<classpathentry kind="lib" path="testsrc/lib/testng-5.10-jdk15.jar"/>\r
<classpathentry kind="lib" path="lib/servlet-api.jar"/>\r
<classpathentry kind="lib" path="WEB-INF/lib/drmaa.jar"/>\r
- <classpathentry kind="lib" path="WEB-INF/lib/compbio-util-1.3.jar"/>\r
<classpathentry kind="lib" path="WEB-INF/lib/compbio-annotations-1.0.jar"/>\r
+ <classpathentry kind="lib" path="WEB-INF/lib/compbio-util-1.3.jar"/>\r
<classpathentry kind="lib" path="binaries/aaconservation.jar"/>\r
<classpathentry kind="output" path="WEB-INF/classes"/>\r
</classpath>\r
/homes/ws-dev1/servers/Test/webapps/JalviewWS/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise\r
/homes/ws-dev1/servers/Test/webapps/TestJWS/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise\r
/homes/ws-dev1/servers/Test/webapps/JalviewWS-back/WEB-INF/classes/vamsas/pl/bin/jpred3_submit_concise\r
+\r
+\r
+JAXB - cannot serialize Maps and instance variables in Enums!\r
+Best replacement for Maps is a custom object for key->value pair and a HashSet for storing the pairs.\r
+JaxB cannot serialize instances of generic classes(?) \r
\ No newline at end of file
TODO: \r
\r
-Publish jabaws-discuss contact information\r
+Replace conservation.Method with server.ws.Method \r
+and try building WS. If this does not work - get rid of Method\r
\r
Output file parsing for stat reporting\r
cluster engine stat of www-jws2 user\r
--- /dev/null
+package compbio.data.sequence;\r
+\r
+import java.util.Arrays;\r
+import java.util.List;\r
+\r
+import javax.xml.bind.annotation.XmlAccessType;\r
+import javax.xml.bind.annotation.XmlAccessorType;\r
+\r
+import compbio.conservation.Method;\r
+import compbio.util.annotation.Immutable;\r
+\r
+@XmlAccessorType(XmlAccessType.FIELD)\r
+@Immutable\r
+public class Score {\r
+\r
+ private Method method;\r
+\r
+ private List<Float> scores;\r
+\r
+ private Score() {\r
+ // JaXB default constructor\r
+ }\r
+\r
+ public Score(Method method, List<Float> scores) {\r
+ this.method = method;\r
+ this.scores = scores;\r
+ }\r
+\r
+ public Method getMethod() {\r
+ return method;\r
+ }\r
+\r
+ public List<Float> getScores() {\r
+ return scores;\r
+ }\r
+\r
+ @Override\r
+ public String toString() {\r
+ return "Score [method=" + method + ", scores=" + scores + "]";\r
+ }\r
+\r
+ @Override\r
+ public int hashCode() {\r
+ final int prime = 31;\r
+ int result = 1;\r
+ result = prime * result + ((method == null) ? 0 : method.hashCode());\r
+ result = prime * result + ((scores == null) ? 0 : scores.hashCode());\r
+ return result;\r
+ }\r
+\r
+ /*\r
+ * TODO test ! (non-Javadoc)\r
+ * \r
+ * @see java.lang.Object#equals(java.lang.Object)\r
+ */\r
+ @Override\r
+ public boolean equals(Object obj) {\r
+ if (this == obj)\r
+ return true;\r
+ if (obj == null)\r
+ return false;\r
+ if (getClass() != obj.getClass())\r
+ return false;\r
+ Score other = (Score) obj;\r
+ if (method != other.method)\r
+ return false;\r
+ if (scores == other.scores) {\r
+ return true;\r
+ }\r
+ if (scores == null) {\r
+ return false;\r
+ }\r
+ if (!Arrays.deepEquals(scores.toArray(), other.scores.toArray()))\r
+ return false;\r
+ return true;\r
+ }\r
+}\r
import java.io.OutputStream;\r
import java.io.OutputStreamWriter;\r
import java.util.ArrayList;\r
+import java.util.HashSet;\r
import java.util.List;\r
import java.util.Scanner;\r
import java.util.logging.Level;\r
* \r
* @param results\r
* output file of AAConservation\r
- * @return {@link MultiAnnotatedSequence}\r
+ * @return Map with keys {@link Method} -> float[]\r
*/\r
- public static MultiAnnotatedSequence<Method> readResults(InputStream results) {\r
+ public static HashSet<Score> readAAConResults(InputStream results) {\r
if (results == null) {\r
throw new NullPointerException(\r
"InputStream with results must be provided");\r
}\r
- MultiAnnotatedSequence<Method> annotations = new MultiAnnotatedSequence<Method>(\r
- Method.class);\r
+ HashSet<Score> annotations = new HashSet<Score>();\r
Scanner sc = new Scanner(results);\r
sc.useDelimiter("#");\r
while (sc.hasNext()) {\r
Double value = valuesScanner.nextDouble();\r
values.add(value.floatValue());\r
}\r
- annotations.addAnnotation(method, values);\r
+ annotations.add(new Score(method, values));\r
}\r
return annotations;\r
}\r
import java.io.IOException;\r
import java.io.InputStream;\r
import java.util.Arrays;\r
-import java.util.HashMap;\r
+import java.util.HashSet;\r
import java.util.List;\r
\r
import org.apache.log4j.Logger;\r
\r
-import compbio.conservation.Method;\r
+import compbio.data.sequence.Score;\r
+import compbio.data.sequence.SequenceUtil;\r
import compbio.engine.client.CommandBuilder;\r
import compbio.engine.client.Executable;\r
import compbio.engine.client.SkeletalExecutable;\r
}\r
// HashMap<Method, float[]>\r
@Override\r
- public HashMap<Method, float[]> getResults(String workDirectory)\r
+ public HashSet<Score> getResults(String workDirectory)\r
throws ResultNotAvailableException {\r
- // MultiAnnotatedSequence<Method> annotations = null;\r
+ HashSet<Score> annotations = null;\r
try {\r
InputStream inStream = new FileInputStream(new File(workDirectory,\r
getOutput()));\r
- // annotations = SequenceUtil.readResults(inStream);\r
+ annotations = SequenceUtil.readAAConResults(inStream);\r
inStream.close();\r
} catch (FileNotFoundException e) {\r
log.error(e.getMessage(), e.getCause());\r
log.error(e.getMessage(), e.getCause());\r
throw new ResultNotAvailableException(e);\r
}\r
- return null;\r
+ return annotations;\r
}\r
\r
private static String getLibPath() {\r
import java.io.FileOutputStream;\r
import java.io.IOException;\r
import java.io.InputStream;\r
+import java.util.HashSet;\r
import java.util.List;\r
\r
import org.testng.annotations.Test;\r
assertNotNull(aseqs);\r
\r
/*\r
- * MultiAnnotatedSequence ma = new MultiAnnotatedSequence();\r
* Map<Trial, List<Number>> val = ma.getInstance(Trial.class);\r
* List<Number> list = new ArrayList<Number>(); list.add(new\r
* Float(1.2)); list.add(new Double(5.662)); val.put(Trial.one,\r
}\r
\r
@Test\r
- public void testReadResults() throws FileNotFoundException {\r
- InputStream inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
- + "aacon_results.txt");\r
-// /System.out.println(SequenceUtil.readResults(inStream));\r
+ public void testReadAAConResults() {\r
+ try {\r
+ InputStream inStream = new FileInputStream(\r
+ AllTestSuit.TEST_DATA_PATH + "aacon_results.txt");\r
+ HashSet<Score> result = SequenceUtil.readAAConResults(inStream);\r
+ inStream.close();\r
+ assertNotNull(result);\r
+ assertEquals(result.size(), 18);\r
+\r
+ inStream = new FileInputStream(AllTestSuit.TEST_DATA_PATH\r
+ + "aacon_result_single.out");\r
+ result = SequenceUtil.readAAConResults(inStream);\r
+ inStream.close();\r
+ assertNotNull(result);\r
+ assertEquals(result.size(), 1);\r
+ assertEquals(result.iterator().next().getScores().size(), 568);\r
+ } catch (IOException e) {\r
+ e.printStackTrace();\r
+ fail(e.getMessage());\r
+ }\r
}\r
}\r
package compbio.ws.client;\r
\r
+import static org.testng.Assert.assertEquals;\r
import static org.testng.Assert.assertNotNull;\r
import static org.testng.Assert.fail;\r
\r
import java.io.FileNotFoundException;\r
import java.io.IOException;\r
import java.net.URL;\r
+import java.util.HashSet;\r
import java.util.List;\r
\r
import javax.xml.namespace.QName;\r
\r
import org.testng.annotations.Test;\r
\r
-import compbio.data.msa.MsaWS;\r
-import compbio.data.sequence.Alignment;\r
+import compbio.conservation.Method;\r
+import compbio.data.msa.Annotation;\r
import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Score;\r
import compbio.data.sequence.SequenceUtil;\r
import compbio.metadata.JobSubmissionException;\r
import compbio.metadata.LimitExceededException;\r
import compbio.metadata.ResultNotAvailableException;\r
import compbio.metadata.UnsupportedRuntimeException;\r
import compbio.util.SysPrefs;\r
-import compbio.ws.server.ClustalWS;\r
+import compbio.ws.server.AAConWS;\r
\r
public class TestWSClient {\r
\r
@Test\r
public void test() throws FileNotFoundException, IOException {\r
\r
- URL url = new URL("http://localhost:8080/jaba/ClustalWS?wsdl");\r
- String namespace = "http://msa.data.compbio/01/01/2010/";\r
- QName qname = new QName(namespace, "ClustalWS");\r
+ URL url = new URL("http://localhost:8080/jabaws/AAConWS?wsdl");\r
+ String namespace = "http://msa.data.compbio/01/12/2010/";\r
+ QName qname = new QName(namespace, "AAConWS");\r
Service serv = Service.create(url, qname);\r
/*\r
* MsaWS msaws = serv.getPort(new QName(\r
// Annotation<AACon> msaws = serv.getPort(new QName(namespace,\r
// "ClustalWSPort"), Annotation.class);\r
\r
- MsaWS<ClustalWS> msaws = serv.getPort(new QName(namespace,\r
- "ClustalWSPort"), MsaWS.class);\r
+ Annotation<AAConWS> msaws = serv.getPort(new QName(namespace,\r
+ "AAConWSPort"), Annotation.class);\r
\r
// List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
// AAConTester.test_alignment_input));\r
\r
List<FastaSequence> fsl = SequenceUtil.readFasta(new FileInputStream(\r
CURRENT_DIRECTORY + "testsrc" + File.separator + "testdata"\r
- + File.separator + "testlimit.in"));\r
+ + File.separator + "TO1381.fasta.aln"));\r
\r
try {\r
- String jobId = msaws.align(fsl);\r
- Alignment result = msaws.getResult(jobId);\r
+ System.out.println("Pres: "\r
+ + msaws.getPresets().getPresets().get(0));\r
+ String jobId = msaws.analize(fsl);\r
+ System.out.println("J: " + jobId);\r
+ HashSet<Score> result = msaws.getConservation(jobId);\r
assertNotNull(result);\r
- System.out.println(result);\r
+ assertEquals(result.size(), 1);\r
+ assertEquals(result.iterator().next().getMethod(), Method.SHENKIN);\r
+ List<Float> scores = result.iterator().next().getScores();\r
+ assertNotNull(scores);\r
+ assertEquals(scores.size(), 568);\r
+\r
} catch (UnsupportedRuntimeException e) {\r
e.printStackTrace();\r
fail(e.getMessage());\r
e.printStackTrace();\r
fail(e.getMessage());\r
}\r
- System.out.println("Pres: " + msaws.getPresets());\r
+\r
}\r
}\r
--- /dev/null
+#SHENKIN 8.653 12.481 12.481 12.481 12.481 12.481 12.481 12.481 12.481 7.862 12.481 12.481 12.481 12.481 7.862 12.481 12.481 12.481 12.481 12.481 12.481 12.481 12.481 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 7.862 6 6 6 6 6 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 8.653 7.862 7.862 7.862 7.862 6 6 6 6 6 6 6 6 6 6 6 6 6 6 11.339 11.339 12.481 12.481 12.481 12.481 12.481 12.481 8.653 8.653 8.653 8.653 8.653 8.653 8.653 8.653 8.653 8.653 8.653 8.653 8.653 7.862 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 11.339 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 7.862 \r
+\r
package compbio.data.msa;\r
\r
import java.security.InvalidParameterException;\r
+import java.util.HashSet;\r
import java.util.List;\r
\r
+import javax.jws.WebMethod;\r
import javax.jws.WebParam;\r
import javax.jws.WebService;\r
\r
import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Score;\r
import compbio.metadata.JobSubmissionException;\r
import compbio.metadata.LimitExceededException;\r
import compbio.metadata.Option;\r
* is throw if the input sequences number or average length\r
* exceeds what is defined by the limit\r
*/\r
+ @WebMethod\r
String analize(\r
@WebParam(name = "fastaSequences") List<FastaSequence> sequences)\r
throws UnsupportedRuntimeException, LimitExceededException,\r
* is throw if the input sequences number or average length\r
* exceeds what is defined by the limit\r
*/\r
+ @WebMethod\r
String customAnalize(\r
@WebParam(name = "fastaSequences") List<FastaSequence> sequences,\r
@WebParam(name = "options") List<Option<T>> options)\r
* is throw if the input sequences number or average length\r
* exceeds what is defined by the limit\r
*/\r
+ @WebMethod\r
String presetAnalize(\r
@WebParam(name = "fastaSequences") List<FastaSequence> sequences,\r
@WebParam(name = "preset") Preset<T> preset)\r
* thrown if jobId is empty or cannot be recognised e.g. in\r
* invalid format\r
*/\r
- String getResult(@WebParam(name = "jobId") String jobId)\r
+ @WebMethod\r
+ HashSet<Score> getConservation(@WebParam(name = "jobId") String jobId)\r
throws ResultNotAvailableException;\r
+\r
}\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
+import compbio.data.sequence.FastaSequence;\r
\r
@XmlRootElement(name = "align", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class Align {\r
\r
@XmlElement(name = "fastaSequences", namespace = "")\r
- private List<compbio.data.sequence.FastaSequence> fastaSequences;\r
+ private List<FastaSequence> fastaSequences;\r
\r
/**\r
* \r
* @return\r
* returns List<FastaSequence>\r
*/\r
- public List<compbio.data.sequence.FastaSequence> getFastaSequences() {\r
+ public List<FastaSequence> getFastaSequences() {\r
return this.fastaSequences;\r
}\r
\r
* @param fastaSequences\r
* the value for the fastaSequences property\r
*/\r
- public void setFastaSequences(List<compbio.data.sequence.FastaSequence> fastaSequences) {\r
+ public void setFastaSequences(List<FastaSequence> fastaSequences) {\r
this.fastaSequences = fastaSequences;\r
}\r
\r
--- /dev/null
+\r
+package compbio.data.msa.jaxws;\r
+\r
+import java.util.List;\r
+import javax.xml.bind.annotation.XmlAccessType;\r
+import javax.xml.bind.annotation.XmlAccessorType;\r
+import javax.xml.bind.annotation.XmlElement;\r
+import javax.xml.bind.annotation.XmlRootElement;\r
+import javax.xml.bind.annotation.XmlType;\r
+import compbio.data.sequence.FastaSequence;\r
+\r
+@XmlRootElement(name = "analize", namespace = "http://msa.data.compbio/01/12/2010/")\r
+@XmlAccessorType(XmlAccessType.FIELD)\r
+@XmlType(name = "analize", namespace = "http://msa.data.compbio/01/12/2010/")\r
+public class Analize {\r
+\r
+ @XmlElement(name = "fastaSequences", namespace = "")\r
+ private List<FastaSequence> fastaSequences;\r
+\r
+ /**\r
+ * \r
+ * @return\r
+ * returns List<FastaSequence>\r
+ */\r
+ public List<FastaSequence> getFastaSequences() {\r
+ return this.fastaSequences;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param fastaSequences\r
+ * the value for the fastaSequences property\r
+ */\r
+ public void setFastaSequences(List<FastaSequence> fastaSequences) {\r
+ this.fastaSequences = fastaSequences;\r
+ }\r
+\r
+}\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
\r
-@XmlRootElement(name = "getProgressResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "analizeResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getProgressResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
-public class GetProgressResponse {\r
+@XmlType(name = "analizeResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
+public class AnalizeResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private byte _return;\r
+ private String _return;\r
\r
/**\r
* \r
* @return\r
- * returns byte\r
+ * returns String\r
*/\r
- public byte getReturn() {\r
+ public String getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(byte _return) {\r
+ public void setReturn(String _return) {\r
this._return = _return;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.metadata.Option;\r
\r
@XmlRootElement(name = "customAlign", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class CustomAlign {\r
\r
@XmlElement(name = "fastaSequences", namespace = "")\r
- private List<compbio.data.sequence.FastaSequence> fastaSequences;\r
+ private List<FastaSequence> fastaSequences;\r
@XmlElement(name = "options", namespace = "")\r
- private List<compbio.metadata.Option> options;\r
+ private List<Option> options;\r
\r
/**\r
* \r
* @return\r
* returns List<FastaSequence>\r
*/\r
- public List<compbio.data.sequence.FastaSequence> getFastaSequences() {\r
+ public List<FastaSequence> getFastaSequences() {\r
return this.fastaSequences;\r
}\r
\r
* @param fastaSequences\r
* the value for the fastaSequences property\r
*/\r
- public void setFastaSequences(List<compbio.data.sequence.FastaSequence> fastaSequences) {\r
+ public void setFastaSequences(List<FastaSequence> fastaSequences) {\r
this.fastaSequences = fastaSequences;\r
}\r
\r
* @return\r
* returns List<Option>\r
*/\r
- public List<compbio.metadata.Option> getOptions() {\r
+ public List<Option> getOptions() {\r
return this.options;\r
}\r
\r
* @param options\r
* the value for the options property\r
*/\r
- public void setOptions(List<compbio.metadata.Option> options) {\r
+ public void setOptions(List<Option> options) {\r
this.options = options;\r
}\r
\r
--- /dev/null
+\r
+package compbio.data.msa.jaxws;\r
+\r
+import java.util.List;\r
+import javax.xml.bind.annotation.XmlAccessType;\r
+import javax.xml.bind.annotation.XmlAccessorType;\r
+import javax.xml.bind.annotation.XmlElement;\r
+import javax.xml.bind.annotation.XmlRootElement;\r
+import javax.xml.bind.annotation.XmlType;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.metadata.Option;\r
+\r
+@XmlRootElement(name = "customAnalize", namespace = "http://msa.data.compbio/01/12/2010/")\r
+@XmlAccessorType(XmlAccessType.FIELD)\r
+@XmlType(name = "customAnalize", namespace = "http://msa.data.compbio/01/12/2010/", propOrder = {\r
+ "fastaSequences",\r
+ "options"\r
+})\r
+public class CustomAnalize {\r
+\r
+ @XmlElement(name = "fastaSequences", namespace = "")\r
+ private List<FastaSequence> fastaSequences;\r
+ @XmlElement(name = "options", namespace = "")\r
+ private List<Option> options;\r
+\r
+ /**\r
+ * \r
+ * @return\r
+ * returns List<FastaSequence>\r
+ */\r
+ public List<FastaSequence> getFastaSequences() {\r
+ return this.fastaSequences;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param fastaSequences\r
+ * the value for the fastaSequences property\r
+ */\r
+ public void setFastaSequences(List<FastaSequence> fastaSequences) {\r
+ this.fastaSequences = fastaSequences;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return\r
+ * returns List<Option>\r
+ */\r
+ public List<Option> getOptions() {\r
+ return this.options;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param options\r
+ * the value for the options property\r
+ */\r
+ public void setOptions(List<Option> options) {\r
+ this.options = options;\r
+ }\r
+\r
+}\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
\r
-@XmlRootElement(name = "pullFileResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "customAnalizeResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "pullFileResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
-public class PullFileResponse {\r
+@XmlType(name = "customAnalizeResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
+public class CustomAnalizeResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private compbio.metadata.ChunkHolder _return;\r
+ private String _return;\r
\r
/**\r
* \r
* @return\r
- * returns ChunkHolder\r
+ * returns String\r
*/\r
- public compbio.metadata.ChunkHolder getReturn() {\r
+ public String getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(compbio.metadata.ChunkHolder _return) {\r
+ public void setReturn(String _return) {\r
this._return = _return;\r
}\r
\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
\r
-@XmlRootElement(name = "getProgress", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "getConservation", namespace = "http://msa.data.compbio/01/12/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getProgress", namespace = "http://msa.data.compbio/01/01/2010/")\r
-public class GetProgress {\r
+@XmlType(name = "getConservation", namespace = "http://msa.data.compbio/01/12/2010/")\r
+public class GetConservation {\r
\r
@XmlElement(name = "jobId", namespace = "")\r
private String jobId;\r
--- /dev/null
+\r
+package compbio.data.msa.jaxws;\r
+\r
+import java.util.HashSet;\r
+import javax.xml.bind.annotation.XmlAccessType;\r
+import javax.xml.bind.annotation.XmlAccessorType;\r
+import javax.xml.bind.annotation.XmlElement;\r
+import javax.xml.bind.annotation.XmlRootElement;\r
+import javax.xml.bind.annotation.XmlType;\r
+\r
+@XmlRootElement(name = "getConservationResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
+@XmlAccessorType(XmlAccessType.FIELD)\r
+@XmlType(name = "getConservationResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
+public class GetConservationResponse {\r
+\r
+ @XmlElement(name = "return", namespace = "")\r
+ private HashSet<compbio.data.sequence.Score> _return;\r
+\r
+ /**\r
+ * \r
+ * @return\r
+ * returns HashSet<Score>\r
+ */\r
+ public HashSet<compbio.data.sequence.Score> getReturn() {\r
+ return this._return;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param _return\r
+ * the value for the _return property\r
+ */\r
+ public void setReturn(HashSet<compbio.data.sequence.Score> _return) {\r
+ this._return = _return;\r
+ }\r
+\r
+}\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
+import compbio.metadata.JobStatus;\r
\r
@XmlRootElement(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class GetJobStatusResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private compbio.metadata.JobStatus _return;\r
+ private JobStatus _return;\r
\r
/**\r
* \r
* @return\r
* returns JobStatus\r
*/\r
- public compbio.metadata.JobStatus getReturn() {\r
+ public JobStatus getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(compbio.metadata.JobStatus _return) {\r
+ public void setReturn(JobStatus _return) {\r
this._return = _return;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
+import compbio.metadata.Limit;\r
\r
@XmlRootElement(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class GetLimitResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private compbio.metadata.Limit _return;\r
+ private Limit _return;\r
\r
/**\r
* \r
* @return\r
* returns Limit\r
*/\r
- public compbio.metadata.Limit getReturn() {\r
+ public Limit getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(compbio.metadata.Limit _return) {\r
+ public void setReturn(Limit _return) {\r
this._return = _return;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
+import compbio.metadata.LimitsManager;\r
\r
@XmlRootElement(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class GetLimitsResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private compbio.metadata.LimitsManager _return;\r
+ private LimitsManager _return;\r
\r
/**\r
* \r
* @return\r
* returns LimitsManager\r
*/\r
- public compbio.metadata.LimitsManager getReturn() {\r
+ public LimitsManager getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(compbio.metadata.LimitsManager _return) {\r
+ public void setReturn(LimitsManager _return) {\r
this._return = _return;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
+import compbio.metadata.PresetManager;\r
\r
@XmlRootElement(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class GetPresetsResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private compbio.metadata.PresetManager _return;\r
+ private PresetManager _return;\r
\r
/**\r
* \r
* @return\r
* returns PresetManager\r
*/\r
- public compbio.metadata.PresetManager getReturn() {\r
+ public PresetManager getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(compbio.metadata.PresetManager _return) {\r
+ public void setReturn(PresetManager _return) {\r
this._return = _return;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
+import compbio.data.sequence.Alignment;\r
\r
@XmlRootElement(name = "getResultResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class GetResultResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private compbio.data.sequence.Alignment _return;\r
+ private Alignment _return;\r
\r
/**\r
* \r
* @return\r
* returns Alignment\r
*/\r
- public compbio.data.sequence.Alignment getReturn() {\r
+ public Alignment getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(compbio.data.sequence.Alignment _return) {\r
+ public void setReturn(Alignment _return) {\r
this._return = _return;\r
}\r
\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
+import compbio.metadata.RunnerConfig;\r
\r
@XmlRootElement(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class GetRunnerOptionsResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private compbio.metadata.RunnerConfig _return;\r
+ private RunnerConfig _return;\r
\r
/**\r
* \r
* @return\r
* returns RunnerConfig\r
*/\r
- public compbio.metadata.RunnerConfig getReturn() {\r
+ public RunnerConfig getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(compbio.metadata.RunnerConfig _return) {\r
+ public void setReturn(RunnerConfig _return) {\r
this._return = _return;\r
}\r
\r
+++ /dev/null
-\r
-package compbio.data.msa.jaxws;\r
-\r
-import javax.xml.bind.annotation.XmlAccessType;\r
-import javax.xml.bind.annotation.XmlAccessorType;\r
-import javax.xml.bind.annotation.XmlRootElement;\r
-import javax.xml.bind.annotation.XmlType;\r
-\r
-\r
-/**\r
- * This class was generated by the JAX-WS RI.\r
- * JAX-WS RI 2.1.7-hudson-48-\r
- * Generated source version: 2.1.7\r
- * \r
- */\r
-@XmlRootElement(name = "JobExecutionException", namespace = "http://msa.data.compbio/01/01/2010/")\r
-@XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "JobExecutionException", namespace = "http://msa.data.compbio/01/01/2010/")\r
-public class JobExecutionExceptionBean {\r
-\r
- private String message;\r
-\r
- /**\r
- * \r
- * @return\r
- * returns String\r
- */\r
- public String getMessage() {\r
- return this.message;\r
- }\r
-\r
- /**\r
- * \r
- * @param message\r
- * the value for the message property\r
- */\r
- public void setMessage(String message) {\r
- this.message = message;\r
- }\r
-\r
-}\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.metadata.Preset;\r
\r
@XmlRootElement(name = "presetAlign", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class PresetAlign {\r
\r
@XmlElement(name = "fastaSequences", namespace = "")\r
- private List<compbio.data.sequence.FastaSequence> fastaSequences;\r
+ private List<FastaSequence> fastaSequences;\r
@XmlElement(name = "preset", namespace = "")\r
- private compbio.metadata.Preset preset;\r
+ private Preset preset;\r
\r
/**\r
* \r
* @return\r
* returns List<FastaSequence>\r
*/\r
- public List<compbio.data.sequence.FastaSequence> getFastaSequences() {\r
+ public List<FastaSequence> getFastaSequences() {\r
return this.fastaSequences;\r
}\r
\r
* @param fastaSequences\r
* the value for the fastaSequences property\r
*/\r
- public void setFastaSequences(List<compbio.data.sequence.FastaSequence> fastaSequences) {\r
+ public void setFastaSequences(List<FastaSequence> fastaSequences) {\r
this.fastaSequences = fastaSequences;\r
}\r
\r
* @return\r
* returns Preset\r
*/\r
- public compbio.metadata.Preset getPreset() {\r
+ public Preset getPreset() {\r
return this.preset;\r
}\r
\r
* @param preset\r
* the value for the preset property\r
*/\r
- public void setPreset(compbio.metadata.Preset preset) {\r
+ public void setPreset(Preset preset) {\r
this.preset = preset;\r
}\r
\r
--- /dev/null
+\r
+package compbio.data.msa.jaxws;\r
+\r
+import java.util.List;\r
+import javax.xml.bind.annotation.XmlAccessType;\r
+import javax.xml.bind.annotation.XmlAccessorType;\r
+import javax.xml.bind.annotation.XmlElement;\r
+import javax.xml.bind.annotation.XmlRootElement;\r
+import javax.xml.bind.annotation.XmlType;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.metadata.Preset;\r
+\r
+@XmlRootElement(name = "presetAnalize", namespace = "http://msa.data.compbio/01/12/2010/")\r
+@XmlAccessorType(XmlAccessType.FIELD)\r
+@XmlType(name = "presetAnalize", namespace = "http://msa.data.compbio/01/12/2010/", propOrder = {\r
+ "fastaSequences",\r
+ "preset"\r
+})\r
+public class PresetAnalize {\r
+\r
+ @XmlElement(name = "fastaSequences", namespace = "")\r
+ private List<FastaSequence> fastaSequences;\r
+ @XmlElement(name = "preset", namespace = "")\r
+ private Preset preset;\r
+\r
+ /**\r
+ * \r
+ * @return\r
+ * returns List<FastaSequence>\r
+ */\r
+ public List<FastaSequence> getFastaSequences() {\r
+ return this.fastaSequences;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param fastaSequences\r
+ * the value for the fastaSequences property\r
+ */\r
+ public void setFastaSequences(List<FastaSequence> fastaSequences) {\r
+ this.fastaSequences = fastaSequences;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return\r
+ * returns Preset\r
+ */\r
+ public Preset getPreset() {\r
+ return this.preset;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param preset\r
+ * the value for the preset property\r
+ */\r
+ public void setPreset(Preset preset) {\r
+ this.preset = preset;\r
+ }\r
+\r
+}\r
--- /dev/null
+\r
+package compbio.data.msa.jaxws;\r
+\r
+import javax.xml.bind.annotation.XmlAccessType;\r
+import javax.xml.bind.annotation.XmlAccessorType;\r
+import javax.xml.bind.annotation.XmlElement;\r
+import javax.xml.bind.annotation.XmlRootElement;\r
+import javax.xml.bind.annotation.XmlType;\r
+\r
+@XmlRootElement(name = "presetAnalizeResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
+@XmlAccessorType(XmlAccessType.FIELD)\r
+@XmlType(name = "presetAnalizeResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
+public class PresetAnalizeResponse {\r
+\r
+ @XmlElement(name = "return", namespace = "")\r
+ private String _return;\r
+\r
+ /**\r
+ * \r
+ * @return\r
+ * returns String\r
+ */\r
+ public String getReturn() {\r
+ return this._return;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param _return\r
+ * the value for the _return property\r
+ */\r
+ public void setReturn(String _return) {\r
+ this._return = _return;\r
+ }\r
+\r
+}\r
import javax.xml.bind.annotation.XmlElement;\r
import javax.xml.bind.annotation.XmlRootElement;\r
import javax.xml.bind.annotation.XmlType;\r
+import compbio.metadata.ChunkHolder;\r
\r
@XmlRootElement(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
@XmlAccessorType(XmlAccessType.FIELD)\r
public class PullExecStatisticsResponse {\r
\r
@XmlElement(name = "return", namespace = "")\r
- private compbio.metadata.ChunkHolder _return;\r
+ private ChunkHolder _return;\r
\r
/**\r
* \r
* @return\r
* returns ChunkHolder\r
*/\r
- public compbio.metadata.ChunkHolder getReturn() {\r
+ public ChunkHolder getReturn() {\r
return this._return;\r
}\r
\r
* @param _return\r
* the value for the _return property\r
*/\r
- public void setReturn(compbio.metadata.ChunkHolder _return) {\r
+ public void setReturn(ChunkHolder _return) {\r
this._return = _return;\r
}\r
\r
+++ /dev/null
-\r
-package compbio.data.msa.jaxws;\r
-\r
-import javax.xml.bind.annotation.XmlAccessType;\r
-import javax.xml.bind.annotation.XmlAccessorType;\r
-import javax.xml.bind.annotation.XmlElement;\r
-import javax.xml.bind.annotation.XmlRootElement;\r
-import javax.xml.bind.annotation.XmlType;\r
-\r
-@XmlRootElement(name = "pullFile", namespace = "http://msa.data.compbio/01/01/2010/")\r
-@XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "pullFile", namespace = "http://msa.data.compbio/01/01/2010/", propOrder = {\r
- "jobId",\r
- "position"\r
-})\r
-public class PullFile {\r
-\r
- @XmlElement(name = "jobId", namespace = "")\r
- private String jobId;\r
- @XmlElement(name = "position", namespace = "")\r
- private long position;\r
-\r
- /**\r
- * \r
- * @return\r
- * returns String\r
- */\r
- public String getJobId() {\r
- return this.jobId;\r
- }\r
-\r
- /**\r
- * \r
- * @param jobId\r
- * the value for the jobId property\r
- */\r
- public void setJobId(String jobId) {\r
- this.jobId = jobId;\r
- }\r
-\r
- /**\r
- * \r
- * @return\r
- * returns long\r
- */\r
- public long getPosition() {\r
- return this.position;\r
- }\r
-\r
- /**\r
- * \r
- * @param position\r
- * the value for the position property\r
- */\r
- public void setPosition(long position) {\r
- this.position = position;\r
- }\r
-\r
-}\r
\r
import java.io.File;\r
import java.util.Arrays;\r
+import java.util.HashSet;\r
import java.util.List;\r
\r
import javax.annotation.Resource;\r
\r
import compbio.data.msa.Annotation;\r
import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Score;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.client.ConfiguredExecutable;\r
return Configurator.configureExecutable(aacon, sequences);\r
}\r
\r
- // HashMap<Method, float[]>\r
- @SuppressWarnings("unchecked")\r
- public String getResult(String jobId) throws ResultNotAvailableException {\r
+ @Override\r
+ public HashSet<Score> getConservation(String jobId)\r
+ throws ResultNotAvailableException {\r
WSUtil.validateJobId(jobId);\r
AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
ConfiguredExecutable<AACon> aacon = (ConfiguredExecutable<AACon>) asyncEngine\r
.getResults(jobId);\r
- // MultiAnnotatedSequence<Method> mas = aacon.getResults();\r
- // log(jobId, "getResults");\r
- return "";// new HashMap<Method, float[]>();\r
+ HashSet<Score> mas = aacon.getResults();\r
+ log.info(jobId + " getConservation : " + mas);\r
+ return mas;\r
}\r
-\r
/*\r
* @SuppressWarnings("unchecked") public JalviewAnnotation\r
* getJalviewAnnotation(String jobId) throws ResultNotAvailableException {\r
--- /dev/null
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<!-- Generated by JAX-WS RI at http://jax-ws.dev.java.net. RI's version is JAX-WS RI 2.2.1-hudson-28-. -->
+<definitions targetNamespace="http://msa.data.compbio/01/12/2010/" name="AAConWS" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:wsp="http://www.w3.org/ns/ws-policy" xmlns:tns="http://msa.data.compbio/01/12/2010/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:wsp1_2="http://schemas.xmlsoap.org/ws/2004/09/policy" xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/" xmlns:wsam="http://www.w3.org/2007/05/addressing/metadata" xmlns:wsu="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd">
+ <types>
+ <xsd:schema>
+ <xsd:import namespace="http://msa.data.compbio/01/12/2010/" schemaLocation="AAConWS_schema1.xsd"/>
+ </xsd:schema>
+ </types>
+ <message name="getConservation">
+ <part name="parameters" element="tns:getConservation"/>
+ </message>
+ <message name="getConservationResponse">
+ <part name="parameters" element="tns:getConservationResponse"/>
+ </message>
+ <message name="ResultNotAvailableException">
+ <part name="fault" element="tns:ResultNotAvailableException"/>
+ </message>
+ <message name="analize">
+ <part name="parameters" element="tns:analize"/>
+ </message>
+ <message name="analizeResponse">
+ <part name="parameters" element="tns:analizeResponse"/>
+ </message>
+ <message name="UnsupportedRuntimeException">
+ <part name="fault" element="tns:UnsupportedRuntimeException"/>
+ </message>
+ <message name="LimitExceededException">
+ <part name="fault" element="tns:LimitExceededException"/>
+ </message>
+ <message name="JobSubmissionException">
+ <part name="fault" element="tns:JobSubmissionException"/>
+ </message>
+ <message name="customAnalize">
+ <part name="parameters" element="tns:customAnalize"/>
+ </message>
+ <message name="customAnalizeResponse">
+ <part name="parameters" element="tns:customAnalizeResponse"/>
+ </message>
+ <message name="WrongParameterException">
+ <part name="fault" element="tns:WrongParameterException"/>
+ </message>
+ <message name="presetAnalize">
+ <part name="parameters" element="tns:presetAnalize"/>
+ </message>
+ <message name="presetAnalizeResponse">
+ <part name="parameters" element="tns:presetAnalizeResponse"/>
+ </message>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
+ </message>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+ </message>
+ <message name="cancelJob">
+ <part name="parameters" element="tns:cancelJob"/>
+ </message>
+ <message name="cancelJobResponse">
+ <part name="parameters" element="tns:cancelJobResponse"/>
+ </message>
+ <message name="getJobStatus">
+ <part name="parameters" element="tns:getJobStatus"/>
+ </message>
+ <message name="getJobStatusResponse">
+ <part name="parameters" element="tns:getJobStatusResponse"/>
+ </message>
+ <message name="getPresets">
+ <part name="parameters" element="tns:getPresets"/>
+ </message>
+ <message name="getPresetsResponse">
+ <part name="parameters" element="tns:getPresetsResponse"/>
+ </message>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
+ </message>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getLimits">
+ <part name="parameters" element="tns:getLimits"/>
+ </message>
+ <message name="getLimitsResponse">
+ <part name="parameters" element="tns:getLimitsResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ </message>
+ <portType name="Annotation">
+ <operation name="getConservation">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/getConservationRequest" message="tns:getConservation"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/getConservationResponse" message="tns:getConservationResponse"/>
+ <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/getConservation/Fault/ResultNotAvailableException"/>
+ </operation>
+ <operation name="analize">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/analizeRequest" message="tns:analize"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/analizeResponse" message="tns:analizeResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/analize/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/analize/Fault/LimitExceededException"/>
+ <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/analize/Fault/JobSubmissionException"/>
+ </operation>
+ <operation name="customAnalize">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/customAnalizeRequest" message="tns:customAnalize"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/customAnalizeResponse" message="tns:customAnalizeResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/customAnalize/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/customAnalize/Fault/LimitExceededException"/>
+ <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/customAnalize/Fault/JobSubmissionException"/>
+ <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/customAnalize/Fault/WrongParameterException"/>
+ </operation>
+ <operation name="presetAnalize">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/presetAnalizeRequest" message="tns:presetAnalize"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/presetAnalizeResponse" message="tns:presetAnalizeResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/presetAnalize/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/presetAnalize/Fault/LimitExceededException"/>
+ <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/presetAnalize/Fault/JobSubmissionException"/>
+ <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/presetAnalize/Fault/WrongParameterException"/>
+ </operation>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+ </operation>
+ <operation name="cancelJob">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/cancelJobRequest" message="tns:cancelJob"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/cancelJobResponse" message="tns:cancelJobResponse"/>
+ </operation>
+ <operation name="getJobStatus">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/getJobStatusRequest" message="tns:getJobStatus"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/getJobStatusResponse" message="tns:getJobStatusResponse"/>
+ </operation>
+ <operation name="getPresets">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/getPresetsRequest" message="tns:getPresets"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/getPresetsResponse" message="tns:getPresetsResponse"/>
+ </operation>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getLimits">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/getLimitsRequest" message="tns:getLimits"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/getLimitsResponse" message="tns:getLimitsResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/Annotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ </operation>
+ </portType>
+ <binding name="AAConWSPortBinding" type="tns:Annotation">
+ <soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
+ <operation name="getConservation">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ <fault name="ResultNotAvailableException">
+ <soap:fault name="ResultNotAvailableException" use="literal"/>
+ </fault>
+ </operation>
+ <operation name="analize">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ <fault name="UnsupportedRuntimeException">
+ <soap:fault name="UnsupportedRuntimeException" use="literal"/>
+ </fault>
+ <fault name="LimitExceededException">
+ <soap:fault name="LimitExceededException" use="literal"/>
+ </fault>
+ <fault name="JobSubmissionException">
+ <soap:fault name="JobSubmissionException" use="literal"/>
+ </fault>
+ </operation>
+ <operation name="customAnalize">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ <fault name="UnsupportedRuntimeException">
+ <soap:fault name="UnsupportedRuntimeException" use="literal"/>
+ </fault>
+ <fault name="LimitExceededException">
+ <soap:fault name="LimitExceededException" use="literal"/>
+ </fault>
+ <fault name="JobSubmissionException">
+ <soap:fault name="JobSubmissionException" use="literal"/>
+ </fault>
+ <fault name="WrongParameterException">
+ <soap:fault name="WrongParameterException" use="literal"/>
+ </fault>
+ </operation>
+ <operation name="presetAnalize">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ <fault name="UnsupportedRuntimeException">
+ <soap:fault name="UnsupportedRuntimeException" use="literal"/>
+ </fault>
+ <fault name="LimitExceededException">
+ <soap:fault name="LimitExceededException" use="literal"/>
+ </fault>
+ <fault name="JobSubmissionException">
+ <soap:fault name="JobSubmissionException" use="literal"/>
+ </fault>
+ <fault name="WrongParameterException">
+ <soap:fault name="WrongParameterException" use="literal"/>
+ </fault>
+ </operation>
+ <operation name="pullExecStatistics">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ <operation name="cancelJob">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ <operation name="getJobStatus">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ <operation name="getPresets">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ <operation name="getLimit">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ <operation name="getLimits">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ <operation name="getRunnerOptions">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ </binding>
+ <service name="AAConWS">
+ <port name="AAConWSPort" binding="tns:AAConWSPortBinding">
+ <soap:address location="REPLACE_WITH_ACTUAL_URL"/>
+ </port>
+ </service>
+</definitions>
+
--- /dev/null
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<xs:schema version="1.0" targetNamespace="http://msa.data.compbio/01/12/2010/" xmlns:tns="http://msa.data.compbio/01/12/2010/" xmlns:xs="http://www.w3.org/2001/XMLSchema">
+
+ <xs:element name="JobSubmissionException" type="tns:JobSubmissionException"/>
+
+ <xs:element name="LimitExceededException" type="tns:LimitExceededException"/>
+
+ <xs:element name="ResultNotAvailableException" type="tns:ResultNotAvailableException"/>
+
+ <xs:element name="UnsupportedRuntimeException" type="tns:UnsupportedRuntimeException"/>
+
+ <xs:element name="WrongParameterException" type="tns:WrongParameterException"/>
+
+ <xs:element name="analize" type="tns:analize"/>
+
+ <xs:element name="analizeResponse" type="tns:analizeResponse"/>
+
+ <xs:element name="cancelJob" type="tns:cancelJob"/>
+
+ <xs:element name="cancelJobResponse" type="tns:cancelJobResponse"/>
+
+ <xs:element name="customAnalize" type="tns:customAnalize"/>
+
+ <xs:element name="customAnalizeResponse" type="tns:customAnalizeResponse"/>
+
+ <xs:element name="getConservation" type="tns:getConservation"/>
+
+ <xs:element name="getConservationResponse" type="tns:getConservationResponse"/>
+
+ <xs:element name="getJobStatus" type="tns:getJobStatus"/>
+
+ <xs:element name="getJobStatusResponse" type="tns:getJobStatusResponse"/>
+
+ <xs:element name="getLimit" type="tns:getLimit"/>
+
+ <xs:element name="getLimitResponse" type="tns:getLimitResponse"/>
+
+ <xs:element name="getLimits" type="tns:getLimits"/>
+
+ <xs:element name="getLimitsResponse" type="tns:getLimitsResponse"/>
+
+ <xs:element name="getPresets" type="tns:getPresets"/>
+
+ <xs:element name="getPresetsResponse" type="tns:getPresetsResponse"/>
+
+ <xs:element name="getRunnerOptions" type="tns:getRunnerOptions"/>
+
+ <xs:element name="getRunnerOptionsResponse" type="tns:getRunnerOptionsResponse"/>
+
+ <xs:element name="presetAnalize" type="tns:presetAnalize"/>
+
+ <xs:element name="presetAnalizeResponse" type="tns:presetAnalizeResponse"/>
+
+ <xs:element name="pullExecStatistics" type="tns:pullExecStatistics"/>
+
+ <xs:element name="pullExecStatisticsResponse" type="tns:pullExecStatisticsResponse"/>
+
+ <xs:complexType name="getJobStatus">
+ <xs:sequence>
+ <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="getJobStatusResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:jobStatus" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="analize">
+ <xs:sequence>
+ <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="fastaSequence">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="analizeResponse">
+ <xs:sequence>
+ <xs:element name="return" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="UnsupportedRuntimeException">
+ <xs:sequence>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="LimitExceededException">
+ <xs:sequence>
+ <xs:element name="actualNumberofSequences" type="xs:int"/>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
+ <xs:element name="numberOfSequencesAllowed" type="xs:int"/>
+ <xs:element name="sequenceLenghtActual" type="xs:int"/>
+ <xs:element name="sequenceLenghtAllowed" type="xs:int"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="JobSubmissionException">
+ <xs:sequence>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="getRunnerOptions">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getRunnerOptionsResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:runnerConfig" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="runnerConfig">
+ <xs:sequence>
+ <xs:element name="options" type="tns:option" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="parameters" type="tns:parameter" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="prmSeparator" type="xs:string" minOccurs="0"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="option">
+ <xs:sequence>
+ <xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
+ <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element name="furtherDetails" type="xs:anyURI" minOccurs="0"/>
+ <xs:element name="name" type="xs:string" minOccurs="0"/>
+ <xs:element name="required" type="xs:boolean"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="parameter">
+ <xs:complexContent>
+ <xs:extension base="tns:option">
+ <xs:sequence>
+ <xs:element name="optionName" type="xs:string" minOccurs="0"/>
+ <xs:element name="validValue" type="tns:valueConstrain" minOccurs="0"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+
+ <xs:complexType name="valueConstrain">
+ <xs:sequence>
+ <xs:element name="type" type="tns:type" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="presetAnalize">
+ <xs:sequence>
+ <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="preset" type="tns:preset" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="preset">
+ <xs:sequence>
+ <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element name="name" type="xs:string" minOccurs="0"/>
+ <xs:element name="options" type="xs:string" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="presetAnalizeResponse">
+ <xs:sequence>
+ <xs:element name="return" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="WrongParameterException">
+ <xs:sequence>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="getLimits">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getLimitsResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="limitsManager">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getLimit">
+ <xs:sequence>
+ <xs:element name="presetName" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="getLimitResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:limit" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="limit">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getPresets">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getPresetsResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="presetManager">
+ <xs:sequence>
+ <xs:element name="presets" type="tns:preset" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="cancelJob">
+ <xs:sequence>
+ <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="cancelJobResponse">
+ <xs:sequence>
+ <xs:element name="return" type="xs:boolean"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="customAnalize">
+ <xs:sequence>
+ <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="options" type="tns:option" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="customAnalizeResponse">
+ <xs:sequence>
+ <xs:element name="return" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="getConservation">
+ <xs:sequence>
+ <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="getConservationResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:score" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="score">
+ <xs:sequence>
+ <xs:element name="method" type="tns:method" minOccurs="0"/>
+ <xs:element name="scores" type="xs:float" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="ResultNotAvailableException">
+ <xs:sequence>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="pullExecStatistics">
+ <xs:sequence>
+ <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+ <xs:element name="position" type="xs:long"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="pullExecStatisticsResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:chunkHolder" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="chunkHolder">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:simpleType name="jobStatus">
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="PENDING"/>
+ <xs:enumeration value="RUNNING"/>
+ <xs:enumeration value="CANCELLED"/>
+ <xs:enumeration value="FINISHED"/>
+ <xs:enumeration value="FAILED"/>
+ <xs:enumeration value="UNDEFINED"/>
+ <xs:enumeration value="STARTED"/>
+ <xs:enumeration value="SUBMITTED"/>
+ <xs:enumeration value="COLLECTED"/>
+ </xs:restriction>
+ </xs:simpleType>
+
+ <xs:simpleType name="type">
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="Integer"/>
+ <xs:enumeration value="Float"/>
+ </xs:restriction>
+ </xs:simpleType>
+
+ <xs:simpleType name="method">
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="KABAT"/>
+ <xs:enumeration value="JORES"/>
+ <xs:enumeration value="SCHNEIDER"/>
+ <xs:enumeration value="SHENKIN"/>
+ <xs:enumeration value="GERSTEIN"/>
+ <xs:enumeration value="TAYLOR_GAPS"/>
+ <xs:enumeration value="TAYLOR_NO_GAPS"/>
+ <xs:enumeration value="ZVELIBIL"/>
+ <xs:enumeration value="KARLIN"/>
+ <xs:enumeration value="ARMON"/>
+ <xs:enumeration value="THOMPSON"/>
+ <xs:enumeration value="NOT_LANCET"/>
+ <xs:enumeration value="MIRNY"/>
+ <xs:enumeration value="WILLIAMSON"/>
+ <xs:enumeration value="LANDGRAF"/>
+ <xs:enumeration value="SANDER"/>
+ <xs:enumeration value="VALDAR"/>
+ <xs:enumeration value="SMERFS"/>
+ </xs:restriction>
+ </xs:simpleType>
+</xs:schema>
+
<xsd:import namespace="http://msa.data.compbio/01/01/2010/" schemaLocation="ClustalWS_schema1.xsd"/>
</xsd:schema>
</types>
- <message name="getPresets">
- <part name="parameters" element="tns:getPresets"/>
- </message>
- <message name="getPresetsResponse">
- <part name="parameters" element="tns:getPresetsResponse"/>
+ <message name="getResult">
+ <part name="parameters" element="tns:getResult"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
+ <message name="getResultResponse">
+ <part name="parameters" element="tns:getResultResponse"/>
</message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
+ <message name="ResultNotAvailableException">
+ <part name="fault" element="tns:ResultNotAvailableException"/>
</message>
<message name="presetAlign">
<part name="parameters" element="tns:presetAlign"/>
<message name="customAlignResponse">
<part name="parameters" element="tns:customAlignResponse"/>
</message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
- </message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
- </message>
- <message name="getResult">
- <part name="parameters" element="tns:getResult"/>
- </message>
- <message name="getResultResponse">
- <part name="parameters" element="tns:getResultResponse"/>
+ <message name="align">
+ <part name="parameters" element="tns:align"/>
</message>
- <message name="ResultNotAvailableException">
- <part name="fault" element="tns:ResultNotAvailableException"/>
+ <message name="alignResponse">
+ <part name="parameters" element="tns:alignResponse"/>
</message>
- <message name="getLimits">
- <part name="parameters" element="tns:getLimits"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getLimitsResponse">
- <part name="parameters" element="tns:getLimitsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
+ <message name="getPresets">
+ <part name="parameters" element="tns:getPresets"/>
</message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+ <message name="getPresetsResponse">
+ <part name="parameters" element="tns:getPresetsResponse"/>
</message>
- <message name="align">
- <part name="parameters" element="tns:align"/>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
</message>
- <message name="alignResponse">
- <part name="parameters" element="tns:alignResponse"/>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getLimits">
+ <part name="parameters" element="tns:getLimits"/>
+ </message>
+ <message name="getLimitsResponse">
+ <part name="parameters" element="tns:getLimitsResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
</message>
<portType name="MsaWS">
- <operation name="getPresets">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
- </operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
+ <operation name="getResult">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
+ <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
</operation>
<operation name="presetAlign">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignRequest" message="tns:presetAlign"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException"/>
</operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
- </operation>
- <operation name="getResult">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
- <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
+ <operation name="align">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
+ <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
</operation>
- <operation name="getLimits">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="cancelJob">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+ <operation name="getPresets">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
</operation>
- <operation name="align">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
- <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/UnsupportedRuntimeException"/>
- <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
- <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getLimits">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
</operation>
</portType>
<binding name="ClustalWSPortBinding" type="tns:MsaWS">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
- <operation name="getPresets">
+ <operation name="getResult">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
+ <fault name="ResultNotAvailableException">
+ <soap:fault name="ResultNotAvailableException" use="literal"/>
+ </fault>
</operation>
- <operation name="getLimit">
+ <operation name="presetAlign">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
+ <fault name="UnsupportedRuntimeException">
+ <soap:fault name="UnsupportedRuntimeException" use="literal"/>
+ </fault>
+ <fault name="LimitExceededException">
+ <soap:fault name="LimitExceededException" use="literal"/>
+ </fault>
+ <fault name="JobSubmissionException">
+ <soap:fault name="JobSubmissionException" use="literal"/>
+ </fault>
+ <fault name="WrongParameterException">
+ <soap:fault name="WrongParameterException" use="literal"/>
+ </fault>
</operation>
- <operation name="presetAlign">
+ <operation name="customAlign">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="customAlign">
+ <operation name="align">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<fault name="JobSubmissionException">
<soap:fault name="JobSubmissionException" use="literal"/>
</fault>
- <fault name="WrongParameterException">
- <soap:fault name="WrongParameterException" use="literal"/>
- </fault>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getResult">
+ <operation name="cancelJob">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
- <fault name="ResultNotAvailableException">
- <soap:fault name="ResultNotAvailableException" use="literal"/>
- </fault>
</operation>
- <operation name="getLimits">
+ <operation name="getJobStatus">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="cancelJob">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getJobStatus">
+ <operation name="getLimit">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="align">
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
- <fault name="UnsupportedRuntimeException">
- <soap:fault name="UnsupportedRuntimeException" use="literal"/>
- </fault>
- <fault name="LimitExceededException">
- <soap:fault name="LimitExceededException" use="literal"/>
- </fault>
- <fault name="JobSubmissionException">
- <soap:fault name="JobSubmissionException" use="literal"/>
- </fault>
</operation>
</binding>
<service name="ClustalWS">
<xs:element name="getRunnerOptionsResponse" type="tns:getRunnerOptionsResponse"/>
- <xs:element name="limits" type="tns:limitsManager"/>
-
<xs:element name="presetAlign" type="tns:presetAlign"/>
<xs:element name="presetAlignResponse" type="tns:presetAlignResponse"/>
- <xs:element name="presets" type="tns:presetManager"/>
-
<xs:element name="pullExecStatistics" type="tns:pullExecStatistics"/>
<xs:element name="pullExecStatisticsResponse" type="tns:pullExecStatisticsResponse"/>
- <xs:element name="runnerConfig" type="tns:runnerConfig"/>
-
<xs:complexType name="getJobStatus">
<xs:sequence>
<xs:element name="jobId" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getResult">
- <xs:sequence>
- <xs:element name="jobId" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="getResultResponse">
- <xs:sequence>
- <xs:element name="return" type="tns:alignment" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="alignment" final="extension restriction">
- <xs:sequence>
- <xs:element name="metadata" type="tns:alignmentMetadata" minOccurs="0"/>
- <xs:element name="sequences" type="tns:fastaSequence" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="alignmentMetadata">
- <xs:sequence>
- <xs:element name="program" type="tns:program" minOccurs="0"/>
- <xs:element name="gapchar" type="xs:unsignedShort"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="fastaSequence">
- <xs:sequence>
- <xs:element name="id" type="xs:string" minOccurs="0"/>
- <xs:element name="sequence" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="ResultNotAvailableException">
- <xs:sequence>
- <xs:element name="message" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
<xs:complexType name="getRunnerOptions">
<xs:sequence/>
</xs:complexType>
<xs:element name="options" type="tns:option" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="parameters" type="tns:parameter" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="prmSeparator" type="xs:string" minOccurs="0"/>
- <xs:element name="runnerClassName" type="xs:string"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="option">
<xs:sequence>
- <xs:element name="description" type="xs:string"/>
- <xs:element name="optionNames" type="xs:string" maxOccurs="unbounded"/>
- <xs:element name="name" type="xs:string"/>
- <xs:element name="furtherDetails" type="xs:anyURI" minOccurs="0"/>
<xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
+ <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element name="furtherDetails" type="xs:anyURI" minOccurs="0"/>
+ <xs:element name="name" type="xs:string" minOccurs="0"/>
+ <xs:element name="required" type="xs:boolean"/>
</xs:sequence>
- <xs:attribute name="isRequired" type="xs:boolean" use="required"/>
</xs:complexType>
<xs:complexType name="parameter">
<xs:complexContent>
<xs:extension base="tns:option">
<xs:sequence>
- <xs:element name="possibleValues" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="optionName" type="xs:string" minOccurs="0"/>
<xs:element name="validValue" type="tns:valueConstrain" minOccurs="0"/>
</xs:sequence>
</xs:extension>
<xs:complexType name="valueConstrain">
<xs:sequence>
- <xs:element name="type" type="tns:type"/>
- <xs:element name="max" type="xs:string" minOccurs="0"/>
- <xs:element name="min" type="xs:string" minOccurs="0"/>
+ <xs:element name="type" type="tns:type" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="cancelJob">
+ <xs:complexType name="getResult">
<xs:sequence>
<xs:element name="jobId" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="cancelJobResponse">
+ <xs:complexType name="getResultResponse">
<xs:sequence>
- <xs:element name="return" type="xs:boolean"/>
+ <xs:element name="return" type="tns:alignment" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimits">
+ <xs:complexType name="alignment" final="extension restriction">
<xs:sequence/>
</xs:complexType>
- <xs:complexType name="getLimitsResponse">
+ <xs:complexType name="ResultNotAvailableException">
<xs:sequence>
- <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="limitsManager">
- <xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
- </xs:sequence>
+ <xs:complexType name="getLimits">
+ <xs:sequence/>
</xs:complexType>
- <xs:complexType name="limit">
+ <xs:complexType name="getLimitsResponse">
<xs:sequence>
- <xs:element name="preset" type="xs:string" minOccurs="0"/>
- <xs:element name="seqNumber" type="xs:int"/>
- <xs:element name="seqLength" type="xs:int"/>
+ <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
</xs:sequence>
- <xs:attribute name="isDefault" type="xs:boolean" use="required"/>
+ </xs:complexType>
+
+ <xs:complexType name="limitsManager">
+ <xs:sequence/>
</xs:complexType>
<xs:complexType name="getLimit">
</xs:sequence>
</xs:complexType>
+ <xs:complexType name="limit">
+ <xs:sequence/>
+ </xs:complexType>
+
<xs:complexType name="getPresets">
<xs:sequence/>
</xs:complexType>
<xs:complexType name="presetManager">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string"/>
- <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
+ <xs:element name="presets" type="tns:preset" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="preset">
<xs:sequence>
- <xs:element name="name" type="xs:string"/>
<xs:element name="description" type="xs:string" minOccurs="0"/>
- <xs:element name="optlist" minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="option" type="xs:string" maxOccurs="unbounded"/>
- </xs:sequence>
- </xs:complexType>
- </xs:element>
+ <xs:element name="name" type="xs:string" minOccurs="0"/>
+ <xs:element name="options" type="xs:string" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="cancelJob">
+ <xs:sequence>
+ <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="cancelJobResponse">
+ <xs:sequence>
+ <xs:element name="return" type="xs:boolean"/>
</xs:sequence>
</xs:complexType>
</xs:sequence>
</xs:complexType>
+ <xs:complexType name="fastaSequence">
+ <xs:sequence/>
+ </xs:complexType>
+
<xs:complexType name="presetAlignResponse">
<xs:sequence>
<xs:element name="return" type="xs:string" minOccurs="0"/>
</xs:complexType>
<xs:complexType name="chunkHolder">
- <xs:sequence>
- <xs:element name="chunk" type="xs:string" minOccurs="0"/>
- <xs:element name="position" type="xs:long"/>
- </xs:sequence>
+ <xs:sequence/>
</xs:complexType>
<xs:complexType name="align">
</xs:restriction>
</xs:simpleType>
- <xs:simpleType name="program">
- <xs:restriction base="xs:string">
- <xs:enumeration value="CLUSTAL"/>
- <xs:enumeration value="MAFFT"/>
- <xs:enumeration value="MUSCLE"/>
- <xs:enumeration value="Tcoffee"/>
- <xs:enumeration value="Probcons"/>
- </xs:restriction>
- </xs:simpleType>
-
<xs:simpleType name="type">
<xs:restriction base="xs:string">
<xs:enumeration value="Integer"/>
<xsd:import namespace="http://msa.data.compbio/01/01/2010/" schemaLocation="MafftWS_schema1.xsd"/>
</xsd:schema>
</types>
- <message name="getPresets">
- <part name="parameters" element="tns:getPresets"/>
- </message>
- <message name="getPresetsResponse">
- <part name="parameters" element="tns:getPresetsResponse"/>
+ <message name="getResult">
+ <part name="parameters" element="tns:getResult"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
+ <message name="getResultResponse">
+ <part name="parameters" element="tns:getResultResponse"/>
</message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
+ <message name="ResultNotAvailableException">
+ <part name="fault" element="tns:ResultNotAvailableException"/>
</message>
<message name="presetAlign">
<part name="parameters" element="tns:presetAlign"/>
<message name="customAlignResponse">
<part name="parameters" element="tns:customAlignResponse"/>
</message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
- </message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
- </message>
- <message name="getResult">
- <part name="parameters" element="tns:getResult"/>
- </message>
- <message name="getResultResponse">
- <part name="parameters" element="tns:getResultResponse"/>
+ <message name="align">
+ <part name="parameters" element="tns:align"/>
</message>
- <message name="ResultNotAvailableException">
- <part name="fault" element="tns:ResultNotAvailableException"/>
+ <message name="alignResponse">
+ <part name="parameters" element="tns:alignResponse"/>
</message>
- <message name="getLimits">
- <part name="parameters" element="tns:getLimits"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getLimitsResponse">
- <part name="parameters" element="tns:getLimitsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
+ <message name="getPresets">
+ <part name="parameters" element="tns:getPresets"/>
</message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+ <message name="getPresetsResponse">
+ <part name="parameters" element="tns:getPresetsResponse"/>
</message>
- <message name="align">
- <part name="parameters" element="tns:align"/>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
</message>
- <message name="alignResponse">
- <part name="parameters" element="tns:alignResponse"/>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getLimits">
+ <part name="parameters" element="tns:getLimits"/>
+ </message>
+ <message name="getLimitsResponse">
+ <part name="parameters" element="tns:getLimitsResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
</message>
<portType name="MsaWS">
- <operation name="getPresets">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
- </operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
+ <operation name="getResult">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
+ <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
</operation>
<operation name="presetAlign">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignRequest" message="tns:presetAlign"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException"/>
</operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
- </operation>
- <operation name="getResult">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
- <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
+ <operation name="align">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
+ <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
</operation>
- <operation name="getLimits">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="cancelJob">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+ <operation name="getPresets">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
</operation>
- <operation name="align">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
- <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/UnsupportedRuntimeException"/>
- <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
- <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getLimits">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
</operation>
</portType>
<binding name="MafftWSPortBinding" type="tns:MsaWS">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
- <operation name="getPresets">
+ <operation name="getResult">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
+ <fault name="ResultNotAvailableException">
+ <soap:fault name="ResultNotAvailableException" use="literal"/>
+ </fault>
</operation>
- <operation name="getLimit">
+ <operation name="presetAlign">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
+ <fault name="UnsupportedRuntimeException">
+ <soap:fault name="UnsupportedRuntimeException" use="literal"/>
+ </fault>
+ <fault name="LimitExceededException">
+ <soap:fault name="LimitExceededException" use="literal"/>
+ </fault>
+ <fault name="JobSubmissionException">
+ <soap:fault name="JobSubmissionException" use="literal"/>
+ </fault>
+ <fault name="WrongParameterException">
+ <soap:fault name="WrongParameterException" use="literal"/>
+ </fault>
</operation>
- <operation name="presetAlign">
+ <operation name="customAlign">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="customAlign">
+ <operation name="align">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<fault name="JobSubmissionException">
<soap:fault name="JobSubmissionException" use="literal"/>
</fault>
- <fault name="WrongParameterException">
- <soap:fault name="WrongParameterException" use="literal"/>
- </fault>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getResult">
+ <operation name="cancelJob">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
- <fault name="ResultNotAvailableException">
- <soap:fault name="ResultNotAvailableException" use="literal"/>
- </fault>
</operation>
- <operation name="getLimits">
+ <operation name="getJobStatus">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="cancelJob">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getJobStatus">
+ <operation name="getLimit">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="align">
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
- <fault name="UnsupportedRuntimeException">
- <soap:fault name="UnsupportedRuntimeException" use="literal"/>
- </fault>
- <fault name="LimitExceededException">
- <soap:fault name="LimitExceededException" use="literal"/>
- </fault>
- <fault name="JobSubmissionException">
- <soap:fault name="JobSubmissionException" use="literal"/>
- </fault>
</operation>
</binding>
<service name="MafftWS">
<xs:element name="getRunnerOptionsResponse" type="tns:getRunnerOptionsResponse"/>
- <xs:element name="limits" type="tns:limitsManager"/>
-
<xs:element name="presetAlign" type="tns:presetAlign"/>
<xs:element name="presetAlignResponse" type="tns:presetAlignResponse"/>
- <xs:element name="presets" type="tns:presetManager"/>
-
<xs:element name="pullExecStatistics" type="tns:pullExecStatistics"/>
<xs:element name="pullExecStatisticsResponse" type="tns:pullExecStatisticsResponse"/>
- <xs:element name="runnerConfig" type="tns:runnerConfig"/>
-
<xs:complexType name="getJobStatus">
<xs:sequence>
<xs:element name="jobId" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getResult">
- <xs:sequence>
- <xs:element name="jobId" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="getResultResponse">
- <xs:sequence>
- <xs:element name="return" type="tns:alignment" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="alignment" final="extension restriction">
- <xs:sequence>
- <xs:element name="metadata" type="tns:alignmentMetadata" minOccurs="0"/>
- <xs:element name="sequences" type="tns:fastaSequence" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="alignmentMetadata">
- <xs:sequence>
- <xs:element name="program" type="tns:program" minOccurs="0"/>
- <xs:element name="gapchar" type="xs:unsignedShort"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="fastaSequence">
- <xs:sequence>
- <xs:element name="id" type="xs:string" minOccurs="0"/>
- <xs:element name="sequence" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="ResultNotAvailableException">
- <xs:sequence>
- <xs:element name="message" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
<xs:complexType name="getRunnerOptions">
<xs:sequence/>
</xs:complexType>
<xs:element name="options" type="tns:option" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="parameters" type="tns:parameter" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="prmSeparator" type="xs:string" minOccurs="0"/>
- <xs:element name="runnerClassName" type="xs:string"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="option">
<xs:sequence>
- <xs:element name="description" type="xs:string"/>
- <xs:element name="optionNames" type="xs:string" maxOccurs="unbounded"/>
- <xs:element name="name" type="xs:string"/>
- <xs:element name="furtherDetails" type="xs:anyURI" minOccurs="0"/>
<xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
+ <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element name="furtherDetails" type="xs:anyURI" minOccurs="0"/>
+ <xs:element name="name" type="xs:string" minOccurs="0"/>
+ <xs:element name="required" type="xs:boolean"/>
</xs:sequence>
- <xs:attribute name="isRequired" type="xs:boolean" use="required"/>
</xs:complexType>
<xs:complexType name="parameter">
<xs:complexContent>
<xs:extension base="tns:option">
<xs:sequence>
- <xs:element name="possibleValues" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="optionName" type="xs:string" minOccurs="0"/>
<xs:element name="validValue" type="tns:valueConstrain" minOccurs="0"/>
</xs:sequence>
</xs:extension>
<xs:complexType name="valueConstrain">
<xs:sequence>
- <xs:element name="type" type="tns:type"/>
- <xs:element name="max" type="xs:string" minOccurs="0"/>
- <xs:element name="min" type="xs:string" minOccurs="0"/>
+ <xs:element name="type" type="tns:type" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="cancelJob">
+ <xs:complexType name="getResult">
<xs:sequence>
<xs:element name="jobId" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="cancelJobResponse">
+ <xs:complexType name="getResultResponse">
<xs:sequence>
- <xs:element name="return" type="xs:boolean"/>
+ <xs:element name="return" type="tns:alignment" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimits">
+ <xs:complexType name="alignment" final="extension restriction">
<xs:sequence/>
</xs:complexType>
- <xs:complexType name="getLimitsResponse">
+ <xs:complexType name="ResultNotAvailableException">
<xs:sequence>
- <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="limitsManager">
- <xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
- </xs:sequence>
+ <xs:complexType name="getLimits">
+ <xs:sequence/>
</xs:complexType>
- <xs:complexType name="limit">
+ <xs:complexType name="getLimitsResponse">
<xs:sequence>
- <xs:element name="preset" type="xs:string" minOccurs="0"/>
- <xs:element name="seqNumber" type="xs:int"/>
- <xs:element name="seqLength" type="xs:int"/>
+ <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
</xs:sequence>
- <xs:attribute name="isDefault" type="xs:boolean" use="required"/>
+ </xs:complexType>
+
+ <xs:complexType name="limitsManager">
+ <xs:sequence/>
</xs:complexType>
<xs:complexType name="getLimit">
</xs:sequence>
</xs:complexType>
+ <xs:complexType name="limit">
+ <xs:sequence/>
+ </xs:complexType>
+
<xs:complexType name="getPresets">
<xs:sequence/>
</xs:complexType>
<xs:complexType name="presetManager">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string"/>
- <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
+ <xs:element name="presets" type="tns:preset" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="preset">
<xs:sequence>
- <xs:element name="name" type="xs:string"/>
<xs:element name="description" type="xs:string" minOccurs="0"/>
- <xs:element name="optlist" minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="option" type="xs:string" maxOccurs="unbounded"/>
- </xs:sequence>
- </xs:complexType>
- </xs:element>
+ <xs:element name="name" type="xs:string" minOccurs="0"/>
+ <xs:element name="options" type="xs:string" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="cancelJob">
+ <xs:sequence>
+ <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="cancelJobResponse">
+ <xs:sequence>
+ <xs:element name="return" type="xs:boolean"/>
</xs:sequence>
</xs:complexType>
</xs:sequence>
</xs:complexType>
+ <xs:complexType name="fastaSequence">
+ <xs:sequence/>
+ </xs:complexType>
+
<xs:complexType name="presetAlignResponse">
<xs:sequence>
<xs:element name="return" type="xs:string" minOccurs="0"/>
</xs:complexType>
<xs:complexType name="chunkHolder">
- <xs:sequence>
- <xs:element name="chunk" type="xs:string" minOccurs="0"/>
- <xs:element name="position" type="xs:long"/>
- </xs:sequence>
+ <xs:sequence/>
</xs:complexType>
<xs:complexType name="align">
</xs:restriction>
</xs:simpleType>
- <xs:simpleType name="program">
- <xs:restriction base="xs:string">
- <xs:enumeration value="CLUSTAL"/>
- <xs:enumeration value="MAFFT"/>
- <xs:enumeration value="MUSCLE"/>
- <xs:enumeration value="Tcoffee"/>
- <xs:enumeration value="Probcons"/>
- </xs:restriction>
- </xs:simpleType>
-
<xs:simpleType name="type">
<xs:restriction base="xs:string">
<xs:enumeration value="Integer"/>
<xsd:import namespace="http://msa.data.compbio/01/01/2010/" schemaLocation="MuscleWS_schema1.xsd"/>
</xsd:schema>
</types>
- <message name="getPresets">
- <part name="parameters" element="tns:getPresets"/>
- </message>
- <message name="getPresetsResponse">
- <part name="parameters" element="tns:getPresetsResponse"/>
+ <message name="getResult">
+ <part name="parameters" element="tns:getResult"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
+ <message name="getResultResponse">
+ <part name="parameters" element="tns:getResultResponse"/>
</message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
+ <message name="ResultNotAvailableException">
+ <part name="fault" element="tns:ResultNotAvailableException"/>
</message>
<message name="presetAlign">
<part name="parameters" element="tns:presetAlign"/>
<message name="customAlignResponse">
<part name="parameters" element="tns:customAlignResponse"/>
</message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
- </message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
- </message>
- <message name="getResult">
- <part name="parameters" element="tns:getResult"/>
- </message>
- <message name="getResultResponse">
- <part name="parameters" element="tns:getResultResponse"/>
+ <message name="align">
+ <part name="parameters" element="tns:align"/>
</message>
- <message name="ResultNotAvailableException">
- <part name="fault" element="tns:ResultNotAvailableException"/>
+ <message name="alignResponse">
+ <part name="parameters" element="tns:alignResponse"/>
</message>
- <message name="getLimits">
- <part name="parameters" element="tns:getLimits"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getLimitsResponse">
- <part name="parameters" element="tns:getLimitsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
+ <message name="getPresets">
+ <part name="parameters" element="tns:getPresets"/>
</message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+ <message name="getPresetsResponse">
+ <part name="parameters" element="tns:getPresetsResponse"/>
</message>
- <message name="align">
- <part name="parameters" element="tns:align"/>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
</message>
- <message name="alignResponse">
- <part name="parameters" element="tns:alignResponse"/>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getLimits">
+ <part name="parameters" element="tns:getLimits"/>
+ </message>
+ <message name="getLimitsResponse">
+ <part name="parameters" element="tns:getLimitsResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
</message>
<portType name="MsaWS">
- <operation name="getPresets">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
- </operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
+ <operation name="getResult">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
+ <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
</operation>
<operation name="presetAlign">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignRequest" message="tns:presetAlign"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException"/>
</operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
- </operation>
- <operation name="getResult">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
- <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
+ <operation name="align">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
+ <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
</operation>
- <operation name="getLimits">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="cancelJob">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+ <operation name="getPresets">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
</operation>
- <operation name="align">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
- <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/UnsupportedRuntimeException"/>
- <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
- <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getLimits">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
</operation>
</portType>
<binding name="MuscleWSPortBinding" type="tns:MsaWS">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
- <operation name="getPresets">
+ <operation name="getResult">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
+ <fault name="ResultNotAvailableException">
+ <soap:fault name="ResultNotAvailableException" use="literal"/>
+ </fault>
</operation>
- <operation name="getLimit">
+ <operation name="presetAlign">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
+ <fault name="UnsupportedRuntimeException">
+ <soap:fault name="UnsupportedRuntimeException" use="literal"/>
+ </fault>
+ <fault name="LimitExceededException">
+ <soap:fault name="LimitExceededException" use="literal"/>
+ </fault>
+ <fault name="JobSubmissionException">
+ <soap:fault name="JobSubmissionException" use="literal"/>
+ </fault>
+ <fault name="WrongParameterException">
+ <soap:fault name="WrongParameterException" use="literal"/>
+ </fault>
</operation>
- <operation name="presetAlign">
+ <operation name="customAlign">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="customAlign">
+ <operation name="align">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<fault name="JobSubmissionException">
<soap:fault name="JobSubmissionException" use="literal"/>
</fault>
- <fault name="WrongParameterException">
- <soap:fault name="WrongParameterException" use="literal"/>
- </fault>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getResult">
+ <operation name="cancelJob">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
- <fault name="ResultNotAvailableException">
- <soap:fault name="ResultNotAvailableException" use="literal"/>
- </fault>
</operation>
- <operation name="getLimits">
+ <operation name="getJobStatus">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="cancelJob">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getJobStatus">
+ <operation name="getLimit">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="align">
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
- <fault name="UnsupportedRuntimeException">
- <soap:fault name="UnsupportedRuntimeException" use="literal"/>
- </fault>
- <fault name="LimitExceededException">
- <soap:fault name="LimitExceededException" use="literal"/>
- </fault>
- <fault name="JobSubmissionException">
- <soap:fault name="JobSubmissionException" use="literal"/>
- </fault>
</operation>
</binding>
<service name="MuscleWS">
<xs:element name="getRunnerOptionsResponse" type="tns:getRunnerOptionsResponse"/>
- <xs:element name="limits" type="tns:limitsManager"/>
-
<xs:element name="presetAlign" type="tns:presetAlign"/>
<xs:element name="presetAlignResponse" type="tns:presetAlignResponse"/>
- <xs:element name="presets" type="tns:presetManager"/>
-
<xs:element name="pullExecStatistics" type="tns:pullExecStatistics"/>
<xs:element name="pullExecStatisticsResponse" type="tns:pullExecStatisticsResponse"/>
- <xs:element name="runnerConfig" type="tns:runnerConfig"/>
-
<xs:complexType name="pullExecStatistics">
<xs:sequence>
<xs:element name="jobId" type="xs:string" minOccurs="0"/>
</xs:complexType>
<xs:complexType name="chunkHolder">
- <xs:sequence>
- <xs:element name="chunk" type="xs:string" minOccurs="0"/>
- <xs:element name="position" type="xs:long"/>
- </xs:sequence>
+ <xs:sequence/>
</xs:complexType>
<xs:complexType name="align">
</xs:complexType>
<xs:complexType name="fastaSequence">
- <xs:sequence>
- <xs:element name="id" type="xs:string" minOccurs="0"/>
- <xs:element name="sequence" type="xs:string" minOccurs="0"/>
- </xs:sequence>
+ <xs:sequence/>
</xs:complexType>
<xs:complexType name="alignResponse">
<xs:complexType name="option">
<xs:sequence>
- <xs:element name="description" type="xs:string"/>
- <xs:element name="optionNames" type="xs:string" maxOccurs="unbounded"/>
- <xs:element name="name" type="xs:string"/>
- <xs:element name="furtherDetails" type="xs:anyURI" minOccurs="0"/>
<xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
+ <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element name="furtherDetails" type="xs:anyURI" minOccurs="0"/>
+ <xs:element name="name" type="xs:string" minOccurs="0"/>
+ <xs:element name="required" type="xs:boolean"/>
</xs:sequence>
- <xs:attribute name="isRequired" type="xs:boolean" use="required"/>
</xs:complexType>
<xs:complexType name="customAlignResponse">
</xs:sequence>
</xs:complexType>
- <xs:complexType name="cancelJob">
- <xs:sequence>
- <xs:element name="jobId" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="cancelJobResponse">
- <xs:sequence>
- <xs:element name="return" type="xs:boolean"/>
- </xs:sequence>
- </xs:complexType>
-
<xs:complexType name="getLimits">
<xs:sequence/>
</xs:complexType>
</xs:complexType>
<xs:complexType name="limitsManager">
- <xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="limit">
- <xs:sequence>
- <xs:element name="preset" type="xs:string" minOccurs="0"/>
- <xs:element name="seqNumber" type="xs:int"/>
- <xs:element name="seqLength" type="xs:int"/>
- </xs:sequence>
- <xs:attribute name="isDefault" type="xs:boolean" use="required"/>
+ <xs:sequence/>
</xs:complexType>
<xs:complexType name="getLimit">
</xs:sequence>
</xs:complexType>
+ <xs:complexType name="limit">
+ <xs:sequence/>
+ </xs:complexType>
+
<xs:complexType name="getPresets">
<xs:sequence/>
</xs:complexType>
<xs:complexType name="presetManager">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string"/>
- <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
+ <xs:element name="presets" type="tns:preset" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="preset">
<xs:sequence>
- <xs:element name="name" type="xs:string"/>
<xs:element name="description" type="xs:string" minOccurs="0"/>
- <xs:element name="optlist" minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="option" type="xs:string" maxOccurs="unbounded"/>
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="presetAlign">
- <xs:sequence>
- <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="preset" type="tns:preset" minOccurs="0"/>
+ <xs:element name="name" type="xs:string" minOccurs="0"/>
+ <xs:element name="options" type="xs:string" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="presetAlignResponse">
- <xs:sequence>
- <xs:element name="return" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="getResult">
+ <xs:complexType name="cancelJob">
<xs:sequence>
<xs:element name="jobId" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getResultResponse">
- <xs:sequence>
- <xs:element name="return" type="tns:alignment" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="alignment" final="extension restriction">
+ <xs:complexType name="cancelJobResponse">
<xs:sequence>
- <xs:element name="metadata" type="tns:alignmentMetadata" minOccurs="0"/>
- <xs:element name="sequences" type="tns:fastaSequence" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="return" type="xs:boolean"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="alignmentMetadata">
+ <xs:complexType name="presetAlign">
<xs:sequence>
- <xs:element name="program" type="tns:program" minOccurs="0"/>
- <xs:element name="gapchar" type="xs:unsignedShort"/>
+ <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="preset" type="tns:preset" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="ResultNotAvailableException">
+ <xs:complexType name="presetAlignResponse">
<xs:sequence>
- <xs:element name="message" type="xs:string" minOccurs="0"/>
+ <xs:element name="return" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:element name="options" type="tns:option" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="parameters" type="tns:parameter" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="prmSeparator" type="xs:string" minOccurs="0"/>
- <xs:element name="runnerClassName" type="xs:string"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:complexContent>
<xs:extension base="tns:option">
<xs:sequence>
- <xs:element name="possibleValues" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="optionName" type="xs:string" minOccurs="0"/>
<xs:element name="validValue" type="tns:valueConstrain" minOccurs="0"/>
</xs:sequence>
</xs:extension>
<xs:complexType name="valueConstrain">
<xs:sequence>
- <xs:element name="type" type="tns:type"/>
- <xs:element name="max" type="xs:string" minOccurs="0"/>
- <xs:element name="min" type="xs:string" minOccurs="0"/>
+ <xs:element name="type" type="tns:type" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="getResult">
+ <xs:sequence>
+ <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="getResultResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:alignment" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="alignment" final="extension restriction">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="ResultNotAvailableException">
+ <xs:sequence>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
</xs:sequence>
</xs:complexType>
- <xs:simpleType name="program">
- <xs:restriction base="xs:string">
- <xs:enumeration value="CLUSTAL"/>
- <xs:enumeration value="MAFFT"/>
- <xs:enumeration value="MUSCLE"/>
- <xs:enumeration value="Tcoffee"/>
- <xs:enumeration value="Probcons"/>
- </xs:restriction>
- </xs:simpleType>
-
<xs:simpleType name="type">
<xs:restriction base="xs:string">
<xs:enumeration value="Integer"/>
<xsd:import namespace="http://msa.data.compbio/01/01/2010/" schemaLocation="TcoffeeWS_schema1.xsd"/>
</xsd:schema>
</types>
- <message name="getPresets">
- <part name="parameters" element="tns:getPresets"/>
- </message>
- <message name="getPresetsResponse">
- <part name="parameters" element="tns:getPresetsResponse"/>
+ <message name="getResult">
+ <part name="parameters" element="tns:getResult"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
+ <message name="getResultResponse">
+ <part name="parameters" element="tns:getResultResponse"/>
</message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
+ <message name="ResultNotAvailableException">
+ <part name="fault" element="tns:ResultNotAvailableException"/>
</message>
<message name="presetAlign">
<part name="parameters" element="tns:presetAlign"/>
<message name="customAlignResponse">
<part name="parameters" element="tns:customAlignResponse"/>
</message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
- </message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
- </message>
- <message name="getResult">
- <part name="parameters" element="tns:getResult"/>
- </message>
- <message name="getResultResponse">
- <part name="parameters" element="tns:getResultResponse"/>
+ <message name="align">
+ <part name="parameters" element="tns:align"/>
</message>
- <message name="ResultNotAvailableException">
- <part name="fault" element="tns:ResultNotAvailableException"/>
+ <message name="alignResponse">
+ <part name="parameters" element="tns:alignResponse"/>
</message>
- <message name="getLimits">
- <part name="parameters" element="tns:getLimits"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getLimitsResponse">
- <part name="parameters" element="tns:getLimitsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
+ <message name="getPresets">
+ <part name="parameters" element="tns:getPresets"/>
</message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+ <message name="getPresetsResponse">
+ <part name="parameters" element="tns:getPresetsResponse"/>
</message>
- <message name="align">
- <part name="parameters" element="tns:align"/>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
</message>
- <message name="alignResponse">
- <part name="parameters" element="tns:alignResponse"/>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getLimits">
+ <part name="parameters" element="tns:getLimits"/>
+ </message>
+ <message name="getLimitsResponse">
+ <part name="parameters" element="tns:getLimitsResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
</message>
<portType name="MsaWS">
- <operation name="getPresets">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
- </operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
+ <operation name="getResult">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
+ <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
</operation>
<operation name="presetAlign">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignRequest" message="tns:presetAlign"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException"/>
</operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
- </operation>
- <operation name="getResult">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
- <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
+ <operation name="align">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
+ <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
</operation>
- <operation name="getLimits">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="cancelJob">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+ <operation name="getPresets">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
</operation>
- <operation name="align">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
- <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/UnsupportedRuntimeException"/>
- <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
- <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getLimits">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
</operation>
</portType>
<binding name="TcoffeeWSPortBinding" type="tns:MsaWS">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
- <operation name="getPresets">
+ <operation name="getResult">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
+ <fault name="ResultNotAvailableException">
+ <soap:fault name="ResultNotAvailableException" use="literal"/>
+ </fault>
</operation>
- <operation name="getLimit">
+ <operation name="presetAlign">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
+ <fault name="UnsupportedRuntimeException">
+ <soap:fault name="UnsupportedRuntimeException" use="literal"/>
+ </fault>
+ <fault name="LimitExceededException">
+ <soap:fault name="LimitExceededException" use="literal"/>
+ </fault>
+ <fault name="JobSubmissionException">
+ <soap:fault name="JobSubmissionException" use="literal"/>
+ </fault>
+ <fault name="WrongParameterException">
+ <soap:fault name="WrongParameterException" use="literal"/>
+ </fault>
</operation>
- <operation name="presetAlign">
+ <operation name="customAlign">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="customAlign">
+ <operation name="align">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<fault name="JobSubmissionException">
<soap:fault name="JobSubmissionException" use="literal"/>
</fault>
- <fault name="WrongParameterException">
- <soap:fault name="WrongParameterException" use="literal"/>
- </fault>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getResult">
+ <operation name="cancelJob">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
- <fault name="ResultNotAvailableException">
- <soap:fault name="ResultNotAvailableException" use="literal"/>
- </fault>
</operation>
- <operation name="getLimits">
+ <operation name="getJobStatus">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="cancelJob">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getJobStatus">
+ <operation name="getLimit">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="align">
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
- <fault name="UnsupportedRuntimeException">
- <soap:fault name="UnsupportedRuntimeException" use="literal"/>
- </fault>
- <fault name="LimitExceededException">
- <soap:fault name="LimitExceededException" use="literal"/>
- </fault>
- <fault name="JobSubmissionException">
- <soap:fault name="JobSubmissionException" use="literal"/>
- </fault>
</operation>
</binding>
<service name="TcoffeeWS">
<xs:element name="getRunnerOptionsResponse" type="tns:getRunnerOptionsResponse"/>
- <xs:element name="limits" type="tns:limitsManager"/>
-
<xs:element name="presetAlign" type="tns:presetAlign"/>
<xs:element name="presetAlignResponse" type="tns:presetAlignResponse"/>
- <xs:element name="presets" type="tns:presetManager"/>
-
<xs:element name="pullExecStatistics" type="tns:pullExecStatistics"/>
<xs:element name="pullExecStatisticsResponse" type="tns:pullExecStatisticsResponse"/>
- <xs:element name="runnerConfig" type="tns:runnerConfig"/>
-
<xs:complexType name="pullExecStatistics">
<xs:sequence>
<xs:element name="jobId" type="xs:string" minOccurs="0"/>
</xs:complexType>
<xs:complexType name="chunkHolder">
- <xs:sequence>
- <xs:element name="chunk" type="xs:string" minOccurs="0"/>
- <xs:element name="position" type="xs:long"/>
- </xs:sequence>
+ <xs:sequence/>
</xs:complexType>
<xs:complexType name="customAlign">
</xs:complexType>
<xs:complexType name="fastaSequence">
- <xs:sequence>
- <xs:element name="id" type="xs:string" minOccurs="0"/>
- <xs:element name="sequence" type="xs:string" minOccurs="0"/>
- </xs:sequence>
+ <xs:sequence/>
</xs:complexType>
<xs:complexType name="option">
<xs:sequence>
- <xs:element name="description" type="xs:string"/>
- <xs:element name="optionNames" type="xs:string" maxOccurs="unbounded"/>
- <xs:element name="name" type="xs:string"/>
- <xs:element name="furtherDetails" type="xs:anyURI" minOccurs="0"/>
<xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
+ <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element name="furtherDetails" type="xs:anyURI" minOccurs="0"/>
+ <xs:element name="name" type="xs:string" minOccurs="0"/>
+ <xs:element name="required" type="xs:boolean"/>
</xs:sequence>
- <xs:attribute name="isRequired" type="xs:boolean" use="required"/>
</xs:complexType>
<xs:complexType name="customAlignResponse">
</xs:sequence>
</xs:complexType>
- <xs:complexType name="cancelJob">
- <xs:sequence>
- <xs:element name="jobId" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="cancelJobResponse">
- <xs:sequence>
- <xs:element name="return" type="xs:boolean"/>
- </xs:sequence>
- </xs:complexType>
-
<xs:complexType name="getLimits">
<xs:sequence/>
</xs:complexType>
</xs:complexType>
<xs:complexType name="limitsManager">
- <xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="limit">
- <xs:sequence>
- <xs:element name="preset" type="xs:string" minOccurs="0"/>
- <xs:element name="seqNumber" type="xs:int"/>
- <xs:element name="seqLength" type="xs:int"/>
- </xs:sequence>
- <xs:attribute name="isDefault" type="xs:boolean" use="required"/>
+ <xs:sequence/>
</xs:complexType>
<xs:complexType name="getLimit">
</xs:sequence>
</xs:complexType>
+ <xs:complexType name="limit">
+ <xs:sequence/>
+ </xs:complexType>
+
<xs:complexType name="getPresets">
<xs:sequence/>
</xs:complexType>
<xs:complexType name="presetManager">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string"/>
- <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
+ <xs:element name="presets" type="tns:preset" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:complexType name="preset">
<xs:sequence>
- <xs:element name="name" type="xs:string"/>
<xs:element name="description" type="xs:string" minOccurs="0"/>
- <xs:element name="optlist" minOccurs="0">
- <xs:complexType>
- <xs:sequence>
- <xs:element name="option" type="xs:string" maxOccurs="unbounded"/>
- </xs:sequence>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="presetAlign">
- <xs:sequence>
- <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="preset" type="tns:preset" minOccurs="0"/>
+ <xs:element name="name" type="xs:string" minOccurs="0"/>
+ <xs:element name="options" type="xs:string" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="presetAlignResponse">
- <xs:sequence>
- <xs:element name="return" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="getResult">
+ <xs:complexType name="cancelJob">
<xs:sequence>
<xs:element name="jobId" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getResultResponse">
- <xs:sequence>
- <xs:element name="return" type="tns:alignment" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="alignment" final="extension restriction">
+ <xs:complexType name="cancelJobResponse">
<xs:sequence>
- <xs:element name="metadata" type="tns:alignmentMetadata" minOccurs="0"/>
- <xs:element name="sequences" type="tns:fastaSequence" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="return" type="xs:boolean"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="alignmentMetadata">
+ <xs:complexType name="presetAlign">
<xs:sequence>
- <xs:element name="program" type="tns:program" minOccurs="0"/>
- <xs:element name="gapchar" type="xs:unsignedShort"/>
+ <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="preset" type="tns:preset" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="ResultNotAvailableException">
+ <xs:complexType name="presetAlignResponse">
<xs:sequence>
- <xs:element name="message" type="xs:string" minOccurs="0"/>
+ <xs:element name="return" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:element name="options" type="tns:option" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="parameters" type="tns:parameter" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="prmSeparator" type="xs:string" minOccurs="0"/>
- <xs:element name="runnerClassName" type="xs:string"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:complexContent>
<xs:extension base="tns:option">
<xs:sequence>
- <xs:element name="possibleValues" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="optionName" type="xs:string" minOccurs="0"/>
<xs:element name="validValue" type="tns:valueConstrain" minOccurs="0"/>
</xs:sequence>
</xs:extension>
<xs:complexType name="valueConstrain">
<xs:sequence>
- <xs:element name="type" type="tns:type"/>
- <xs:element name="max" type="xs:string" minOccurs="0"/>
- <xs:element name="min" type="xs:string" minOccurs="0"/>
+ <xs:element name="type" type="tns:type" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="getResult">
+ <xs:sequence>
+ <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="getResultResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:alignment" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="alignment" final="extension restriction">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="ResultNotAvailableException">
+ <xs:sequence>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
</xs:sequence>
</xs:complexType>
- <xs:simpleType name="program">
- <xs:restriction base="xs:string">
- <xs:enumeration value="CLUSTAL"/>
- <xs:enumeration value="MAFFT"/>
- <xs:enumeration value="MUSCLE"/>
- <xs:enumeration value="Tcoffee"/>
- <xs:enumeration value="Probcons"/>
- </xs:restriction>
- </xs:simpleType>
-
<xs:simpleType name="type">
<xs:restriction base="xs:string">
<xs:enumeration value="Integer"/>
git://source.jalview.org / jabaws.git / commitdiff