X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=f3db9be7a1b8d9215b6d2d815f5d6583226fac4f;hb=fbec1b33d0fc169d72be059a5d2cf12b248270e1;hp=4998360a1eef268f4084dbc2d07947f00595ffc0;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 4998360..f3db9be 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,21 +1,21 @@
 /*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 
 package jalview.appletgui;
 
@@ -24,47 +24,75 @@ import java.awt.event.*;
 
 import jalview.datamodel.*;
 
-public class IdPanel extends Panel implements MouseListener, MouseMotionListener {
+public class IdPanel
+    extends Panel implements MouseListener, MouseMotionListener
+{
 
-  protected IdCanvas       idCanvas;
-  protected AlignViewport  av;
+  protected IdCanvas idCanvas;
+  protected AlignViewport av;
   protected AlignmentPanel alignPanel;
   ScrollThread scrollThread = null;
 
-  int            offy;
-  int            width;
+  int offy;
+  int width;
   int lastid = -1;
   boolean mouseDragging = false;
+  java.util.Vector links = new java.util.Vector();
 
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
-    this.av         = av;
+    this.av = av;
     alignPanel = parent;
     idCanvas = new IdCanvas(av);
     setLayout(new BorderLayout());
     add(idCanvas, BorderLayout.CENTER);
     idCanvas.addMouseListener(this);
     idCanvas.addMouseMotionListener(this);
-  }
 
-  public void mouseMoved(MouseEvent e) {}
+    String label, url;
+    for(int i=1; i<10; i++)
+    {
+      label = parent.alignFrame.applet.getParameter("linkLabel_"+i);
+      url = parent.alignFrame.applet.getParameter("linkURL_"+i);
 
+      if(label!=null && url!=null)
+        links.addElement(label+"|"+url);
 
-  public void mouseDragged(MouseEvent e) {
+    }
+    if (links.size() < 1)
+    {
+      links = new java.util.Vector();
+      links.addElement("SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");
+    }
+  }
+
+  public void mouseMoved(MouseEvent e)
+  {}
+
+  public void mouseDragged(MouseEvent e)
+  {
     mouseDragging = true;
 
     int y = e.getY();
-    if(av.getWrapAlignment())
-      y-=2*av.charHeight;
+    if (av.getWrapAlignment())
+    {
+      y -= 2 * av.charHeight;
+    }
     int seq = av.getIndex(y);
 
-    if(seq<0)
+    if (seq < 0)
+    {
       return;
+    }
 
     if (seq < lastid)
+    {
       selectSeqs(lastid - 1, seq);
+    }
     else if (seq > lastid)
+    {
       selectSeqs(lastid + 1, seq);
+    }
 
     lastid = seq;
     alignPanel.repaint();
@@ -72,91 +100,127 @@ public class IdPanel extends Panel implements MouseListener, MouseMotionListener
 
   public void mouseClicked(MouseEvent e)
   {
-    if (e.getClickCount() == 2)
+    if (e.getClickCount() < 2)
+        return;
+
+    int y = e.getY();
+
+    if (av.getWrapAlignment())
     {
-       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.bin.JalviewLite.showURL(
-             "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +
-             "]+-vn+2");
-       }catch(Exception ex){ex.printStackTrace();}
+      y -= (2 * av.charHeight);
     }
 
+    //DEFAULT LINK IS FIRST IN THE LINK LIST
+    int seq = av.getIndex(y);
+    String id = av.getAlignment().getSequenceAt(seq).getName();
+
+    String target = links.elementAt(0).toString();
+    target = target.substring(0, target.indexOf("|"));
+    String url = links.elementAt(0).toString();
+    url = url.substring(url.indexOf("|")+1);
+
+    int index = url.indexOf("$SEQUENCE_ID$");
+    url = url.substring(0, index)+ id + url.substring(index+13);
+
+    try
+    {
+      jalview.bin.JalviewLite.showURL(url, target);
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
   }
+
   public void mouseEntered(MouseEvent e)
   {
-    if(scrollThread!=null)
+    if (scrollThread != null)
+    {
       scrollThread.running = false;
+    }
   }
 
-  public void mouseExited (MouseEvent e)
+  public void mouseExited(MouseEvent e)
   {
-    if(av.getWrapAlignment())
+    if (av.getWrapAlignment())
+    {
       return;
+    }
 
-    if(mouseDragging && e.getY()<0 && av.getStartSeq()>0)
+    if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
     {
       scrollThread = new ScrollThread(true);
     }
 
-    if(mouseDragging && e.getY()>=getSize().height && av.alignment.getHeight()>av.getEndSeq())
+    if (mouseDragging && e.getY() >= getSize().height &&
+        av.alignment.getHeight() > av.getEndSeq())
     {
       scrollThread = new ScrollThread(false);
     }
   }
 
-
-  public void mousePressed(MouseEvent e) {
-    if (e.getClickCount() == 2)
+  public void mousePressed(MouseEvent e)
+  {
+    if (e.getClickCount() >1 )
+    {
       return;
+    }
 
     int y = e.getY();
-    if(av.getWrapAlignment())
-      y-=2*av.charHeight;
+    if (av.getWrapAlignment())
+    {
+      y -= 2 * av.charHeight;
+    }
 
     int seq = av.getIndex(y);
     if (seq == -1)
+    {
       return;
+    }
 
-    if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+    if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==
+        InputEvent.BUTTON3_MASK)
     {
-      APopupMenu popup = new APopupMenu(alignPanel, null);
+      APopupMenu popup = new APopupMenu(alignPanel, (Sequence) av.getAlignment().getSequenceAt(seq), links);
       this.add(popup);
       popup.show(this, e.getX(), e.getY());
       return;
     }
 
-
-    if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null)
+    if (!e.isControlDown() && !e.isShiftDown() &&
+        av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null)
     {
 
       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));
+      selection.setEndRes(av.alignment.getWidth() - 1);
+      for (int i = 0; i < sg.getSize(); i++)
+      {
+        selection.addSequence(sg.getSequenceAt(i), true);
+      }
 
       av.setSelectionGroup(selection);
       return;
     }
 
-    if(av.getSelectionGroup()==null || ( !e.isControlDown() && av.getSelectionGroup()!=null))
+    if (av.getSelectionGroup() == null ||
+        (!e.isControlDown() && av.getSelectionGroup() != null))
+    {
       av.setSelectionGroup(new SequenceGroup());
+    }
 
     av.getSelectionGroup().setStartRes(0);
-    av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);
+    av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
 
-    if(e.isShiftDown() && lastid!=-1)
+    if (e.isShiftDown() && lastid != -1)
+    {
       selectSeqs(lastid, seq);
+    }
     else
+    {
       selectSeq(seq);
+    }
 
     alignPanel.repaint();
   }
@@ -165,47 +229,58 @@ public class IdPanel extends Panel implements MouseListener, MouseMotionListener
   {
     lastid = seq;
     SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
-    av.getSelectionGroup().addOrRemove(pickedSeq);
+    av.getSelectionGroup().addOrRemove(pickedSeq, false);
   }
 
-  void selectSeqs(int start, int end) {
+  void selectSeqs(int start, int end)
+  {
 
     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));
+    {
+      int tmp = start;
+      start = end;
+      end = tmp;
+      lastid = end;
+    }
 
-   }
+    for (int i = start; i <= end; i++)
+    {
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false);
+    }
 
+  }
 
   public void mouseReleased(MouseEvent e)
   {
-    if(scrollThread!=null)
+    if (scrollThread != null)
+    {
       scrollThread.running = false;
+    }
+
+    if(av.getSelectionGroup()!=null)
+      av.getSelectionGroup().recalcConservation();
 
     mouseDragging = false;
-    PaintRefresher.Refresh(this);
+    PaintRefresher.Refresh(this, av.alignment);
   }
 
-  public void highlightSearchResults( java.util.Vector found )
+  public void highlightSearchResults(java.util.Vector found)
   {
-    idCanvas.setHighlighted( found );
+    idCanvas.setHighlighted(found);
 
-    if(found == null)
+    if (found == null)
+    {
       return;
+    }
 
-    int index = av.alignment.findIndex( (SequenceI)found.elementAt(0));
+    int index = av.alignment.findIndex( (SequenceI) found.elementAt(0));
 
     // do we need to scroll the panel?
-    if(av.getStartSeq()>index || av.getEndSeq()<index)
-        alignPanel.setScrollValues( av.getStartRes(), index);
+    if (av.getStartSeq() > index || av.getEndSeq() < index)
+    {
+      alignPanel.setScrollValues(av.getStartRes(), index);
+    }
   }
 
   // this class allows scrolling off the bottom of the visible alignment
@@ -230,22 +305,30 @@ public class IdPanel extends Panel implements MouseListener, MouseMotionListener
       running = true;
       while (running)
       {
-        if(alignPanel.scrollUp(up))
+        if (alignPanel.scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
           int seq = av.getStartSeq();
-          if(!up)
+          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
@@ -256,6 +339,6 @@ public class IdPanel extends Panel implements MouseListener, MouseMotionListener
         {}
       }
     }
-}
+  }
 
 }