X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=examples%2Fgroovy%2FalignLoadedFile.groovy;h=df68e2b772e23a9b0bfa277c146eb1188dc138d5;hb=741d85487592809427ffd6d58b0d02efb8338c61;hp=6d8f8070f1e5cc71dac8ae6975c62315b94734b0;hpb=b340cf1b50a8d941f78e7031ea5f453550e95f36;p=jalview.git

diff --git a/examples/groovy/alignLoadedFile.groovy b/examples/groovy/alignLoadedFile.groovy
index 6d8f807..df68e2b 100644
--- a/examples/groovy/alignLoadedFile.groovy
+++ b/examples/groovy/alignLoadedFile.groovy
@@ -1,5 +1,26 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 // run an alignment on the current alignFrame
 import jalview.ws.jws2.*;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
 import jalview.datamodel.*;
 
 // First get the JABA service discoverer and see if there are any services.
@@ -13,7 +34,7 @@ if (!disc.isRunning() && !disc.hasServices())
   disc.run();
 }
 
-for (jalview.ws.jws2.Jws2Discoverer.Jws2Instance service: disc.getServices()) {
+for (jalview.ws.jws2.jabaws2.Jws2Instance service: disc.getServices()) {
 
 if (service.serviceType.indexOf("uscle")>-1) {
   // now - go through the services if any, and find a Muscle service
@@ -23,7 +44,7 @@ if (service.serviceType.indexOf("uscle")>-1) {
   } catch (q) {
         // currentAlFrame is not defined - so we were run as an interactive script from the Groovy console
 	// in that case, just pick the first alignmentFrame in the stack.
-	msaf = Jalview.getAlignframes()[0]
+	msaf = Jalview.getAlignFrames()[0]
   };
   // Finally start Jalview's JabaWS MSA Client with the alignment from msaf
   new MsaWSClient(service, msaf.getTitle(), msaf.gatherSequencesForAlignment(), false,