From b340cf1b50a8d941f78e7031ea5f453550e95f36 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 5 Aug 2011 16:52:30 +0100
Subject: [PATCH] example script that will submit a muscle jabaws job using
 the currently loaded alignment (JAL-894)

---
 examples/groovy/alignLoadedFile.groovy |   34 ++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)
 create mode 100644 examples/groovy/alignLoadedFile.groovy

diff --git a/examples/groovy/alignLoadedFile.groovy b/examples/groovy/alignLoadedFile.groovy
new file mode 100644
index 0000000..6d8f807
--- /dev/null
+++ b/examples/groovy/alignLoadedFile.groovy
@@ -0,0 +1,34 @@
+// run an alignment on the current alignFrame
+import jalview.ws.jws2.*;
+import jalview.datamodel.*;
+
+// First get the JABA service discoverer and see if there are any services.
+jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer.getDiscoverer();
+while (disc.isRunning()) {
+Thread.sleep(50);
+}
+if (!disc.isRunning() && !disc.hasServices())
+{
+  // discoverer is not running, and has no services - so run it again.
+  disc.run();
+}
+
+for (jalview.ws.jws2.Jws2Discoverer.Jws2Instance service: disc.getServices()) {
+
+if (service.serviceType.indexOf("uscle")>-1) {
+  // now - go through the services if any, and find a Muscle service
+  def msaf;
+  try {
+	msaf = currentAlFrame;
+  } 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]
+  };
+  // Finally start Jalview's JabaWS MSA Client with the alignment from msaf
+  new MsaWSClient(service, msaf.getTitle(), msaf.gatherSequencesForAlignment(), false,
+                true, msaf.getViewport().getAlignment()
+                .getDataset(), msaf);
+  break;
+}
+}
-- 
1.7.10.2