeqPanel extends JPanel
     if(seq>=av.getAlignment().getHeight())
       return;
 
-    Object obj = ResidueProperties.aa2Triplet.get( av.getAlignment().getSequenceAt(seq).getCharAt(res)+"" ) ;
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+    if(res>sequence.getLength())
+      return;
+
+    Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
     String aa = "";
     if(obj!=null)
          aa = obj.toString();
 
-    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+av.getAlignment().getSequenceAt(seq).getName());
+    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
     if(aa!="")
       text.append("  Residue: "+aa+" ("+  av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
 
-    parent.alignFrame.statusBar.setText(text.toString());
+    ap.alignFrame.statusBar.setText(text.toString());
+
+    // 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 sf = (SequenceFeature) e.nextElement();
+        if (sf.getStart() <= sequence.findPosition(res) &&
+            sf.getEnd() >= sequence.findPosition(res))
+        {
+          if(sbuffer.length()>0)
+            sbuffer.append("; ");
+          sbuffer.append(sf.getType() + " " + sf.getDescription());
+          if(sf.getStatus().length()>0)
+            sbuffer.append(" ("+sf.getStatus()+")");
+        }
+
+      }
+
+      ToolTipManager.sharedInstance().registerComponent(this);
+      this.setToolTipText(sbuffer.toString());
+    }
+
 
   }
 
   public void doMouseDragged(MouseEvent evt) {
     // If we're dragging we're editing
 
+    if(lastres==-1)
+      return;
+
     int x = evt.getX();
 
     int res = x/av.getCharWidth() + av.getStartRes();
@@ -186,7 +245,9 @@ public class SeqPanel extends JPanel
 	// Group editing
 	if (evt.isAltDown() || evt.isControlDown())
         {
-	  SequenceGroup sg = av.getAlignment().findGroup(startseq);
+	  SequenceGroup sg = av.getSelectionGroup();
+          if(sg==null)
+            av.getAlignment().findGroup(startseq);
           if (sg != null)
           {
             boolean deleteAllowed = false;
@@ -286,31 +347,29 @@ public class SeqPanel extends JPanel
   {
 
     if ( jalview.util.Comparison.isGap( av.alignment.getSequenceAt(seq).getSequence().charAt(j)))
-        av.alignment.getSequenceAt(seq).deleteCharAt(j);
+      av.alignment.getSequenceAt(seq).deleteCharAt(j);
 
     av.alignment.getWidth();
     repaint();
     seqEditOccurred=seq;
+
   }
 
 
   void updateConservation(int i)
   {
-  /*  Alignment al = (Alignment) av.getAlignment();
-    SequenceGroup sg = av.alignment.findGroup( al.getSequenceAt(i));
-    if(sg==null || !(sg.cs instanceof ConservationColourScheme))
-      return;
+    av.updateConservation();
+    av.updateConsensus();
 
-    Conservation c = sg.getConservation();
+    ColourSchemeI cs = av.getGlobalColourScheme();
+    if(cs instanceof ConservationColourScheme)
+      cs = ( (ConservationColourScheme) cs).cs;
+
+    if(cs instanceof ClustalxColourScheme)
+      cs = new ClustalxColourScheme(av.alignment.getSequences(), av.alignment.getWidth());
+
+    ap.alignFrame.changeColour(cs);
 
-    c = new Conservation("All", al.cons,
-                         ResidueProperties.propHash, 3, sg.sequences, 0,
-                         al.getWidth());
-    c.calculate();
-    c.verdict(false, 100);
-    sg.setConservation(c);
-    ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;
-    ccs.conserve = c;*/
   }
 
 //////////////////////////////////////////
@@ -323,16 +382,39 @@ public class SeqPanel extends JPanel
     int seq = evt.getY()/av.getCharHeight() + av.getStartSeq();
     oldSeq = seq;
 
-    stretchGroup = av.getRubberbandGroup();
+    SequenceI sequence = (Sequence) av.getAlignment().getSequenceAt(seq);
+
+    if(sequence==null || res>sequence.getLength())
+      return;
+
+    stretchGroup = av.getSelectionGroup();
 
     if(stretchGroup == null)
-        stretchGroup = av.alignment.findGroup((Sequence)av.getAlignment().getSequenceAt(seq));
+     {
+       stretchGroup = av.alignment.findGroup( sequence );
+       if(stretchGroup!=null && res>stretchGroup.getStartRes() && res<stretchGroup.getEndRes())
+         av.setSelectionGroup(stretchGroup);
+       else
+         stretchGroup = null;
+     }
 
-    else if(!stretchGroup.sequences.contains((Sequence)av.getAlignment().getSequenceAt(seq))
+    else if(!stretchGroup.sequences.contains(sequence)
             || stretchGroup.getStartRes()>res
             || stretchGroup.getEndRes()<res)
      {
        stretchGroup = null;
+
+       SequenceGroup[] allGroups = av.alignment.findAllGroups( sequence );
+
+       if (allGroups != null)
+         for (int i = 0; i < allGroups.length; i++)
+           if (allGroups[i].getStartRes() <= res &&
+               allGroups[i].getEndRes() >= res)
+           {
+             stretchGroup = allGroups[i];
+             av.setSelectionGroup(stretchGroup);
+             break;
+           }
      }
 
     if(stretchGroup==null)
@@ -341,13 +423,19 @@ public class SeqPanel extends JPanel
       SequenceGroup sg = new SequenceGroup();
       sg.setStartRes(res);
       sg.setEndRes(res);
-      sg.addSequence( (Sequence)av.getAlignment().getSequenceAt(seq) );
-      av.setRubberbandGroup( sg );
+      sg.addSequence( sequence );
+      av.setSelectionGroup( sg );
       stretchGroup = sg;
+
+      if(av.getConservationSelected())
+        SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), "Background");
+      if(av.getAbovePIDThreshold())
+        SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), "Background");
+
     }
     else if( javax.swing.SwingUtilities.isRightMouseButton(evt))
     {
-        jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( parent , null);
+        jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu( ap , null);
         pop.show(this, evt.getX(), evt.getY());
 
     // edit the properties of existing group
@@ -362,10 +450,8 @@ public class SeqPanel extends JPanel
       changeStartRes = true;
 
 
-    seqCanvas.paintFlag = true;
     repaint();
 
-
   }
 
   boolean changeEndSeq = false;
@@ -376,9 +462,40 @@ public class SeqPanel extends JPanel
 
   public void doMouseReleasedDefineMode(MouseEvent evt)
   {
+    mouseDragging = false;
+
+    if(stretchGroup==null)
+      return;
+
+    if(stretchGroup.cs instanceof ClustalxColourScheme)
+    {
+      stretchGroup.cs = new ClustalxColourScheme(stretchGroup.sequences, av.alignment.getWidth());
+      repaint();
+    }
+
+    else if(stretchGroup.cs instanceof ConservationColourScheme)
+    {
+       ConservationColourScheme ccs = (ConservationColourScheme)stretchGroup.cs;
+       stretchGroup.cs = ccs;
+       SliderPanel.setConservationSlider(ap, stretchGroup.cs, stretchGroup.getName()) ;
+
+       repaint();
+    }
+    else
+    {
+      if(stretchGroup.cs !=null && stretchGroup.cs.canThreshold())
+      {
+        ResidueColourScheme rcs =  (ResidueColourScheme) stretchGroup.cs;
+        SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, stretchGroup.getName());
+      }
+
+    }
+
+
     changeEndRes = false;
     changeStartRes = false;
     stretchGroup = null;
+    ap.idPanel.repaint();
   }
 
 
@@ -388,13 +505,19 @@ public class SeqPanel extends JPanel
     int res = evt.getX()/av.getCharWidth() + av.getStartRes();
     int y = evt.getY()/av.getCharHeight() + av.getStartSeq();
 
+    if(stretchGroup==null)
+      return;
+
+    if(res>av.alignment.getWidth())
+      res = av.alignment.getWidth()-1;
+
 
     if(stretchGroup.getEndRes()==res)
       // Edit end res position of selected group
       changeEndRes = true;
 
     else if(stretchGroup.getStartRes()==res)
-      // Edit end res position of selected group
+      // Edit start res position of selected group
       changeStartRes = true;
 
 
@@ -414,14 +537,13 @@ public class SeqPanel extends JPanel
         stretchGroup.setStartRes( res );
     }
 
-
     int dragDirection = 0;
     if (y > oldSeq)
       dragDirection = 1;
     else if (y < oldSeq)
       dragDirection = -1;
 
-    while (y != oldSeq)
+    while (y != oldSeq && oldSeq>0 && y<av.alignment.getHeight())
     {
       // This routine ensures we don't skip any sequences, as the
       // selection is quite slow.
@@ -437,16 +559,87 @@ public class SeqPanel extends JPanel
       }
       else
       {
+       if(seq!=null)
         stretchGroup.addSequence(seq);
         stretchGroup.addSequence(nextSeq);
       }
     }
     oldSeq = y;
+    mouseDragging = true;
+    if(scrollThread!=null)
+      scrollThread.setEvent(evt);
 
-    seqCanvas.paintFlag = true;
     repaint();
   }
 
+  public void doMouseEnteredDefineMode(MouseEvent e)
+  {
+    if (scrollThread != null)
+      scrollThread.running = false;
+  }
+
+  public void doMouseExitedDefineMode(MouseEvent e)
+  {
+    if (av.getWrapAlignment())
+      return;
+
+    if(mouseDragging)
+      scrollThread = new ScrollThread();
+
+  }
+  // this class allows scrolling off the bottom of the visible alignment
+  class ScrollThread extends Thread
+  {
+    MouseEvent evt;
+    boolean running = false;
+    public ScrollThread()
+    {
+      start();
+    }
+
+    public void setEvent(MouseEvent e)
+    {
+      evt = e;
+    }
+
+    public void stopScrolling()
+    {
+      running = false;
+    }
+
+    public void run()
+    {
+      running = true;
+      while (running)
+      {
+        if(evt!=null)
+        {
+
+          if (mouseDragging && evt.getY() < 0 && av.getStartSeq() > 0)
+            running = ap.scrollUp(true);
+
+          if (mouseDragging && evt.getY() >= getHeight() &&
+              av.alignment.getHeight() > av.getEndSeq())
+            running = ap.scrollUp(false);
+
+          if (mouseDragging && evt.getX() < 0)
+            running = ap.scrollRight(true);
+
+          else if (mouseDragging && evt.getX() >= getWidth())
+            running = ap.scrollRight(false);
+        }
+
+        try
+        {
+          Thread.sleep(75);
+        }
+        catch (Exception ex)
+        {}
+      }
+    }
+}
+
+
 
 }