X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=fee5dd4bcf0c1ca0d214e29fb100242d5f8eddea;hb=4f1f764c09427cd63c3e355fa729da86735a8194;hp=33463d43f1274d48daf581d6d1f591da8bb46f6f;hpb=4ebc6d5b362bc093c39312aa1a69836e3dd6ae84;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index 33463d4..fee5dd4 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -37,6 +37,7 @@ public class IdPanel
   int width;
   int lastid = -1;
   boolean mouseDragging = false;
+  java.util.Vector links = new java.util.Vector();
 
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
@@ -47,26 +48,64 @@ public class IdPanel
     add(idCanvas, BorderLayout.CENTER);
     idCanvas.addMouseListener(this);
     idCanvas.addMouseMotionListener(this);
+
+    String label, url;
+    if (av.applet != null)
+    {
+      for (int i = 1; i < 10; i++)
+      {
+        label = av.applet.getParameter("linkLabel_" + i);
+        url = av.applet.getParameter("linkURL_" + i);
+
+        if (label != null && url != null)
+        {
+          links.addElement(label + "|" + url);
+        }
+
+      }
+    }
+    if (links.size() < 1)
+    {
+      links = new java.util.Vector();
+      links.addElement("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+    }
   }
 
+  Tooltip tooltip;
   public void mouseMoved(MouseEvent e)
-  {}
-
-  public void mouseDragged(MouseEvent e)
   {
-    mouseDragging = true;
+    int seq = alignPanel.seqPanel.findSeq(e);
 
-    int y = e.getY();
-    if (av.getWrapAlignment())
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+    if (sequence.getDescription() == null)
     {
-      y -= 2 * av.charHeight;
+      if (tooltip != null)
+      {
+        tooltip.setVisible(false);
+      }
+      tooltip = null;
+      return;
     }
-    int seq = av.getIndex(y);
 
-    if (seq < 0)
+    if (tooltip == null)
     {
-      return;
+      tooltip = new Tooltip(
+          sequence.getDisplayId(true)
+          + "\n" + sequence.getDescription(), idCanvas);
+    }
+    else
+    {
+      tooltip.setTip(sequence.getDisplayId(true)
+                     + "\n" + sequence.getDescription());
     }
+  }
+
+  public void mouseDragged(MouseEvent e)
+  {
+    mouseDragging = true;
+
+    int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
 
     if (seq < lastid)
     {
@@ -78,34 +117,41 @@ public class IdPanel
     }
 
     lastid = seq;
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   public void mouseClicked(MouseEvent e)
   {
-    if (e.getClickCount() == 2)
+    if (e.getClickCount() < 2)
     {
-      int y = e.getY();
-      if (av.getWrapAlignment())
-      {
-        y -= 2 * av.charHeight;
-      }
-
-      int seq = av.getIndex(y);
-      String id = av.getAlignment().getSequenceAt(seq).getName();
+      return;
+    }
 
-      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();
-      }
+    //DEFAULT LINK IS FIRST IN THE LINK LIST
+    int seq = alignPanel.seqPanel.findSeq(e);
+    String id = av.getAlignment().getSequenceAt(seq).getName();
+    if (id.indexOf("|") > -1)
+    {
+      id = id.substring(id.lastIndexOf("|") + 1);
     }
 
+    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
+    {
+
+      alignPanel.alignFrame.showURL(url, target);
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
   }
 
   public void mouseEntered(MouseEvent e)
@@ -137,7 +183,7 @@ public class IdPanel
 
   public void mousePressed(MouseEvent e)
   {
-    if (e.getClickCount() == 2)
+    if (e.getClickCount() > 1)
     {
       return;
     }
@@ -148,47 +194,27 @@ public class IdPanel
       y -= 2 * av.charHeight;
     }
 
-    int seq = av.getIndex(y);
-    if (seq == -1)
-    {
-      return;
-    }
+    int seq = alignPanel.seqPanel.findSeq(e);
 
     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)
-    {
-
-      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), true);
-      }
-
-      av.setSelectionGroup(selection);
-      return;
-    }
-
-    if (av.getSelectionGroup() == null ||
-        (!e.isControlDown() && av.getSelectionGroup() != null))
+    if ( (av.getSelectionGroup() == null) ||
+        ( (!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
+      av.getSelectionGroup().setStartRes(0);
+      av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
     }
 
-    av.getSelectionGroup().setStartRes(0);
-    av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
-
     if (e.isShiftDown() && lastid != -1)
     {
       selectSeqs(lastid, seq);
@@ -198,7 +224,7 @@ public class IdPanel
       selectSeq(seq);
     }
 
-    alignPanel.repaint();
+    alignPanel.paintAlignment(true);
   }
 
   void selectSeq(int seq)
@@ -212,6 +238,12 @@ public class IdPanel
   {
 
     lastid = start;
+
+    if (end >= av.getAlignment().getHeight())
+    {
+      end = av.getAlignment().getHeight() - 1;
+    }
+
     if (end < start)
     {
       int tmp = start;
@@ -234,11 +266,13 @@ public class IdPanel
       scrollThread.running = false;
     }
 
-    if(av.getSelectionGroup()!=null)
+    if (av.getSelectionGroup() != null)
+    {
       av.getSelectionGroup().recalcConservation();
+    }
 
     mouseDragging = false;
-    PaintRefresher.Refresh(this);
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
   }
 
   public void highlightSearchResults(java.util.Vector found)
@@ -294,7 +328,7 @@ public class IdPanel
           {
             selectSeqs(lastid - 1, seq);
           }
-          else if (seq > lastid)
+          else if (seq > lastid && seq < av.alignment.getHeight())
           {
             selectSeqs(lastid + 1, seq);
           }
@@ -306,7 +340,7 @@ public class IdPanel
           running = false;
         }
 
-        alignPanel.repaint();
+        alignPanel.paintAlignment(true);
         try
         {
           Thread.sleep(100);