X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fserver%2FTcoffeeWS.java;h=72291dc0e04f298ba9f0acb19e04a22d9bd4c79b;hb=1059f954bc521e5ee59ec084ed066268a802ceaf;hp=086d870bf9594a18c931aa194f96bb36ed0cfd85;hpb=73ea919f7892867d1a841d91dd8e2166679fe720;p=jabaws.git

diff --git a/webservices/compbio/ws/server/TcoffeeWS.java b/webservices/compbio/ws/server/TcoffeeWS.java
index 086d870..72291dc 100644
--- a/webservices/compbio/ws/server/TcoffeeWS.java
+++ b/webservices/compbio/ws/server/TcoffeeWS.java
@@ -29,6 +29,7 @@ import compbio.data.msa.JABAService;
 import compbio.data.msa.MsaWS;
 import compbio.data.sequence.Alignment;
 import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.Program;
 import compbio.engine.AsyncExecutor;
 import compbio.engine.Configurator;
 import compbio.engine.client.ConfiguredExecutable;
@@ -53,14 +54,11 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 
 	private static Logger log = Logger.getLogger(TcoffeeWS.class);
 
-	private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util
-			.getSupportedOptions(Tcoffee.class);
+	private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util.getSupportedOptions(Tcoffee.class);
 
-	private static final PresetManager<Tcoffee> tcoffeePresets = Util
-			.getPresets(Tcoffee.class);
+	private static final PresetManager<Tcoffee> tcoffeePresets = Util.getPresets(Tcoffee.class);
 
-	private static final LimitsManager<Tcoffee> limitMan = compbio.engine.client.Util
-			.getLimits(new Tcoffee().getType());
+	private static final LimitsManager<Tcoffee> limitMan = compbio.engine.client.Util.getLimits(new Tcoffee().getType());
 
 	@Override
 	public String align(List<FastaSequence> sequences)
@@ -96,12 +94,10 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 
 		WSUtil.validateFastaInput(sequences);
 		ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);
-		List<String> params = WSUtil.getCommands(options,
-				Tcoffee.KEY_VALUE_SEPARATOR);
+		List<String> params = WSUtil.getCommands(options, Tcoffee.KEY_VALUE_SEPARATOR);
 		log.info("Setting parameters:" + params);
 		confTcoffee.addParameters(params);
-		return WSUtil.align(sequences, confTcoffee, log, "customAlign",
-				getLimit(""));
+		return WSUtil.align(sequences, confTcoffee, log, "customAlign", getLimit(""));
 	}
 
 	@Override
@@ -126,8 +122,7 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 		ConfiguredExecutable<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine
 				.getResults(jobId);
 		Alignment al = tcoffee.getResults();
-		// log(jobId, "getResults");
-		return al;
+		return new Alignment (al.getSequences(), Program.Tcoffee, '-');
 	}
 
 	@Override