X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=5db5e2e97ddafb9850dab16236862b62f13c6169;hb=2ba9716bbffe4b35f640f8a85be4b60fe5fb2fdd;hp=ff175aa3a885a003c1d34eece767b871a8bb413b;hpb=5f0327b9a1f7adedb23e9188aef61e98dd14a1c2;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index ff175aa..5db5e2e 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -12,12 +12,12 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
   protected IdCanvas       idCanvas;
   protected AlignViewport  av;
   protected AlignmentPanel alignPanel;
+  ScrollThread scrollThread = null;
 
-  protected int            offy;
-  public    int            width;
-  public    int            lastid;
-
-  SequenceGroup selectedSequenceGroup;
+  int            offy;
+  int            width;
+  int lastid = -1;
+  boolean mouseDragging = false;
 
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
@@ -32,113 +32,214 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
 
   public void mouseMoved(MouseEvent e) {}
 
-  public void selectSeqs(int start, int end) {
-     if (end < start)
-     {
-       int tmp = start;
-       start = end;
-       end   = tmp;
-     }
-
-     for (int i = start; i <= end; i++)
-     {
-       SequenceI pickedSeq = av.getAlignment().getSequenceAt(i);
-       if (av.getSelection().contains(pickedSeq))
-       {
-         av.getSelection().removeElement(pickedSeq);
-         selectedSequenceGroup.deleteSequence(pickedSeq);
-       }
-       else
-       {
-         av.getSelection().addElement(pickedSeq);
-         if(selectedSequenceGroup==null)
-         {
-           selectedSequenceGroup = new SequenceGroup();
-           av.setRubberbandGroup( selectedSequenceGroup );
-          // av.alignment.addGroup( selectedSequenceGroup );
-           selectedSequenceGroup.setStartRes(0);
-           selectedSequenceGroup.setEndRes( pickedSeq.getSequence().length());
-         }
-
-         selectedSequenceGroup.addSequence( pickedSeq );
-       }
-
-     }
-
-     alignPanel.seqPanel.seqCanvas.paintFlag=true;
-     alignPanel.repaint();
-     repaint();
-
-   }
 
   public void mouseDragged(MouseEvent e) {
+    mouseDragging = true;
+
     int y = e.getY();
+    if(av.getWrapAlignment())
+      y-=2*av.charHeight;
     int seq = av.getIndex(y);
 
+    if(seq<0)
+      return;
+
     if (seq < lastid)
       selectSeqs(lastid - 1, seq);
     else if (seq > lastid)
       selectSeqs(lastid + 1, seq);
 
     lastid = seq;
-
-    return;
+    alignPanel.repaint();
   }
 
   public void mouseClicked(MouseEvent e)
   {
     if (e.getClickCount() == 2)
     {
-       int seq = av.getIndex(e.getY());
+       int y = e.getY();
+       if(av.getWrapAlignment())
+         y-=2*av.charHeight;
+
+       int seq = av.getIndex(y);
        String id = av.getAlignment().getSequenceAt(seq).getName();
 
        try{
          jalview.util.BrowserLauncher.openURL(
              "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +
              "]+-vn+2");
-       }catch(Exception ex){ex.printStackTrace();}
+       }catch(Exception ex){System.err.println(
+           "Try adding the jalview.browser property to your jalview.properties file:\n"
+                            +"jalview.browser=firefox"); ex.printStackTrace();}
     }
 
   }
-  public void mouseEntered(MouseEvent e) { }
-  public void mouseExited (MouseEvent e) { }
+  public void mouseEntered(MouseEvent e)
+  {
+    if(scrollThread!=null)
+      scrollThread.running = false;
+  }
+
+  public void mouseExited (MouseEvent e)
+  {
+    if(av.getWrapAlignment())
+      return;
+
+    if(mouseDragging && e.getY()<0 && av.getStartSeq()>0)
+    {
+      scrollThread = new ScrollThread(true);
+    }
+
+    if(mouseDragging && e.getY()>=getHeight() && av.alignment.getHeight()>av.getEndSeq())
+    {
+      scrollThread = new ScrollThread(false);
+    }
+  }
+
 
   public void mousePressed(MouseEvent e) {
     if (e.getClickCount() == 2)
       return;
 
     int y = e.getY();
+    if(av.getWrapAlignment())
+      y-=2*av.charHeight;
+
     int seq = av.getIndex(y);
+    if (seq == -1)
+      return;
+
+    if (javax.swing.SwingUtilities.isRightMouseButton(e))
+    {
+      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
+          (Sequence)av.getAlignment().getSequenceAt(seq));
+      pop.show(this, e.getX(), y);
+      return;
+    }
 
-    selectedSequenceGroup = av.getRubberbandGroup();
-    if (selectedSequenceGroup == null)
+    if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null)
     {
-      selectedSequenceGroup = new SequenceGroup();
-      av.setRubberbandGroup(selectedSequenceGroup);
+
+      SequenceGroup selection = new SequenceGroup();
+      SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq));
+      selection.setStartRes(0);
+      selection.setEndRes(av.alignment.getWidth()-1);
+      for (int i =0; i< sg.getSize(); i++)
+        selection.addSequence(sg.getSequenceAt(i));
+
+      av.setSelectionGroup(selection);
+      return;
     }
 
-    selectedSequenceGroup.setStartRes(0);
-    selectedSequenceGroup.setEndRes(av.getAlignment().getWidth() - 1);
+    if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null))
+      av.setSelectionGroup(new SequenceGroup());
+
+    av.getSelectionGroup().setStartRes(0);
+    av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);
 
-    if (seq != -1)
-      selectSeqs(seq, seq);
+    if(e.isShiftDown() && lastid!=-1)
+      selectSeqs(lastid, seq);
+    else
+      selectSeq(seq);
 
+    alignPanel.repaint();
+  }
+
+  void selectSeq(int seq)
+  {
     lastid = seq;
+    SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+    av.getSelectionGroup().addOrRemove(pickedSeq);
+  }
+
+  void selectSeqs(int start, int end) {
 
-    if( javax.swing.SwingUtilities.isRightMouseButton(e))
+    lastid = start;
+    if (end < start)
      {
-       jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, av.getAlignment().getSequenceAt(seq) );
-       pop.show(this, e.getX(), y);
+       int tmp = start;
+       start = end;
+       end   = tmp;
+       lastid = end;
      }
 
+     for (int i = start; i <= end; i++)
+        av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));
+
+   }
 
-    return;
-  }
 
   public void mouseReleased(MouseEvent e)
   {
-    lastid = -1;
+    if(scrollThread!=null)
+      scrollThread.running = false;
+
+    mouseDragging = false;
     PaintRefresher.Refresh(this);
-    selectedSequenceGroup = null;
   }
+
+  public void highlightSearchResults( java.util.Vector found )
+  {
+    idCanvas.setHighlighted( found );
+
+    if(found == null)
+      return;
+
+    int index = av.alignment.findIndex( (SequenceI)found.get(0));
+
+    // do we need to scroll the panel?
+    if(av.getStartSeq()>index || av.getEndSeq()<index)
+        alignPanel.setScrollValues( av.getStartRes(), index);
+  }
+
+  // this class allows scrolling off the bottom of the visible alignment
+  class ScrollThread
+      extends Thread
+  {
+    boolean running = false;
+    boolean up = true;
+    public ScrollThread(boolean up)
+    {
+      this.up = up;
+      start();
+    }
+
+    public void stopScrolling()
+    {
+      running = false;
+    }
+
+    public void run()
+    {
+      running = true;
+      while (running)
+      {
+        if(alignPanel.scrollUp(up))
+        {
+          // scroll was ok, so add new sequence to selection
+          int seq = av.getStartSeq();
+          if(!up)
+            seq = av.getEndSeq();
+
+          if (seq < lastid)
+            selectSeqs(lastid - 1, seq);
+          else if (seq > lastid)
+            selectSeqs(lastid + 1, seq);
+
+          lastid = seq;
+        }
+        else
+          running = false;
+
+        alignPanel.repaint();
+        try
+        {
+          Thread.sleep(100);
+        }
+        catch (Exception ex)
+        {}
+      }
+    }
+}
+
 }