* \r
* This library is free software; you can redistribute it and/or modify it under the terms of the\r
* Apache License version 2 as published by the Apache Software Foundation\r
* \r
* This library is free software; you can redistribute it and/or modify it under the terms of the\r
* Apache License version 2 as published by the Apache Software Foundation\r
import compbio.data.msa.MsaWS;\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
import compbio.data.msa.MsaWS;\r
import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.client.ConfiguredExecutable;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.client.ConfiguredExecutable;\r
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "TcoffeeWS")\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "TcoffeeWS")\r
\r
@Override\r
public String align(List<FastaSequence> sequences)\r
throws JobSubmissionException {\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\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
throws JobSubmissionException {\r
Tcoffee tcoffee = new Tcoffee();\r
}\r
\r
ConfiguredExecutable<Tcoffee> init(List<FastaSequence> sequences)\r
throws JobSubmissionException {\r
Tcoffee tcoffee = new Tcoffee();\r
ConfiguredExecutable<Tcoffee> confCoffee = Configurator\r
.configureExecutable(tcoffee, sequences);\r
if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {\r
ConfiguredExecutable<Tcoffee> confCoffee = Configurator\r
.configureExecutable(tcoffee, sequences);\r
if (confCoffee.getExecProvider() == Executable.ExecProvider.Cluster) {\r
\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
- return WSUtil.align(sequences, confTcoffee, null, "customAlign",\r
- getLimit(""));\r
+ return WSUtil.align(sequences, confTcoffee, log, "customAlign", getLimit(""));\r
ConfiguredExecutable<Tcoffee> confTcoffee = init(sequences);\r
confTcoffee.addParameters(preset.getOptions());\r
Limit<Tcoffee> limit = getLimit(preset.getName());\r
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
ConfiguredExecutable<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine\r
.getResults(jobId);\r
Alignment al = tcoffee.getResults();\r
ConfiguredExecutable<Tcoffee> tcoffee = (ConfiguredExecutable<Tcoffee>) asyncEngine\r
.getResults(jobId);\r
Alignment al = tcoffee.getResults();\r