From 29f89f52f3fc99e904a55e426c53a830290408cc Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 9 Aug 2005 16:45:05 +0000
Subject: [PATCH] Applet handles multiple sequence links

---
 src/jalview/appletgui/APopupMenu.java |   37 ++++++++++++------
 src/jalview/appletgui/IdPanel.java    |   66 ++++++++++++++++++++++-----------
 src/jalview/appletgui/SeqPanel.java   |    2 +-
 3 files changed, 71 insertions(+), 34 deletions(-)

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index cf854b0..858770a 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -21,6 +21,7 @@ package jalview.appletgui;
 
 import java.awt.*;
 import java.awt.event.*;
+import java.util.Vector;
 
 import jalview.analysis.*;
 import jalview.datamodel.*;
@@ -46,9 +47,6 @@ public class APopupMenu
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
 
   AlignmentPanel ap;
-  Menu sequenceMenu = new Menu();
-  MenuItem sequenceName = new MenuItem();
-  Sequence sequence;
   MenuItem unGroupMenuItem = new MenuItem();
   MenuItem nucleotideMenuItem = new MenuItem();
   Menu colourMenu = new Menu();
@@ -56,7 +54,7 @@ public class APopupMenu
   CheckboxMenuItem showText = new CheckboxMenuItem();
   CheckboxMenuItem showColourText = new CheckboxMenuItem();
 
-  public APopupMenu(AlignmentPanel ap, Sequence seq)
+  public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links)
   {
     ///////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -66,7 +64,6 @@ public class APopupMenu
     //////////////////////////////////////////////////////////
 
     this.ap = ap;
-    sequence = seq;
 
     try
     {
@@ -90,11 +87,31 @@ public class APopupMenu
       groupMenu.remove(unGroupMenuItem);
     }
 
-    if (seq == null)
+    if (seq != null && links!=null)
     {
-      remove(sequenceMenu);
+      Menu linkMenu = new Menu("Link");
+      MenuItem item;
+      String link;
+      for(int i=0; i<links.size(); i++)
+      {
+        link = links.elementAt(i).toString();
+        final String target = link.substring(0, link.indexOf("|"));
+        item = new MenuItem(target);
+        final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
+               + seq.getName() +
+               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+
+           item.addActionListener(new java.awt.event.ActionListener()
+           {
+               public void actionPerformed(ActionEvent e)
+               {
+                  jalview.bin.JalviewLite.showURL(url, target);
+               }
+           });
+          linkMenu.add(item);
+      }
+      add(linkMenu);
     }
-
   }
 
   private void jbInit()
@@ -103,8 +120,6 @@ public class APopupMenu
     groupMenu.setLabel("Group");
     groupMenu.setLabel("Define");
 
-    sequenceMenu.setLabel("Sequence");
-    sequenceName.setLabel("Edit name");
     unGroupMenuItem.setLabel("Remove Group");
     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
     {
@@ -165,14 +180,12 @@ public class APopupMenu
     });
 
     add(groupMenu);
-    this.add(sequenceMenu);
     groupMenu.add(unGroupMenuItem);
     groupMenu.add(colourMenu);
     groupMenu.addSeparator();
     groupMenu.add(showBoxes);
     groupMenu.add(showText);
     groupMenu.add(showColourText);
-    sequenceMenu.add(sequenceName);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(BLOSUM62Colour);
diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index d548936..f3db9be 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -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)
   {
@@ -47,6 +48,22 @@ public class IdPanel
     add(idCanvas, BorderLayout.CENTER);
     idCanvas.addMouseListener(this);
     idCanvas.addMouseMotionListener(this);
+
+    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);
+
+    }
+    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)
@@ -83,29 +100,36 @@ public class IdPanel
 
   public void mouseClicked(MouseEvent e)
   {
-    if (e.getClickCount() == 2)
-    {
-      int y = e.getY();
-      if (av.getWrapAlignment())
-      {
-        y -= 2 * av.charHeight;
-      }
+    if (e.getClickCount() < 2)
+        return;
 
-      int seq = av.getIndex(y);
-      String id = av.getAlignment().getSequenceAt(seq).getName();
+    int y = e.getY();
 
-      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();
-      }
+    if (av.getWrapAlignment())
+    {
+      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)
@@ -137,7 +161,7 @@ public class IdPanel
 
   public void mousePressed(MouseEvent e)
   {
-    if (e.getClickCount() == 2)
+    if (e.getClickCount() >1 )
     {
       return;
     }
@@ -157,7 +181,7 @@ public class IdPanel
     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;
diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 665a444..080dc22 100755
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -566,7 +566,7 @@ public class SeqPanel
     else if ( (evt.getModifiers() & InputEvent.BUTTON3_MASK) ==
              InputEvent.BUTTON3_MASK)
     {
-      APopupMenu popup = new APopupMenu(ap, null);
+      APopupMenu popup = new APopupMenu(ap, null, null);
       this.add(popup);
       popup.show(this, evt.getX(), evt.getY());
     }
-- 
1.7.10.2