no newline after licence comment

[jalview.git] / src / jalview / gui / PopupMenu.java

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 2068b0b..056a983 100755 (executable)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -30,6 +30,7 @@ import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.schemes.*;
+import jalview.util.UrlLink;
 
 /**
  * DOCUMENT ME!
@@ -361,41 +362,67 @@ public class PopupMenu
     if (links != null && links.size() > 0)
     {
       JMenu linkMenu = new JMenu("Link");
-      JMenuItem item;
+
       for (int i = 0; i < links.size(); i++)
       {
         String link = links.elementAt(i).toString();
-        final String label = link.substring(0, link.indexOf("|"));
-        item = new JMenuItem(label);
-        final String url;
-
-        if (link.indexOf("$SEQUENCE_ID$") > -1)
+        UrlLink urlLink = null;
+        try {
+          urlLink = new UrlLink(link);
+        } catch (Exception foo) {
+          jalview.bin.Cache.log.error("Exception for URLLink '"+link+"'",foo);
+          continue;
+        };
+        if (!urlLink.isValid())
         {
-          String id = seq.getName();
-          if (id.indexOf("|") > -1)
-          {
-            id = id.substring(id.lastIndexOf("|") + 1);
-          }
-
-          url = link.substring(link.indexOf("|") + 1,
-                               link.indexOf("$SEQUENCE_ID$"))
-              + id +
-              link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
+          jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+          continue;
         }
-        else
+        final String label = urlLink.getLabel();
+        if (urlLink.isDynamic())
         {
-          url = link.substring(link.lastIndexOf("|") + 1);
-        }
 
-        item.addActionListener(new java.awt.event.ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
+          // collect matching db-refs
+          DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{urlLink.getTarget()});
+          // collect id string too
+          String id = seq.getName();
+          if (dbr!=null)
           {
-            showLink(url);
+            for (int r=0;r<dbr.length; r++)
+            {
+              if (id!=null && dbr[r].getAccessionId().equals(id))
+              {
+                // suppress duplicate link creation for the bare sequence ID string with this link
+                id = null;
+              }
+              // create Bare ID link for this RUL
+              String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
+              if (urls!=null)
+              {
+                for (int u=0; u<urls.length; u+=2)
+                {
+                  addshowLink(linkMenu, label+"|"+urls[u],urls[u+1]); 
+                }
+              }
+            }
           }
-        });
-
-        linkMenu.add(item);
+          if (id!=null)
+          {
+            // create Bare ID link for this RUL
+            String[] urls = urlLink.makeUrls(id, true);
+            if (urls!=null)
+            {
+              for (int u=0; u<urls.length; u+=2)
+              {
+                addshowLink(linkMenu, label,  urls[u+1]);
+              }
+            }
+          }
+        } else
+        {
+          // Add a non-dynamic link
+          addshowLink(linkMenu, label, urlLink.getUrl_prefix());
+        }
       }
       if (sequence != null)
       {
@@ -409,6 +436,34 @@ public class PopupMenu
   }
 
   /**
+   * add a show URL menu item to the given linkMenu
+   * @param linkMenu
+   * @param label - menu label string
+   * @param url - url to open
+   */
+  private void addshowLink(JMenu linkMenu, String label, final String url)
+  {
+    JMenuItem item = new JMenuItem(label);
+    item.setToolTipText("open URL: "+url);
+    item.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        new Thread(new Runnable() {
+
+          public void run()
+          {
+            showLink(url);
+          }
+          
+        }).start();
+      }
+    });
+
+    linkMenu.add(item);    
+  }
+
+  /**
    * DOCUMENT ME!
    *
    * @throws Exception DOCUMENT ME!
@@ -1302,16 +1357,22 @@ public class PopupMenu
 
     String[] omitHidden = null;
 
-    if (ap.av.hasHiddenColumns)
-    {
-      System.out.println("PROMPT USER HERE");
-      omitHidden = ap.av.getViewAsString(true);
+    System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens or we simply trust the user wants wysiwig behaviour
+    SequenceGroup sg = ap.av.getSelectionGroup();
+    ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
+    omitHidden = ap.av.getViewAsString(true);
+    Alignment oal = new Alignment(ap.av.getSequenceSelection());
+    AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
+    for (int i=0; i<nala.length; i++)
+    {
+      AlignmentAnnotation na =nala[i];
+      oal.addAnnotation(na);
     }
-
     cap.setText(new FormatAdapter().formatSequences(
-        e.getActionCommand(),
-        ap.av.getSelectionAsNewSequence(),
-        omitHidden));
+            e.getActionCommand(),
+            oal,
+            omitHidden, csel, sg));
+    oal=null;
   }
 
   public void pdbFromFile_actionPerformed()
@@ -1382,13 +1443,21 @@ public class PopupMenu
 
   public void discoverPDB_actionPerformed()
   {
-    SequenceI[] sequences =
-         ap.av.selectionGroup == null ?
-           new Sequence[]{sequence}
-         : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
-
-    new jalview.ws.DBRefFetcher(sequences,
-        ap.alignFrame).fetchDBRefs(false);
+    
+    final SequenceI[] sequences = 
+      ((ap.av.selectionGroup == null) 
+              ?  new Sequence[]{sequence}
+      : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
+    Thread discpdb = new Thread(new Runnable() {
+      public void run()
+      {
+        
+        new jalview.ws.DBRefFetcher(sequences,
+                ap.alignFrame).fetchDBRefs(false);
+      }
+      
+    });
+    discpdb.start();
   }
 
   public void sequenceFeature_actionPerformed()