Applet handles multiple sequence links

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index cf854b0..858770a 100755 (executable)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -21,6 +21,7 @@ package jalview.appletgui;
 \r
 import java.awt.*;\r
 import java.awt.event.*;\r
+import java.util.Vector;\r
 \r
 import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
@@ -46,9 +47,6 @@ public class APopupMenu
   protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
 \r
   AlignmentPanel ap;\r
-  Menu sequenceMenu = new Menu();\r
-  MenuItem sequenceName = new MenuItem();\r
-  Sequence sequence;\r
   MenuItem unGroupMenuItem = new MenuItem();\r
   MenuItem nucleotideMenuItem = new MenuItem();\r
   Menu colourMenu = new Menu();\r
@@ -56,7 +54,7 @@ public class APopupMenu
   CheckboxMenuItem showText = new CheckboxMenuItem();\r
   CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
 \r
-  public APopupMenu(AlignmentPanel ap, Sequence seq)\r
+  public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links)\r
   {\r
     ///////////////////////////////////////////////////////////\r
     // If this is activated from the sequence panel, the user may want to\r
@@ -66,7 +64,6 @@ public class APopupMenu
     //////////////////////////////////////////////////////////\r
 \r
     this.ap = ap;\r
-    sequence = seq;\r
 \r
     try\r
     {\r
@@ -90,11 +87,31 @@ public class APopupMenu
       groupMenu.remove(unGroupMenuItem);\r
     }\r
 \r
-    if (seq == null)\r
+    if (seq != null && links!=null)\r
     {\r
-      remove(sequenceMenu);\r
+      Menu linkMenu = new Menu("Link");\r
+      MenuItem item;\r
+      String link;\r
+      for(int i=0; i<links.size(); i++)\r
+      {\r
+        link = links.elementAt(i).toString();\r
+        final String target = link.substring(0, link.indexOf("|"));\r
+        item = new MenuItem(target);\r
+        final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
+               + seq.getName() +\r
+               link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+\r
+           item.addActionListener(new java.awt.event.ActionListener()\r
+           {\r
+               public void actionPerformed(ActionEvent e)\r
+               {\r
+                  jalview.bin.JalviewLite.showURL(url, target);\r
+               }\r
+           });\r
+          linkMenu.add(item);\r
+      }\r
+      add(linkMenu);\r
     }\r
-\r
   }\r
 \r
   private void jbInit()\r
@@ -103,8 +120,6 @@ public class APopupMenu
     groupMenu.setLabel("Group");\r
     groupMenu.setLabel("Define");\r
 \r
-    sequenceMenu.setLabel("Sequence");\r
-    sequenceName.setLabel("Edit name");\r
     unGroupMenuItem.setLabel("Remove Group");\r
     unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
     {\r
@@ -165,14 +180,12 @@ public class APopupMenu
     });\r
 \r
     add(groupMenu);\r
-    this.add(sequenceMenu);\r
     groupMenu.add(unGroupMenuItem);\r
     groupMenu.add(colourMenu);\r
     groupMenu.addSeparator();\r
     groupMenu.add(showBoxes);\r
     groupMenu.add(showText);\r
     groupMenu.add(showColourText);\r
-    sequenceMenu.add(sequenceName);\r
     colourMenu.add(noColourmenuItem);\r
     colourMenu.add(clustalColour);\r
     colourMenu.add(BLOSUM62Colour);\r

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index d548936..f3db9be 100755 (executable)
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -37,6 +37,7 @@ public class IdPanel
   int width;\r
   int lastid = -1;\r
   boolean mouseDragging = false;\r
+  java.util.Vector links = new java.util.Vector();\r
 \r
   public IdPanel(AlignViewport av, AlignmentPanel parent)\r
   {\r
@@ -47,6 +48,22 @@ public class IdPanel
     add(idCanvas, BorderLayout.CENTER);\r
     idCanvas.addMouseListener(this);\r
     idCanvas.addMouseMotionListener(this);\r
+\r
+    String label, url;\r
+    for(int i=1; i<10; i++)\r
+    {\r
+      label = parent.alignFrame.applet.getParameter("linkLabel_"+i);\r
+      url = parent.alignFrame.applet.getParameter("linkURL_"+i);\r
+\r
+      if(label!=null && url!=null)\r
+        links.addElement(label+"|"+url);\r
+\r
+    }\r
+    if (links.size() < 1)\r
+    {\r
+      links = new java.util.Vector();\r
+      links.addElement("SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");\r
+    }\r
   }\r
 \r
   public void mouseMoved(MouseEvent e)\r
@@ -83,29 +100,36 @@ public class IdPanel
 \r
   public void mouseClicked(MouseEvent e)\r
   {\r
-    if (e.getClickCount() == 2)\r
-    {\r
-      int y = e.getY();\r
-      if (av.getWrapAlignment())\r
-      {\r
-        y -= 2 * av.charHeight;\r
-      }\r
+    if (e.getClickCount() < 2)\r
+        return;\r
 \r
-      int seq = av.getIndex(y);\r
-      String id = av.getAlignment().getSequenceAt(seq).getName();\r
+    int y = e.getY();\r
 \r
-      try\r
-      {\r
-        jalview.bin.JalviewLite.showURL(\r
-            "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +\r
-            "]+-vn+2");\r
-      }\r
-      catch (Exception ex)\r
-      {\r
-        ex.printStackTrace();\r
-      }\r
+    if (av.getWrapAlignment())\r
+    {\r
+      y -= (2 * av.charHeight);\r
     }\r
 \r
+    //DEFAULT LINK IS FIRST IN THE LINK LIST\r
+    int seq = av.getIndex(y);\r
+    String id = av.getAlignment().getSequenceAt(seq).getName();\r
+\r
+    String target = links.elementAt(0).toString();\r
+    target = target.substring(0, target.indexOf("|"));\r
+    String url = links.elementAt(0).toString();\r
+    url = url.substring(url.indexOf("|")+1);\r
+\r
+    int index = url.indexOf("$SEQUENCE_ID$");\r
+    url = url.substring(0, index)+ id + url.substring(index+13);\r
+\r
+    try\r
+    {\r
+      jalview.bin.JalviewLite.showURL(url, target);\r
+    }\r
+    catch (Exception ex)\r
+    {\r
+      ex.printStackTrace();\r
+    }\r
   }\r
 \r
   public void mouseEntered(MouseEvent e)\r
@@ -137,7 +161,7 @@ public class IdPanel
 \r
   public void mousePressed(MouseEvent e)\r
   {\r
-    if (e.getClickCount() == 2)\r
+    if (e.getClickCount() >1 )\r
     {\r
       return;\r
     }\r
@@ -157,7 +181,7 @@ public class IdPanel
     if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==\r
         InputEvent.BUTTON3_MASK)\r
     {\r
-      APopupMenu popup = new APopupMenu(alignPanel, null);\r
+      APopupMenu popup = new APopupMenu(alignPanel, (Sequence) av.getAlignment().getSequenceAt(seq), links);\r
       this.add(popup);\r
       popup.show(this, e.getX(), e.getY());\r
       return;\r

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index 665a444..080dc22 100755 (executable)
--- 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) ==\r
              InputEvent.BUTTON3_MASK)\r
     {\r
-      APopupMenu popup = new APopupMenu(ap, null);\r
+      APopupMenu popup = new APopupMenu(ap, null, null);\r
       this.add(popup);\r
       popup.show(this, evt.getX(), evt.getY());\r
     }\r