JWS-113 Commented Jpred entries in the datamodel, runner and webservices java source...

[jabaws.git] / webservices / compbio / ws / server / TcoffeeWS.java

diff --git a/webservices/compbio/ws/server/TcoffeeWS.java b/webservices/compbio/ws/server/TcoffeeWS.java
index e9bda4d..ee1c1c6 100644 (file)
--- a/webservices/compbio/ws/server/TcoffeeWS.java
+++ b/webservices/compbio/ws/server/TcoffeeWS.java
@@ -29,11 +29,13 @@ import compbio.data.msa.JABAService;
 import compbio.data.msa.MsaWS;\r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Program;\r
 import compbio.engine.AsyncExecutor;\r
 import compbio.engine.Configurator;\r
 import compbio.engine.client.ConfiguredExecutable;\r
 import compbio.engine.client.Executable;\r
 import compbio.engine.client.SkeletalExecutable;\r
+import compbio.engine.client.EngineUtil;\r
 import compbio.metadata.ChunkHolder;\r
 import compbio.metadata.JobStatus;\r
 import compbio.metadata.JobSubmissionException;\r
@@ -45,30 +47,23 @@ import compbio.metadata.PresetManager;
 import compbio.metadata.ResultNotAvailableException;\r
 import compbio.metadata.RunnerConfig;\r
 import compbio.metadata.WrongParameterException;\r
-import compbio.runner.Util;\r
+import compbio.runner.RunnerUtil;\r
 import compbio.runner.msa.Tcoffee;\r
 \r
 @WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "TcoffeeWS")\r
 public class TcoffeeWS implements MsaWS<Tcoffee> {\r
 \r
        private static Logger log = Logger.getLogger(TcoffeeWS.class);\r
-\r
-       private static final RunnerConfig<Tcoffee> tcoffeeOptions = Util\r
-                       .getSupportedOptions(Tcoffee.class);\r
-\r
-       private static final PresetManager<Tcoffee> tcoffeePresets = Util\r
-                       .getPresets(Tcoffee.class);\r
-\r
-       private static final LimitsManager<Tcoffee> limitMan = compbio.engine.client.Util\r
-                       .getLimits(new Tcoffee().getType());\r
+       private static final RunnerConfig<Tcoffee> tcoffeeOptions = RunnerUtil.getSupportedOptions(Tcoffee.class);\r
+       private static final PresetManager<Tcoffee> tcoffeePresets = RunnerUtil.getPresets(Tcoffee.class);\r
+       private static final LimitsManager<Tcoffee> limitMan = EngineUtil.getLimits(new Tcoffee().getType());\r
 \r
        @Override\r
        public String align(List<FastaSequence> sequences)\r
                        throws JobSubmissionException {\r
                WSUtil.validateFastaInput(sequences);\r
                ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
-               return WSUtil\r
-                               .align(sequences, confTcoffee, null, "align", getLimit(""));\r
+               return WSUtil.align(sequences, confTcoffee, log, "align", getLimit(""));\r
        }\r
 \r
        ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)\r
@@ -97,12 +92,10 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
 \r
                WSUtil.validateFastaInput(sequences);\r
                ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
-               List<String> params = WSUtil.getCommands(options,\r
-                               Tcoffee.KEY_VALUE_SEPARATOR);\r
+               List<String> params = WSUtil.getCommands(options, Tcoffee.KEY_VALUE_SEPARATOR);\r
                log.info("Setting parameters:" + params);\r
                confTcoffee.addParameters(params);\r
-               return WSUtil.align(sequences, confTcoffee, null, "customAlign",\r
-                               getLimit(""));\r
+               return WSUtil.align(sequences, confTcoffee, log, "customAlign", getLimit(""));\r
        }\r
 \r
        @Override\r
@@ -116,7 +109,7 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
                ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
                confTcoffee.addParameters(preset.getOptions());\r
                Limit<Tcoffee> limit = getLimit(preset.getName());\r
-               return WSUtil.align(sequences, confTcoffee, null, "presetAlign", limit);\r
+               return WSUtil.align(sequences, confTcoffee, log, "presetAlign", limit);\r
        }\r
 \r
        @SuppressWarnings("unchecked")\r
@@ -127,8 +120,7 @@ public class TcoffeeWS implements MsaWS<Tcoffee> {
                ConfiguredExecutable<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine\r
                                .getResults(jobId);\r
                Alignment al = tcoffee.getResults();\r
-               // log(jobId, "getResults");\r
-               return al;\r
+               return new Alignment (al.getSequences(), Program.Tcoffee, '-');\r
        }\r
 \r
        @Override\r