X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=5db5e2e97ddafb9850dab16236862b62f13c6169;hb=fe5db5e87fc726b1560d21f97f19b0e04963b72c;hp=5e15283e80671d9eb79730adb8ae155a6b782b5a;hpb=491ef50a485fbff6e610c0cd138e5cf89538aa3d;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 5e15283..5db5e2e 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -12,15 +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;
-
-
-
-  boolean mouseDown;
-  boolean mouseUp;
+  int            offy;
+  int            width;
+  int lastid = -1;
+  boolean mouseDragging = false;
 
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
@@ -35,107 +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);
-       } else {
-         av.getSelection().addElement(pickedSeq);
-       }
-     }
-
-     repaint();
-
-   }
 
   public void mouseDragged(MouseEvent e) {
-    int y = e.getY();
+    mouseDragging = true;
 
+    int y = e.getY();
+    if(av.getWrapAlignment())
+      y-=2*av.charHeight;
     int seq = av.getIndex(y);
 
-    if (mouseDown == true) {
-      if (seq < lastid) {
-        selectSeqs(lastid-1,seq);
-      } else if (seq > lastid) {
-         selectSeqs(lastid+1,seq);
-      }
-      lastid = seq;
-    }
+    if(seq<0)
+      return;
 
-    return;
+    if (seq < lastid)
+      selectSeqs(lastid - 1, seq);
+    else if (seq > lastid)
+      selectSeqs(lastid + 1, seq);
+
+    lastid = seq;
+    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)
+  {
+    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 mouseEntered(MouseEvent e) { }
-  public void mouseExited (MouseEvent e) { }
+
 
   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;
 
-    mouseDown = true;
+    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;
+    }
 
-      if( javax.swing.SwingUtilities.isRightMouseButton(e))
-      {
-        String id = av.getAlignment().getSequenceAt(seq).getName();
-        String s = (String)JOptionPane.showInputDialog(
-                    this,
-                    "Edit sequence name",
-                    "Edit sequence name",
-                    JOptionPane.PLAIN_MESSAGE,
-                    null,
-                    null,
-                    id);
-
-        if(s!=null)
-        {
-          av.getAlignment().getSequenceAt(seq).setName(s);
-          alignPanel.RefreshPanels();
-        }
+    if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null)
+    {
 
-      }
-      else
-      {
-        if (seq != -1)
-          selectSeqs(seq,seq);
+      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));
 
-        lastid = seq;
-      }
-    return;
+      av.setSelectionGroup(selection);
+      return;
+    }
+
+    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(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);
   }
 
-  public void mouseReleased(MouseEvent e) {
-    lastid = -1;
+  void selectSeqs(int start, int end) {
 
-    mouseDown = false;
-    mouseUp   = true;
+    lastid = start;
+    if (end < start)
+     {
+       int tmp = start;
+       start = end;
+       end   = tmp;
+       lastid = end;
+     }
 
+     for (int i = start; i <= end; i++)
+        av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i));
+
+   }
+
+
+  public void mouseReleased(MouseEvent e)
+  {
+    if(scrollThread!=null)
+      scrollThread.running = false;
+
+    mouseDragging = false;
     PaintRefresher.Refresh(this);
+  }
+
+  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)
+        {}
+      }
+    }
+}
+
 }