From 784398bbc60a0e6ae55c6cde1b4f5b1b6f4a5592 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 1 Apr 2010 16:05:03 +0000
Subject: [PATCH] reinstate submission of database Ids as well as sequence Id
 strings.

---
 src/jalview/ws/EnfinEnvision2OneWay.java |   66 +++++++++++++++++-------------
 1 file changed, 37 insertions(+), 29 deletions(-)

diff --git a/src/jalview/ws/EnfinEnvision2OneWay.java b/src/jalview/ws/EnfinEnvision2OneWay.java
index 8e596b7..8905515 100644
--- a/src/jalview/ws/EnfinEnvision2OneWay.java
+++ b/src/jalview/ws/EnfinEnvision2OneWay.java
@@ -142,6 +142,7 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSM
   private boolean running=false;
   private Vector groupURLLinks = null;
   private Vector groupURLdescr = null;
+  private static String[] allowedDb=new String[] {"UNIPROT","EMBL","PDB"} ;
   
   public EnfinEnvision2OneWay() {
     groupURLLinks = new Vector();
@@ -366,40 +367,31 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSM
         final String label = urlLink.getLabel();
         boolean usingNames = false;
         // Now see which parts of the group apply for this URL
-        String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
-        Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
+        String ltarget;
         String[] seqstr,ids; // input to makeUrl
-        if (idset!=null)
-        {
-          int numinput = ((int[])idset[0])[0];
-          String[] allids = ((String[])idset[1]);
-          seqstr = new String[numinput];
-          ids = new String[numinput];
-          for (int sq=0,idcount=0;sq<seqs.length;sq++)
+        for (int t=0;t<allowedDb.length; t++) {
+          ltarget = allowedDb[t]; // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+          Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
+          if (idset!=null)
           {
-            if (allids[sq]!=null) {
-              ids[idcount] = allids[sq];
-              seqstr[idcount++] = idandseqs[1][sq];
+            int numinput = ((int[])idset[0])[0];
+            String[] allids = ((String[])idset[1]);
+            seqstr = new String[numinput];
+            ids = new String[numinput];
+            for (int sq=0,idcount=0;sq<seqs.length;sq++)
+            {
+              if (allids[sq]!=null) {
+                ids[idcount] = allids[sq];
+                seqstr[idcount++] = idandseqs[1][sq];
+              }
             }
+            addMenu = addMenu | createAndAddLinks(linkMenus,false,urlLink,label,ltarget,descr, ids,seqstr);
           }
-        } else {
-          // just use the id/seq set
-          seqstr = idandseqs[1];
-          ids = idandseqs[0];
-          usingNames=true;
-        }
-        // and try and make the groupURL!
-        
-        Object[] urlset = urlLink.makeUrlStubs(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
-        if (urlset!=null)
-        {
-          int type = urlLink.getGroupURLType() & 3;
-          //System.out.println(urlLink.getGroupURLType() +" "+((String[])urlset[3])[0]);
-          // first two bits ofurlLink type bitfield are sequenceids and sequences
-          // TODO: FUTURE: ensure the groupURL menu structure can be generalised
-          addshowLink(linkMenus[type], label + (((type & 1)==1) ? ("("+(usingNames ? "Names" : ltarget)+")") : ""), descr, urlLink, urlset);
-          addMenu = true;
         }
+        // also do names only.
+        seqstr = idandseqs[1];
+        ids = idandseqs[0];
+        addMenu = addMenu | createAndAddLinks(linkMenus,true,urlLink,label,"Names",descr, ids,seqstr);
       }
     if (addMenu)
     {
@@ -417,6 +409,22 @@ public class EnfinEnvision2OneWay extends DefaultHandler implements Runnable,WSM
     return null;
   }
 
+  private boolean createAndAddLinks(JMenu[] linkMenus, boolean usingNames,
+          GroupUrlLink urlLink, String label, String ltarget, String descr, String[] ids,
+          String[] seqstr)
+  {
+    Object[] urlset = urlLink.makeUrlStubs(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
+    if (urlset!=null)
+    {
+      int type = urlLink.getGroupURLType() & 3;
+      //System.out.println(urlLink.getGroupURLType() +" "+((String[])urlset[3])[0]);
+      // first two bits ofurlLink type bitfield are sequenceids and sequences
+      // TODO: FUTURE: ensure the groupURL menu structure can be generalised
+      addshowLink(linkMenus[type], label + (((type & 1)==1) ? ("("+(usingNames ? "Names" : ltarget)+")") : ""), descr, urlLink, urlset);
+      return true;
+    }
+    return false;
+  }
   /// end of stuff copied from popupmenu
   public void attachWSMenuEntry(final JMenu wsmenu, final AlignFrame alignFrame)
   {
-- 
1.7.10.2