2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 // run an alignment on the current alignFrame
22 import jalview.ws.jws2.*;
23 import jalview.ws.jws2.jabaws2.Jws2Instance;
24 import jalview.datamodel.*;
26 // First get the JABA service discoverer and see if there are any services.
27 jalview.ws.jws2.Jws2Discoverer disc = jalview.ws.jws2.Jws2Discoverer.getDiscoverer();
28 while (disc.isRunning()) {
31 if (!disc.isRunning() && !disc.hasServices())
33 // discoverer is not running, and has no services - so run it again.
37 for (jalview.ws.jws2.jabaws2.Jws2Instance service: disc.getServices()) {
39 if (service.serviceType.indexOf("uscle")>-1) {
40 // now - go through the services if any, and find a Muscle service
43 msaf = currentAlFrame;
45 // currentAlFrame is not defined - so we were run as an interactive script from the Groovy console
46 // in that case, just pick the first alignmentFrame in the stack.
47 msaf = Jalview.getAlignFrames()[0]
49 // Finally start Jalview's JabaWS MSA Client with the alignment from msaf
50 new MsaWSClient(service, msaf.getTitle(), msaf.gatherSequencesForAlignment(), false,
51 true, msaf.getViewport().getAlignment()