<endpoint name='ProbconsWS'\r
implementation='compbio.ws.server.ProbconsWS'\r
url-pattern='/ProbconsWS'/>\r
+ <endpoint name='MSAprobsWS'\r
+ implementation='compbio.ws.server.MSAprobsWS'\r
+ url-pattern='/MSAprobsWS'/>\r
+ <endpoint name='GLprobsWS'\r
+ implementation='compbio.ws.server.GLprobsWS'\r
+ url-pattern='/GLprobsWS'/>\r
<endpoint name='AAConWS'\r
implementation='compbio.ws.server.AAConWS'\r
url-pattern='/AAConWS'/>\r
</servlet>\r
\r
<servlet>\r
+ <servlet-name>MSAprobsWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
+ <servlet-name>GLprobsWS</servlet-name>\r
+ <servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
+ <load-on-startup>1</load-on-startup>\r
+ </servlet>\r
+\r
+ <servlet>\r
<servlet-name>AAConWS</servlet-name>\r
<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>\r
<load-on-startup>1</load-on-startup>\r
</servlet-mapping>\r
\r
<servlet-mapping>\r
+ <servlet-name>MSAprobsWS</servlet-name>\r
+ <url-pattern>/MSAprobsWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
+ <servlet-name>GLprobsWS</servlet-name>\r
+ <url-pattern>/GLprobsWS</url-pattern>\r
+ </servlet-mapping>\r
+\r
+ <servlet-mapping>\r
<servlet-name>AAConWS</servlet-name>\r
<url-pattern>/AAConWS</url-pattern>\r
</servlet-mapping>\r
<property name="compbio-ga" value="compbio-ga-1.0.jar"/>
<!-- products -->
- <property name="jabaws_version" value="2.5.0"/>
+ <property name="jabaws_version" value="2.1.0"/>
<property name="datamodel" value="${distdir}/datamodel-${jabaws_version}.jar"/>
<property name="datamodel-src" value="${distdir}/datamodel-src-${jabaws_version}.jar"/>
<property name="min-jabaws-client" value="${distdir}/min-jabaws-client-${jabaws_version}.jar"/>
rnaalifold.limits.file = conf/settings/RNAalifoldLimits.xml\r
rnaalifold.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M\r
\r
+###########################################################################################\r
+# MSAProbs CONFIGURATION #\r
+###########################################################################################\r
+local.msaprobs.bin = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs\r
+cluster.msaprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs\r
+msaprobs.parameters.file = conf/settings/MSAprobsParameters.xml\r
+msaprobs.limits.file = conf/settings/MSAprobsLimits.xml\r
+msaprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M\r
\r
+###########################################################################################\r
+# GLprobs CONFIGURATION #\r
+###########################################################################################\r
+local.glprobs.bin = binaries/src/GLProbs-1.0/glprobs\r
+cluster.glprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/GLProbs-1.0/glprobs\r
+glprobs.parameters.file = conf/settings/GLprobsParameters.xml\r
+glprobs.limits.file = conf/settings/GLprobsLimits.xml\r
+glprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M\r
--- /dev/null
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<limits>\r
+ <runnerClassName>compbio.runner.msa.MSAprobs</runnerClassName>\r
+ <limit isDefault="true">\r
+ <seqNumber>2000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+ <limit isDefault="false">\r
+ <preset># LocalEngineExecutionLimit #</preset>\r
+ <seqNumber>30</seqNumber>\r
+ <seqLength>500</seqLength>\r
+ </limit>\r
+</limits>\r
--- /dev/null
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<runnerConfig>\r
+ <runnerClassName>compbio.runner.msa.GLprobs</runnerClassName>\r
+\r
+ <options isRequired="true">\r
+ <name>CLUSTAL format for output alignment</name>\r
+ <description>\r
+ CLUSTAL output format is used instead of the FASTA format\r
+ </description>\r
+ <optionNames>-clustalw</optionNames>\r
+ <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
+ </options>\r
+\r
+ <options isRequired="true">\r
+ <name>Another order of sequence in output alignment</name>\r
+ <description>\r
+ print sequences in alignment order rather than input order\r
+ </description>\r
+ <optionNames>-a</optionNames>\r
+ <optionNames>--alignment-order</optionNames>\r
+ <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
+ </options>\r
+\r
+ <prmSeparator> </prmSeparator>\r
+\r
+ <parameters isRequired="false">\r
+ <name>passes of consistency transformation</name>\r
+ <description>\r
+ passes of consistency transformation\r
+ </description>\r
+ <optionNames>-c</optionNames>\r
+ <optionNames>--consistency</optionNames>\r
+ <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
+ <defaultValue>2</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>0</min>\r
+ <max>5</max>\r
+ </validValue>\r
+ </parameters>\r
+\r
+ <parameters isRequired="false">\r
+ <name>passes of consistency transformation</name>\r
+ <description>\r
+ number of passes of iterative-refinement\r
+ </description>\r
+ <optionNames>-ir</optionNames>\r
+ <optionNames>--iterative-refinement</optionNames>\r
+ <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
+ <defaultValue>100</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>0</min>\r
+ <max>1000</max>\r
+ </validValue>\r
+ </parameters>\r
+\r
+ <parameters isRequired="false">\r
+ <name>Number of CPUs</name>\r
+ <description>\r
+ Number of CPU used by msaprobs. \r
+ My default the number is equal to the total number of CPU on the system.\r
+ </description>\r
+ <optionNames>-num_threads</optionNames>\r
+ <furtherDetails>prog_docs/glprobs.txt</furtherDetails>\r
+ <defaultValue>1</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ </validValue>\r
+ </parameters>\r
+\r
+</runnerConfig>\r
--- /dev/null
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<presets>\r
+ <runnerClassName>compbio.runner.msa.MSAprobs</runnerClassName>\r
+\r
+ <preset>\r
+ <name>working</name>\r
+ <description>\r
+ Working configuration\r
+ </description>\r
+ <optlist>\r
+ <option>-clustalw</option>\r
+ </optlist>\r
+ </preset>\r
+\r
+</presets>\r
--- /dev/null
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<limits>\r
+ <runnerClassName>compbio.runner.msa.MSAprobs</runnerClassName>\r
+ <limit isDefault="true">\r
+ <seqNumber>2000</seqNumber>\r
+ <seqLength>1000</seqLength>\r
+ </limit>\r
+ <limit isDefault="false">\r
+ <preset># LocalEngineExecutionLimit #</preset>\r
+ <seqNumber>30</seqNumber>\r
+ <seqLength>500</seqLength>\r
+ </limit>\r
+</limits>\r
--- /dev/null
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<runnerConfig>\r
+ <runnerClassName>compbio.runner.msa.MSAprobs</runnerClassName>\r
+\r
+ <options isRequired="true">\r
+ <name>CLUSTAL format for output alignment</name>\r
+ <description>\r
+ CLUSTAL output format is used instead of the FASTA format\r
+ </description>\r
+ <optionNames>-clustalw</optionNames>\r
+ <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>\r
+ </options>\r
+\r
+ <options isRequired="true">\r
+ <name>Another order of sequence in output alignment</name>\r
+ <description>\r
+ print sequences in alignment order rather than input order\r
+ </description>\r
+ <optionNames>-a</optionNames>\r
+ <optionNames>--alignment-order</optionNames>\r
+ <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>\r
+ </options>\r
+\r
+ <prmSeparator> </prmSeparator>\r
+\r
+ <parameters isRequired="false">\r
+ <name>passes of consistency transformation</name>\r
+ <description>\r
+ passes of consistency transformation\r
+ </description>\r
+ <optionNames>-c</optionNames>\r
+ <optionNames>--consistency</optionNames>\r
+ <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>\r
+ <defaultValue>2</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>0</min>\r
+ <max>5</max>\r
+ </validValue>\r
+ </parameters>\r
+\r
+ <parameters isRequired="false">\r
+ <name>passes of consistency transformation</name>\r
+ <description>\r
+ number of passes of iterative-refinement\r
+ </description>\r
+ <optionNames>-ir</optionNames>\r
+ <optionNames>--iterative-refinement</optionNames>\r
+ <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>\r
+ <defaultValue>10</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>0</min>\r
+ <max>1000</max>\r
+ </validValue>\r
+ </parameters>\r
+\r
+ <parameters isRequired="false">\r
+ <name>Number of CPUs</name>\r
+ <description>\r
+ Number of CPU used by msaprobs. \r
+ My default the number is equal to the total number of CPU on the system.\r
+ </description>\r
+ <optionNames>-num_threads</optionNames>\r
+ <furtherDetails>prog_docs/msaprobs.txt</furtherDetails>\r
+ <defaultValue>1</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ </validValue>\r
+ </parameters>\r
+</runnerConfig>\r
--- /dev/null
+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>\r
+<presets>\r
+ <runnerClassName>compbio.runner.msa.MSAprobs</runnerClassName>\r
+\r
+ <preset>\r
+ <name>working</name>\r
+ <description>\r
+ Working configuration\r
+ </description>\r
+ <optlist>\r
+ <option>-clustalw</option>\r
+ </optlist>\r
+ </preset>\r
+\r
+</presets>\r
<prmSeparator> </prmSeparator>\r
\r
<!-- unsupported in practice \r
- <parameters>\r
+ <parameters>\r
<name>MATRIX</name>\r
<description>Protein weight matrix. Specifies the emission probabilities that are to be used for scoring alignments.</description>\r
<optionNames>-m</optionNames>\r
<furtherDetails>http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html</furtherDetails>\r
<defaultValue>BLOSUM62</defaultValue>\r
- <possibleValues>BLOSUM100</possibleValues>\r
- <possibleValues>BLOSUM30</possibleValues>\r
- <possibleValues>BLOSUM35</possibleValues>\r
- <possibleValues>BLOSUM40</possibleValues>\r
- <possibleValues>BLOSUM45</possibleValues>\r
- <possibleValues>BLOSUM50</possibleValues>\r
- <possibleValues>BLOSUM55</possibleValues>\r
- <possibleValues>BLOSUM60</possibleValues>\r
- <possibleValues>BLOSUM62</possibleValues>\r
- <possibleValues>BLOSUM65</possibleValues>\r
- <possibleValues>BLOSUM70</possibleValues>\r
- <possibleValues>BLOSUM75</possibleValues>\r
- <possibleValues>BLOSUM80</possibleValues>\r
- <possibleValues>BLOSUM85</possibleValues>\r
- <possibleValues>BLOSUM90</possibleValues>\r
- <possibleValues>BLOSUMN</possibleValues>\r
- <possibleValues>DAYHOFF</possibleValues>\r
- <possibleValues>GONNET</possibleValues>\r
- <possibleValues>IDENTITY</possibleValues>\r
- <possibleValues>MATCH</possibleValues>\r
- <possibleValues>NUC.4.2</possibleValues>\r
- <possibleValues>NUC.4.4</possibleValues>\r
- <possibleValues>PAM10</possibleValues>\r
- <possibleValues>PAM100</possibleValues>\r
- <possibleValues>PAM110</possibleValues>\r
- <possibleValues>PAM120</possibleValues>\r
- <possibleValues>PAM130</possibleValues>\r
- <possibleValues>PAM140</possibleValues>\r
- <possibleValues>PAM150</possibleValues>\r
- <possibleValues>PAM160</possibleValues>\r
- <possibleValues>PAM170</possibleValues>\r
- <possibleValues>PAM180</possibleValues>\r
- <possibleValues>PAM190</possibleValues>\r
- <possibleValues>PAM20</possibleValues>\r
- <possibleValues>PAM200</possibleValues>\r
- <possibleValues>PAM210</possibleValues>\r
- <possibleValues>PAM220</possibleValues>\r
- <possibleValues>PAM230</possibleValues>\r
- <possibleValues>PAM240</possibleValues>\r
- <possibleValues>PAM250</possibleValues>\r
- <possibleValues>PAM260</possibleValues>\r
- <possibleValues>PAM270</possibleValues>\r
- <possibleValues>PAM280</possibleValues>\r
- <possibleValues>PAM290</possibleValues>\r
- <possibleValues>PAM30</possibleValues>\r
- <possibleValues>PAM300</possibleValues>\r
- <possibleValues>PAM310</possibleValues>\r
- <possibleValues>PAM320</possibleValues>\r
- <possibleValues>PAM330</possibleValues>\r
- <possibleValues>PAM340</possibleValues>\r
- <possibleValues>PAM350</possibleValues>\r
- <possibleValues>PAM360</possibleValues>\r
- <possibleValues>PAM370</possibleValues>\r
- <possibleValues>PAM380</possibleValues>\r
- <possibleValues>PAM390</possibleValues>\r
- <possibleValues>PAM40</possibleValues>\r
- <possibleValues>PAM400</possibleValues>\r
- <possibleValues>PAM410</possibleValues>\r
- <possibleValues>PAM420</possibleValues>\r
- <possibleValues>PAM430</possibleValues>\r
- <possibleValues>PAM440</possibleValues>\r
- <possibleValues>PAM450</possibleValues>\r
- <possibleValues>PAM460</possibleValues>\r
- <possibleValues>PAM470</possibleValues>\r
- <possibleValues>PAM480</possibleValues>\r
- <possibleValues>PAM490</possibleValues>\r
- <possibleValues>PAM50</possibleValues>\r
- <possibleValues>PAM500</possibleValues>\r
- <possibleValues>PAM60</possibleValues>\r
- <possibleValues>PAM70</possibleValues>\r
- <possibleValues>PAM80</possibleValues>\r
- <possibleValues>PAM90</possibleValues>\r
- </parameters>\r
+ <possibleValues>BLOSUM100</possibleValues>\r
+ <possibleValues>BLOSUM30</possibleValues>\r
+ <possibleValues>BLOSUM35</possibleValues>\r
+ <possibleValues>BLOSUM40</possibleValues>\r
+ <possibleValues>BLOSUM45</possibleValues>\r
+ <possibleValues>BLOSUM50</possibleValues>\r
+ <possibleValues>BLOSUM55</possibleValues>\r
+ <possibleValues>BLOSUM60</possibleValues>\r
+ <possibleValues>BLOSUM62</possibleValues>\r
+ <possibleValues>BLOSUM65</possibleValues>\r
+ <possibleValues>BLOSUM70</possibleValues>\r
+ <possibleValues>BLOSUM75</possibleValues>\r
+ <possibleValues>BLOSUM80</possibleValues>\r
+ <possibleValues>BLOSUM85</possibleValues>\r
+ <possibleValues>BLOSUM90</possibleValues>\r
+ <possibleValues>BLOSUMN</possibleValues>\r
+ <possibleValues>DAYHOFF</possibleValues>\r
+ <possibleValues>GONNET</possibleValues>\r
+ <possibleValues>IDENTITY</possibleValues>\r
+ <possibleValues>MATCH</possibleValues>\r
+ <possibleValues>NUC.4.2</possibleValues>\r
+ <possibleValues>NUC.4.4</possibleValues>\r
+ <possibleValues>PAM10</possibleValues>\r
+ <possibleValues>PAM100</possibleValues>\r
+ <possibleValues>PAM110</possibleValues>\r
+ <possibleValues>PAM120</possibleValues>\r
+ <possibleValues>PAM130</possibleValues>\r
+ <possibleValues>PAM140</possibleValues>\r
+ <possibleValues>PAM150</possibleValues>\r
+ <possibleValues>PAM160</possibleValues>\r
+ <possibleValues>PAM170</possibleValues>\r
+ <possibleValues>PAM180</possibleValues>\r
+ <possibleValues>PAM190</possibleValues>\r
+ <possibleValues>PAM20</possibleValues>\r
+ <possibleValues>PAM200</possibleValues>\r
+ <possibleValues>PAM210</possibleValues>\r
+ <possibleValues>PAM220</possibleValues>\r
+ <possibleValues>PAM230</possibleValues>\r
+ <possibleValues>PAM240</possibleValues>\r
+ <possibleValues>PAM250</possibleValues>\r
+ <possibleValues>PAM260</possibleValues>\r
+ <possibleValues>PAM270</possibleValues>\r
+ <possibleValues>PAM280</possibleValues>\r
+ <possibleValues>PAM290</possibleValues>\r
+ <possibleValues>PAM30</possibleValues>\r
+ <possibleValues>PAM300</possibleValues>\r
+ <possibleValues>PAM310</possibleValues>\r
+ <possibleValues>PAM320</possibleValues>\r
+ <possibleValues>PAM330</possibleValues>\r
+ <possibleValues>PAM340</possibleValues>\r
+ <possibleValues>PAM350</possibleValues>\r
+ <possibleValues>PAM360</possibleValues>\r
+ <possibleValues>PAM370</possibleValues>\r
+ <possibleValues>PAM380</possibleValues>\r
+ <possibleValues>PAM390</possibleValues>\r
+ <possibleValues>PAM40</possibleValues>\r
+ <possibleValues>PAM400</possibleValues>\r
+ <possibleValues>PAM410</possibleValues>\r
+ <possibleValues>PAM420</possibleValues>\r
+ <possibleValues>PAM430</possibleValues>\r
+ <possibleValues>PAM440</possibleValues>\r
+ <possibleValues>PAM450</possibleValues>\r
+ <possibleValues>PAM460</possibleValues>\r
+ <possibleValues>PAM470</possibleValues>\r
+ <possibleValues>PAM480</possibleValues>\r
+ <possibleValues>PAM490</possibleValues>\r
+ <possibleValues>PAM50</possibleValues>\r
+ <possibleValues>PAM500</possibleValues>\r
+ <possibleValues>PAM60</possibleValues>\r
+ <possibleValues>PAM70</possibleValues>\r
+ <possibleValues>PAM80</possibleValues>\r
+ <possibleValues>PAM90</possibleValues>\r
+ </parameters>\r
-->\r
\r
<parameters>\r
aligned. This option is used in case the default parameters are not appropriate for the\r
particular sequences being aligned; in general, this option is not recommended as it may\r
lead to unstable alignment parameters.\r
- </description>\r
+ </description>\r
<optionNames>-pre</optionNames>\r
<furtherDetails>prog_docs/probcons.pdf</furtherDetails>\r
<defaultValue>0</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
+ <validValue>\r
+ <type>Integer</type>\r
<min>0</min>\r
<max>20</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters>\r
<name>Passes of iterative refinement</name>\r
- <description>This specifies the number of iterations of iterative refinement to be performed. In each\r
-stage of iterative refinement, the set of sequences in the alignment is randomly\r
-partitioned into two groups. After projecting the alignments to these groups, the two\r
-groups are realigned, resulting in an alignment whose objective score is guaranteed to be\r
-at least that of the original alignment</description>\r
+ <description>\r
+ This specifies the number of iterations of iterative refinement to be performed.\r
+ In each stage of iterative refinement, the set of sequences in the alignment is \r
+ randomly partitioned into two groups. After projecting the alignments to these \r
+ groups, the two groups are realigned, resulting in an alignment whose objective \r
+ score is guaranteed to be at least that of the original alignment\r
+ </description>\r
<optionNames>-ir</optionNames>\r
<furtherDetails>prog_docs/probcons.pdf</furtherDetails>\r
- <defaultValue>100</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
+ <defaultValue>100</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
<min>0</min>\r
<max>1000</max>\r
</validValue>\r
</parameters>\r
+\r
<parameters>\r
<name>Passes of consistency transformation</name>\r
- <description>Each pass applies one round of the consistency transformation on the set of sequences.\r
- The consistency transformation is described in detail in the mentioned papers. In each\r
- round, the aligner computes the consistency transformation for each pair of sequences\r
- using all other sequences. The aligner then updates the posterior probability matrices of\r
- the pairwise alignments.</description>\r
+ <description>\r
+ Each pass applies one round of the consistency transformation on the set of sequences.\r
+ The consistency transformation is described in detail in the mentioned papers. In each\r
+ round, the aligner computes the consistency transformation for each pair of sequences\r
+ using all other sequences. The aligner then updates the posterior probability matrices of\r
+ the pairwise alignments.\r
+ </description>\r
<optionNames>-c</optionNames>\r
<furtherDetails>prog_docs/probcons.pdf</furtherDetails>\r
<defaultValue>2</defaultValue>\r
- <validValue>\r
- <type>Integer</type>\r
+ <validValue>\r
+ <type>Integer</type>\r
<min>0</min>\r
<max>5</max>\r
</validValue>\r
id = str.nextToken();\r
// PROBCONS output clustal formatted file with not mention\r
// of CLUSTAL (:-))\r
- if (id.equals("CLUSTAL") || id.equals("PROBCONS")) {\r
+ if (id.equals("CLUSTAL") || id.equals("PROBCONS") || id.equals("MSAPROBS")) {\r
flag = true;\r
} else {\r
if (flag) {\r
* Probcons\r
*/\r
Probcons,\r
+\r
+ /**\r
+ * MSAprobs\r
+ */\r
+ MSAprobs,\r
+\r
+ /**\r
+ * GLprobs\r
+ */\r
+ GLprobs,\r
+\r
/**\r
* Jpred\r
*/\r
implement a web service which confirms to it within a webservices source \r
folder. \r
\r
-12) Register web service in WEB-INF/ web.xml and sun-jaxws.xml\r
+12) Register web service in WEB-INF/web.xml and WEB-INF/sun-jaxws.xml\r
\r
13) Add generated wsdl to wsbuild.xml ant script to generate the stubs\r
\r
--- /dev/null
+/* Copyright (c) 2011 Peter Troshin\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
+ * \r
+ * This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ * Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ * License for more details.\r
+ * \r
+ * A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
+\r
+package compbio.runner.msa;\r
+\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.util.Arrays;\r
+import java.util.List;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
+import compbio.engine.client.PipedExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.runner.RunnerUtil;\r
+\r
+public class GLprobs extends SkeletalExecutable<GLprobs>\r
+ implements\r
+ PipedExecutable<GLprobs> {\r
+\r
+ private static Logger log = Logger.getLogger(GLprobs.class);\r
+\r
+ private final static String ANNOTATION = "annotation.txt";\r
+\r
+ public static final String KEY_VALUE_SEPARATOR = " ";\r
+\r
+ /**\r
+ */\r
+ public GLprobs() {\r
+ addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION));\r
+ /*\r
+ * Could either have probabilities or the alignment, but not both "-t",\r
+ * "probabilities"\r
+ */\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Alignment getResults(String workDirectory)\r
+ throws ResultNotAvailableException {\r
+ try {\r
+ return RunnerUtil.readClustalFile(workDirectory, getOutput());\r
+ } catch (FileNotFoundException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (IOException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (UnknownFileFormatException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (NullPointerException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public List<String> getCreatedFiles() {\r
+ return Arrays.asList(getOutput(), ANNOTATION, getError());\r
+ }\r
+\r
+ @Override\r
+ public GLprobs setInput(String inFile) {\r
+ String input = getInput();\r
+ super.setInput(inFile);\r
+ // TODO replace with setLast\r
+ cbuilder.setParam(inFile);\r
+ return this;\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Class<GLprobs> getType() {\r
+ return (Class<GLprobs>) this.getClass();\r
+ }\r
+}\r
--- /dev/null
+/* Copyright (c) 2011 Peter Troshin\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
+ * \r
+ * This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ * Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ * License for more details.\r
+ * \r
+ * A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
+\r
+package compbio.runner.msa;\r
+\r
+import java.io.FileNotFoundException;\r
+import java.io.IOException;\r
+import java.util.Arrays;\r
+import java.util.List;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.UnknownFileFormatException;\r
+import compbio.engine.client.PipedExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.runner.RunnerUtil;\r
+\r
+public class MSAprobs extends SkeletalExecutable<MSAprobs>\r
+ implements\r
+ PipedExecutable<MSAprobs> {\r
+\r
+ private static Logger log = Logger.getLogger(MSAprobs.class);\r
+\r
+ private final static String ANNOTATION = "annotation.txt";\r
+\r
+ public static final String KEY_VALUE_SEPARATOR = " ";\r
+\r
+ /**\r
+ */\r
+ public MSAprobs() {\r
+ addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION));\r
+ /*\r
+ * Could either have probabilities or the alignment, but not both "-t",\r
+ * "probabilities"\r
+ */\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Alignment getResults(String workDirectory)\r
+ throws ResultNotAvailableException {\r
+ try {\r
+ return RunnerUtil.readClustalFile(workDirectory, getOutput());\r
+ } catch (FileNotFoundException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (IOException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (UnknownFileFormatException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ } catch (NullPointerException e) {\r
+ log.error(e.getMessage(), e.getCause());\r
+ throw new ResultNotAvailableException(e);\r
+ }\r
+ }\r
+\r
+ @Override\r
+ public List<String> getCreatedFiles() {\r
+ return Arrays.asList(getOutput(), ANNOTATION, getError());\r
+ }\r
+\r
+ @Override\r
+ public MSAprobs setInput(String inFile) {\r
+ String input = getInput();\r
+ super.setInput(inFile);\r
+ // TODO replace with setLast\r
+ cbuilder.setParam(inFile);\r
+ return this;\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Class<MSAprobs> getType() {\r
+ return (Class<MSAprobs>) this.getClass();\r
+ }\r
+}\r
align_services.add(Services.MafftWS);\r
align_services.add(Services.MuscleWS);\r
align_services.add(Services.ProbconsWS);\r
+ align_services.add(Services.MSAprobsWS);\r
+ align_services.add(Services.GLprobsWS);\r
align_services.add(Services.TcoffeeWS);\r
Category alignment = new Category(CATEGORY_ALIGNMENT, align_services);\r
\r
import compbio.data.msa.SequenceAnnotation;\r
\r
/**\r
- * List of web services currently supported by JABAWS version 2\r
+ * List of web services currently supported by JABAWS version 2.1\r
* \r
*/\r
public enum Services {\r
* Make sure this class has NO references to runners or engines as it is a\r
* part of minimal client package. Such things should go into ServicesUtil\r
*/\r
- MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS, JpredWS, RNAalifoldWS;\r
+ MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, MSAprobsWS, GLprobsWS,\r
+ AAConWS, \r
+ JronnWS, DisemblWS, GlobPlotWS, IUPredWS, \r
+ JpredWS, \r
+ RNAalifoldWS;\r
\r
public static Services getService(String servName) {\r
servName = servName.trim().toLowerCase();\r
case MafftWS :\r
case MuscleWS :\r
case ProbconsWS :\r
+ case MSAprobsWS :\r
+ case GLprobsWS :\r
case TcoffeeWS :\r
return MsaWS.class;\r
-\r
default :\r
throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
}\r
case MafftWS :\r
case MuscleWS :\r
case ProbconsWS :\r
+ case MSAprobsWS :\r
+ case GLprobsWS :\r
case TcoffeeWS :\r
return JABAService.SERVICE_NAMESPACE;\r
default :\r
return MUSCLE_INFO.toString();\r
case ProbconsWS :\r
return PROBCONS_INFO.toString();\r
+ case MSAprobsWS :\r
+ return MSAPROBS_INFO.toString();\r
+ case GLprobsWS :\r
+ return GLPROBS_INFO.toString();\r
case TcoffeeWS :\r
return TCOFFEE_INFO.toString();\r
case RNAalifoldWS :\r
return MUSCLE_INFO.getReference();\r
case ProbconsWS :\r
return PROBCONS_INFO.getReference();\r
+ case MSAprobsWS :\r
+ return MSAPROBS_INFO.getReference();\r
+ case GLprobsWS :\r
+ return GLPROBS_INFO.getReference();\r
case TcoffeeWS :\r
return TCOFFEE_INFO.getReference();\r
case RNAalifoldWS :\r
return MUSCLE_INFO.getVersion();\r
case ProbconsWS :\r
return PROBCONS_INFO.getVersion();\r
+ case MSAprobsWS :\r
+ return MSAPROBS_INFO.getVersion();\r
+ case GLprobsWS :\r
+ return GLPROBS_INFO.getVersion();\r
case TcoffeeWS :\r
return TCOFFEE_INFO.getVersion();\r
case RNAalifoldWS :\r
return "alignment";\r
case ProbconsWS :\r
return "alignment";\r
+ case GLprobsWS :\r
+ return "alignment";\r
+ case MSAprobsWS :\r
+ return "alignment";\r
case TcoffeeWS :\r
return "alignment";\r
case RNAalifoldWS :\r
"in preparation", "1.0", "http://www.compbio.dundee.ac.uk/aacon");\r
\r
static ServiceInfo JPRED_INFO = new ServiceInfo(JpredWS,\r
- "Cole C, Barber JD, Barton GJ.reparation" + \r
- "The Jpred 3 secondary structure prediction server\n" +\r
- "Nucl. Acids Res. (2008) 36 (suppl 2): W197-W201., doi: 10.1093/nar/gkn238", \r
+ "Cole C, Barber JD, Barton GJ,\r\n" + \r
+ "\"The Jpred 3 secondary structure prediction server\"\r\n" +\r
+ "Nucl. Acids Res. 36 (suppl 2):W197 (2008)", \r
"3.0.3", "http://www.compbio.dundee.ac.uk/www-jpred");\r
\r
static ServiceInfo CLUSTAL_INFO = new ServiceInfo(ClustalWS,\r
- "Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, " + \r
- "Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG.\n" +\r
- "(2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.",\r
+ "Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG,\r\n" +\r
+ "\"Clustal W and Clustal X version 2.0\"\r\n" + \r
+ "Bioinformatics, 23: 2947 (2007)",\r
"2.0.12", "http://www.clustal.org/clustal2/");\r
\r
static ServiceInfo CLUSTAL_OMEGA_INFO = new ServiceInfo(ClustalOWS,\r
- "Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega\r\n"\r
- + "Fabian Sievers, Andreas Wilm, David Dineen, Toby J. Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D. Thompson, Desmond G. Higgins",\r
- "1.0.2", "http://www.clustal.org/omega");\r
+ "Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG,\r\n" +\r
+ "\"Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega\"\r\n" +\r
+ "Mol Syst Biol. 7:539 (2011)",\r
+ "1.0.2", "http://www.clustal.org/omega/");\r
\r
static ServiceInfo DISEMBL_INFO = new ServiceInfo(DisemblWS,\r
- "R. Linding, L.J. Jensen, F. Diella, P. Bork, T.J. Gibson and R.B. Russell\r\n"\r
- + "Protein disorder prediction: implications for structural proteomics\r\n"\r
- + "Structure Vol 11, Issue 11, 4 November 2003", "1.5",\r
- "http://dis.embl.de/");\r
+ "Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, and Russell RB,\r\n" +\r
+ "\"Protein disorder prediction: implications for structural proteomics\"\r\n" +\r
+ "Structure 11(11):1453 (2003)", \r
+ "1.5", "http://dis.embl.de/");\r
\r
static ServiceInfo GLOBPLOT_INFO = new ServiceInfo(GlobPlotWS,\r
- "Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson " +\r
- "'GlobPlot: exploring protein sequences for globularity and disorder.' " + \r
- "Nucl. Acids Res. (2003) 31 (13): 3701-3708. doi: 10.1093/nar/gkg519\r\n",\r
+ "Linding R, Russell RB, Neduva V and Gibson TJ,\r\n" +\r
+ "GlobPlot: exploring protein sequences for globularity and disorder\r\n" + \r
+ "Nucl. Acids Res. 31 (13):3701 (2003)",\r
"2.3", "http://globplot.embl.de/");\r
\r
static ServiceInfo IUPRED_INFO = new ServiceInfo(IUPredWS,\r
- "The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins\r\n"\r
- + "Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon\r\n"\r
- + "J. Mol. Biol. (2005) 347, 827-839.", "1.0",\r
- "http://iupred.enzim.hu/");\r
+ "Dosztányi Z, Csizmók V, Tompa P, and Simon I,\r\n" +\r
+ "\"The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins\"\r\n" +\r
+ "J. Mol. Biol. 347:827 (2005)", \r
+ "1.0", "http://iupred.enzim.hu/");\r
\r
static ServiceInfo TCOFFEE_INFO = new ServiceInfo(TcoffeeWS,\r
- "T-Coffee: A novel method for multiple sequence alignments "\r
- + "Notredame, Higgins, Heringa, JMB, 302 (205-217) 2000",\r
+ "Notredame C, Higgins DG, Heringa L,\r\n" +\r
+ "\"T-Coffee: A novel method for multiple sequence alignments\"\r\n" + \r
+ "JMB, 302(1):205 (2000)",\r
"8.99", "http://tcoffee.crg.cat/apps/tcoffee/index.html");\r
\r
static ServiceInfo MUSCLE_INFO = new ServiceInfo(MuscleWS,\r
- "Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.\r\n"\r
- + "doi:10.1093/nar/gkh340", "3.8.31",\r
- "http://www.drive5.com/muscle/");\r
+ "Edgar RC,\r\n"+ \r
+ "\"MUSCLE: multiple sequence alignment with high accuracy and high throughput\"\r\n" + \r
+ "Nucleic Acids Res. 32(5):1792 (2004)", \r
+ "3.8.31", "http://www.drive5.com/muscle/");\r
\r
static ServiceInfo PROBCONS_INFO = new ServiceInfo(ProbconsWS,\r
- "Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: "\r
- + "Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. ",\r
+ "Do CB, Mahabhashyam MSP, Brudno M, and Batzoglou S,\r\n" +\r
+ "\"PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment\"\r\n" + \r
+ "Genome Research 15:330 (2005)",\r
"1.12", "http://probcons.stanford.edu/");\r
\r
+ static ServiceInfo MSAPROBS_INFO = new ServiceInfo(MSAprobsWS,\r
+ "Liu Y, Schmidt B, and Maskell DL,\r\n" + \r
+ "\"MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities\"\r\n" +\r
+ "Bioinformatics, 26 (16):1958 (2010)",\r
+ "0.9.7", "http://msaprobs.sourceforge.net/");\r
+\r
+ static ServiceInfo GLPROBS_INFO = new ServiceInfo(GLprobsWS,\r
+ "Yongtao Ye, Siu-Ming Yiu, David W. Cheung, Qing Zhan, Hing-Fung Ting, Yadong Wang, Tak-Wah Lam,\r\n" +\r
+ "\"GLProbs: Aligning multiple sequences adaptively\"\r\n" + \r
+ "in progress (2013)",\r
+ "1.0", "http://sourceforge.net/projects/glprobs/");\r
+\r
static ServiceInfo JRONN_INFO = new ServiceInfo(JronnWS,\r
- "unpublished, original algorithm Yang,Z.R., Thomson,R., McMeil,P. and Esnouf,R.M. (2005) "\r
- + "RONN: the bio-basis function neural network technique applied to the "\r
- + "dectection of natively disordered regions in proteins Bioinformatics 21: 3369-3376\r\n",\r
+ "unpublished, original algorithm Yang ZR, Thomson R, McMeil P, and Esnouf RM,\r\n" + \r
+ "\"RONN: the bio-basis function neural network technique applied to the dectection of natively disordered regions in proteins\"\r\n" +\r
+ "Bioinformatics 21:3369 (2005)\r\n",\r
"1.0", "http://www.compbio.dundee.ac.uk/jabaws/");\r
\r
static ServiceInfo MAFFT_INFO = new ServiceInfo(MafftWS,\r
- "Katoh, Toh 2010 (Bioinformatics 26:1899-1900)\r\n"\r
- + "Parallelization of the MAFFT multiple sequence alignment program. ",\r
+ "Katoh K, Toh H,\r\n" +\r
+ "\"Parallelization of the MAFFT multiple sequence alignment program\"\r\n" + \r
+ "Bioinformatics 26:1899 (2010)",\r
"6.8.57", "http://mafft.cbrc.jp/alignment/software/");\r
\r
static ServiceInfo RNAALIFOLD_INFO = new ServiceInfo(RNAalifoldWS,\r
- "Ivo L. Hofacker, Martin Fekete, and Peter F. Stadler 'Secondary Structure Prediction"\r
- + " for Aligned RNA Sequences'. J.Mol.Biol. 319: 1059-1066, 2002. Stephan H. Bernhart,"\r
- + " Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, and Peter F. Stadler. "\r
- + "'RNAalifold: Improved consensus structure prediction for RNA alignments'. BMC Bioinformatics, 9:474, 2008.\r\n",\r
+ "Hofacker IL, Fekete M, and Stadler PV,\r\n"+ \r
+ "\"Secondary Structure Prediction for Aligned RNA Sequences\"\r\n" + \r
+ "J.Mol.Biol. 319:1059 (2002) and\r\n " + \r
+ "Bernhart SH, Hofacker IL Will S, Gruber AR, and Stadler PF,\r\n" + \r
+ "\"RNAalifold: Improved consensus structure prediction for RNA alignments\"\r\n" +\r
+ "BMC Bioinformatics, 9:474 (2008)\r\n",\r
"2.1.2", "http://www.tbi.univie.ac.at/RNA/");\r
\r
@XmlAccessorType(XmlAccessType.FIELD)\r
String reference;\r
String version;\r
String moreinfo;\r
- final static String jabaws_version = "2.5";\r
+ final static String jabaws_version = "2.1";\r
final static String line_delimiter = "\n";\r
\r
private ServiceInfo() {\r
import compbio.runner.msa.Mafft;\r
import compbio.runner.msa.Muscle;\r
import compbio.runner.msa.Probcons;\r
+import compbio.runner.msa.MSAprobs;\r
+import compbio.runner.msa.GLprobs;\r
import compbio.runner.msa.Tcoffee;\r
import compbio.runner.structure.RNAalifold;\r
\r
return null;\r
}\r
\r
- public static Class<? extends Executable<?>> getServiceImpl(Services service) {\r
+ private static Class<? extends Executable<?>> getServiceImpl(Services service) {\r
switch (service) {\r
case AAConWS :\r
return AACon.class;\r
return Tcoffee.class;\r
case ProbconsWS :\r
return Probcons.class;\r
+ case MSAprobsWS :\r
+ return MSAprobs.class;\r
+ case GLprobsWS :\r
+ return GLprobs.class;\r
case DisemblWS :\r
return Disembl.class;\r
case GlobPlotWS :\r
--- /dev/null
+/* Copyright (c) 2011 Peter Troshin\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
+ * \r
+ * This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ * Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ * License for more details.\r
+ * \r
+ * A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
+\r
+package compbio.ws.server;\r
+\r
+import java.io.File;\r
+import java.util.List;\r
+\r
+import javax.jws.WebService;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.msa.JABAService;\r
+import compbio.data.msa.MsaWS;\r
+import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Program;\r
+import compbio.engine.AsyncExecutor;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.engine.client.EngineUtil;\r
+import compbio.metadata.ChunkHolder;\r
+import compbio.metadata.JobStatus;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.Limit;\r
+import compbio.metadata.LimitsManager;\r
+import compbio.metadata.Option;\r
+import compbio.metadata.Preset;\r
+import compbio.metadata.PresetManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
+import compbio.metadata.WrongParameterException;\r
+import compbio.runner.RunnerUtil;\r
+import compbio.runner.msa.GLprobs;\r
+\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "GLprobsWS")\r
+public class GLprobsWS implements MsaWS<GLprobs> {\r
+\r
+ private static Logger log = Logger.getLogger(GLprobsWS.class);\r
+\r
+ private static final RunnerConfig<GLprobs> GLprobsOptions = RunnerUtil.getSupportedOptions(GLprobs.class);\r
+ private static final LimitsManager<GLprobs> limitMan = EngineUtil.getLimits(new GLprobs().getType());\r
+\r
+ @Override\r
+ public String align(List<FastaSequence> sequences)\r
+ throws JobSubmissionException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<GLprobs> confGLprobs = init(sequences);\r
+ return WSUtil.align(sequences, confGLprobs, log, "align", getLimit(""));\r
+ }\r
+\r
+ ConfiguredExecutable<GLprobs> init(List<FastaSequence> dataSet)\r
+ throws JobSubmissionException {\r
+ GLprobs GLprobs = new GLprobs();\r
+ GLprobs.setInput(SkeletalExecutable.INPUT);\r
+ GLprobs.setOutput(SkeletalExecutable.OUTPUT);\r
+ GLprobs.setError(SkeletalExecutable.ERROR);\r
+ return Configurator.configureExecutable(GLprobs, dataSet);\r
+ }\r
+\r
+ @Override\r
+ public String customAlign(List<FastaSequence> sequences,\r
+ List<Option<GLprobs>> options) throws JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<GLprobs> confGLprobs = init(sequences);\r
+ List<String> params = WSUtil.getCommands(options, GLprobs.KEY_VALUE_SEPARATOR);\r
+ log.info("Setting parameters:" + params);\r
+ confGLprobs.addParameters(params);\r
+ return WSUtil.align(sequences, confGLprobs, log, "customAlign",getLimit(""));\r
+ }\r
+\r
+ @Override\r
+ public String presetAlign(List<FastaSequence> sequences,\r
+ Preset<GLprobs> preset) throws JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ if (preset == null) {\r
+ throw new WrongParameterException("Preset must be provided!");\r
+ }\r
+ ConfiguredExecutable<GLprobs> confGLprobs = init(sequences);\r
+ confGLprobs.addParameters(preset.getOptions());\r
+ Limit<GLprobs> limit = getLimit(preset.getName());\r
+ return WSUtil.align(sequences, confGLprobs, log, "presetAlign", limit);\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
+ WSUtil.validateJobId(jobId);\r
+ AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+ ConfiguredExecutable<GLprobs> GLprobs = (ConfiguredExecutable<GLprobs>) asyncEngine.getResults(jobId);\r
+ Alignment al = GLprobs.getResults();\r
+ return new Alignment (al.getSequences(), Program.GLprobs, '-');\r
+ }\r
+\r
+ @Override\r
+ public Limit<GLprobs> getLimit(String presetName) {\r
+ if (limitMan == null) {\r
+ // Limit is not defined\r
+ return null;\r
+ }\r
+ return limitMan.getLimitByName(presetName);\r
+ }\r
+\r
+ @Override\r
+ public LimitsManager<GLprobs> getLimits() {\r
+ return limitMan;\r
+ }\r
+\r
+ @Override\r
+ public ChunkHolder pullExecStatistics(String jobId, long position) {\r
+ WSUtil.validateJobId(jobId);\r
+ // TODO check if output is the one to return\r
+ String file = Configurator.getWorkDirectory(jobId) + File.separator + new GLprobs().getError();\r
+ return WSUtil.pullFile(file, position);\r
+ }\r
+\r
+ @Override\r
+ public boolean cancelJob(String jobId) {\r
+ WSUtil.validateJobId(jobId);\r
+ return WSUtil.cancelJob(jobId);\r
+ }\r
+\r
+ @Override\r
+ public JobStatus getJobStatus(String jobId) {\r
+ WSUtil.validateJobId(jobId);\r
+ return WSUtil.getJobStatus(jobId);\r
+ }\r
+\r
+ @Override\r
+ public PresetManager<GLprobs> getPresets() {\r
+ return null;\r
+ }\r
+\r
+ @Override\r
+ public RunnerConfig<GLprobs> getRunnerOptions() {\r
+ return GLprobsOptions;\r
+ }\r
+\r
+}\r
--- /dev/null
+/* Copyright (c) 2011 Peter Troshin\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
+ * \r
+ * This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ * Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ * License for more details.\r
+ * \r
+ * A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
+\r
+package compbio.ws.server;\r
+\r
+import java.io.File;\r
+import java.util.List;\r
+\r
+import javax.jws.WebService;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.msa.JABAService;\r
+import compbio.data.msa.MsaWS;\r
+import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.Program;\r
+import compbio.engine.AsyncExecutor;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.SkeletalExecutable;\r
+import compbio.engine.client.EngineUtil;\r
+import compbio.metadata.ChunkHolder;\r
+import compbio.metadata.JobStatus;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.Limit;\r
+import compbio.metadata.LimitsManager;\r
+import compbio.metadata.Option;\r
+import compbio.metadata.Preset;\r
+import compbio.metadata.PresetManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
+import compbio.metadata.WrongParameterException;\r
+import compbio.runner.RunnerUtil;\r
+import compbio.runner.msa.MSAprobs;\r
+\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "MSAprobsWS")\r
+public class MSAprobsWS implements MsaWS<MSAprobs> {\r
+\r
+ private static Logger log = Logger.getLogger(MSAprobsWS.class);\r
+\r
+ private static final RunnerConfig<MSAprobs> MSAprobsOptions = RunnerUtil.getSupportedOptions(MSAprobs.class);\r
+ private static final LimitsManager<MSAprobs> limitMan = EngineUtil.getLimits(new MSAprobs().getType());\r
+\r
+ @Override\r
+ public String align(List<FastaSequence> sequences)\r
+ throws JobSubmissionException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<MSAprobs> confMSAprobs = init(sequences);\r
+ return WSUtil.align(sequences, confMSAprobs, log, "align", getLimit(""));\r
+ }\r
+\r
+ ConfiguredExecutable<MSAprobs> init(List<FastaSequence> dataSet)\r
+ throws JobSubmissionException {\r
+ MSAprobs MSAprobs = new MSAprobs();\r
+ MSAprobs.setInput(SkeletalExecutable.INPUT);\r
+ MSAprobs.setOutput(SkeletalExecutable.OUTPUT);\r
+ MSAprobs.setError(SkeletalExecutable.ERROR);\r
+ return Configurator.configureExecutable(MSAprobs, dataSet);\r
+ }\r
+\r
+ @Override\r
+ public String customAlign(List<FastaSequence> sequences,\r
+ List<Option<MSAprobs>> options) throws JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<MSAprobs> confMSAprobs = init(sequences);\r
+ List<String> params = WSUtil.getCommands(options, MSAprobs.KEY_VALUE_SEPARATOR);\r
+ log.info("Setting parameters:" + params);\r
+ confMSAprobs.addParameters(params);\r
+ return WSUtil.align(sequences, confMSAprobs, log, "customAlign",getLimit(""));\r
+ }\r
+\r
+ @Override\r
+ public String presetAlign(List<FastaSequence> sequences,\r
+ Preset<MSAprobs> preset) throws JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ if (preset == null) {\r
+ throw new WrongParameterException("Preset must be provided!");\r
+ }\r
+ ConfiguredExecutable<MSAprobs> confMSAprobs = init(sequences);\r
+ confMSAprobs.addParameters(preset.getOptions());\r
+ Limit<MSAprobs> limit = getLimit(preset.getName());\r
+ return WSUtil.align(sequences, confMSAprobs, log, "presetAlign", limit);\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
+ WSUtil.validateJobId(jobId);\r
+ AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+ ConfiguredExecutable<MSAprobs> MSAprobs = (ConfiguredExecutable<MSAprobs>) asyncEngine.getResults(jobId);\r
+ Alignment al = MSAprobs.getResults();\r
+ return new Alignment (al.getSequences(), Program.MSAprobs, '-');\r
+ }\r
+\r
+ @Override\r
+ public Limit<MSAprobs> getLimit(String presetName) {\r
+ if (limitMan == null) {\r
+ // Limit is not defined\r
+ return null;\r
+ }\r
+ return limitMan.getLimitByName(presetName);\r
+ }\r
+\r
+ @Override\r
+ public LimitsManager<MSAprobs> getLimits() {\r
+ return limitMan;\r
+ }\r
+\r
+ @Override\r
+ public ChunkHolder pullExecStatistics(String jobId, long position) {\r
+ WSUtil.validateJobId(jobId);\r
+ // TODO check if output is the one to return\r
+ String file = Configurator.getWorkDirectory(jobId) + File.separator + new MSAprobs().getError();\r
+ return WSUtil.pullFile(file, position);\r
+ }\r
+\r
+ @Override\r
+ public boolean cancelJob(String jobId) {\r
+ WSUtil.validateJobId(jobId);\r
+ return WSUtil.cancelJob(jobId);\r
+ }\r
+\r
+ @Override\r
+ public JobStatus getJobStatus(String jobId) {\r
+ WSUtil.validateJobId(jobId);\r
+ return WSUtil.getJobStatus(jobId);\r
+ }\r
+\r
+ @Override\r
+ public PresetManager<MSAprobs> getPresets() {\r
+ return null;\r
+ }\r
+\r
+ @Override\r
+ public RunnerConfig<MSAprobs> getRunnerOptions() {\r
+ return MSAprobsOptions;\r
+ }\r
+\r
+}\r
<xs:enumeration value="Muscle"/>
<xs:enumeration value="Tcoffee"/>
<xs:enumeration value="Probcons"/>
+ <xs:enumeration value="MSAprobs"/>
+ <xs:enumeration value="GLprobs"/>
<xs:enumeration value="Jpred"/>
</xs:restriction>
</xs:simpleType>
--- /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 Metro/2.1 (branches/2.1-6728; 2011-02-03T14:14:58+0000) JAXWS-RI/2.2.3 JAXWS/2.2. -->
+<definitions targetNamespace="http://msa.data.compbio/01/01/2010/" name="GLprobsWS" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:wsp="http://www.w3.org/ns/ws-policy" xmlns:tns="http://msa.data.compbio/01/01/2010/" 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/01/01/2010/" schemaLocation="GLprobsWS_schema1.xsd"/>
+ </xsd:schema>
+ </types>
+ <message name="align">
+ <part name="parameters" element="tns:align"/>
+ </message>
+ <message name="alignResponse">
+ <part name="parameters" element="tns:alignResponse"/>
+ </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="presetAlign">
+ <part name="parameters" element="tns:presetAlign"/>
+ </message>
+ <message name="presetAlignResponse">
+ <part name="parameters" element="tns:presetAlignResponse"/>
+ </message>
+ <message name="WrongParameterException">
+ <part name="fault" element="tns:WrongParameterException"/>
+ </message>
+ <message name="customAlign">
+ <part name="parameters" element="tns:customAlign"/>
+ </message>
+ <message name="customAlignResponse">
+ <part name="parameters" element="tns:customAlignResponse"/>
+ </message>
+ <message name="getResult">
+ <part name="parameters" element="tns:getResult"/>
+ </message>
+ <message name="getResultResponse">
+ <part name="parameters" element="tns:getResultResponse"/>
+ </message>
+ <message name="ResultNotAvailableException">
+ <part name="fault" element="tns:ResultNotAvailableException"/>
+ </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="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
+ </message>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ </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="getPresets">
+ <part name="parameters" element="tns:getPresets"/>
+ </message>
+ <message name="getPresetsResponse">
+ <part name="parameters" element="tns:getPresetsResponse"/>
+ </message>
+ <portType name="MsaWS">
+ <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="presetAlign">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignRequest" message="tns:presetAlign"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignResponse" message="tns:presetAlignResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/LimitExceededException"/>
+ <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/JobSubmissionException"/>
+ <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/WrongParameterException"/>
+ </operation>
+ <operation name="customAlign">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignRequest" message="tns:customAlign"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignResponse" message="tns:customAlignResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/LimitExceededException"/>
+ <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="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="cancelJob">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobResponse" message="tns:cancelJobResponse"/>
+ </operation>
+ <operation name="getJobStatus">
+ <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>
+ <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="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="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>
+ </portType>
+ <binding name="GLprobsWSPortBinding" type="tns:MsaWS">
+ <soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
+ <operation name="align">
+ <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="presetAlign">
+ <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="customAlign">
+ <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="getResult">
+ <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="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="pullExecStatistics">
+ <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>
+ <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="getPresets">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ </binding>
+ <service name="GLprobsWS">
+ <port name="GLprobsWSPort" binding="tns:GLprobsWSPortBinding">
+ <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/01/01/2010/" xmlns:tns="http://msa.data.compbio/01/01/2010/" 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="align" type="tns:align"/>
+
+ <xs:element name="alignResponse" type="tns:alignResponse"/>
+
+ <xs:element name="cancelJob" type="tns:cancelJob"/>
+
+ <xs:element name="cancelJobResponse" type="tns:cancelJobResponse"/>
+
+ <xs:element name="customAlign" type="tns:customAlign"/>
+
+ <xs:element name="customAlignResponse" type="tns:customAlignResponse"/>
+
+ <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="getResult" type="tns:getResult"/>
+
+ <xs:element name="getResultResponse" type="tns:getResultResponse"/>
+
+ <xs:element name="getRunnerOptions" type="tns:getRunnerOptions"/>
+
+ <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="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"/>
+ </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:string" minOccurs="0"/>
+ <xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
+ </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="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"/>
+ <xs:element name="max" type="xs:string" minOccurs="0"/>
+ <xs:element name="min" 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">
+ <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="jpredAlignment">
+ <xs:complexContent>
+ <xs:extension base="tns:alignment">
+ <xs:sequence/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+
+ <xs:complexType name="ResultNotAvailableException">
+ <xs:sequence>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <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="align">
+ <xs:sequence>
+ <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="alignResponse">
+ <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="customAlign">
+ <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="customAlignResponse">
+ <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="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:element name="chunk" type="xs:string" minOccurs="0"/>
+ <xs:element name="position" type="xs:long"/>
+ </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: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="presetAlignResponse">
+ <xs:sequence>
+ <xs:element name="return" type="xs:string" minOccurs="0"/>
+ </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="runnerClassName" type="xs:string"/>
+ <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
+ </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: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: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="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:simpleType name="type">
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="Integer"/>
+ <xs:enumeration value="Float"/>
+ </xs:restriction>
+ </xs:simpleType>
+
+ <xs:simpleType name="program">
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="CLUSTAL"/>
+ <xs:enumeration value="ClustalO"/>
+ <xs:enumeration value="Mafft"/>
+ <xs:enumeration value="Muscle"/>
+ <xs:enumeration value="Tcoffee"/>
+ <xs:enumeration value="Probcons"/>
+ <xs:enumeration value="MSAprobs"/>
+ <xs:enumeration value="GLprobs"/>
+ <xs:enumeration value="Jpred"/>
+ </xs:restriction>
+ </xs:simpleType>
+
+ <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:schema>
+
<xs:enumeration value="Muscle"/>
<xs:enumeration value="Tcoffee"/>
<xs:enumeration value="Probcons"/>
+ <xs:enumeration value="MSAprobs"/>
+ <xs:enumeration value="GLprobs"/>
<xs:enumeration value="Jpred"/>
</xs:restriction>
</xs:simpleType>
--- /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 Metro/2.1 (branches/2.1-6728; 2011-02-03T14:14:58+0000) JAXWS-RI/2.2.3 JAXWS/2.2. -->
+<definitions targetNamespace="http://msa.data.compbio/01/01/2010/" name="MSAprobsWS" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:wsp="http://www.w3.org/ns/ws-policy" xmlns:tns="http://msa.data.compbio/01/01/2010/" 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/01/01/2010/" schemaLocation="MSAprobsWS_schema1.xsd"/>
+ </xsd:schema>
+ </types>
+ <message name="align">
+ <part name="parameters" element="tns:align"/>
+ </message>
+ <message name="alignResponse">
+ <part name="parameters" element="tns:alignResponse"/>
+ </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="presetAlign">
+ <part name="parameters" element="tns:presetAlign"/>
+ </message>
+ <message name="presetAlignResponse">
+ <part name="parameters" element="tns:presetAlignResponse"/>
+ </message>
+ <message name="WrongParameterException">
+ <part name="fault" element="tns:WrongParameterException"/>
+ </message>
+ <message name="customAlign">
+ <part name="parameters" element="tns:customAlign"/>
+ </message>
+ <message name="customAlignResponse">
+ <part name="parameters" element="tns:customAlignResponse"/>
+ </message>
+ <message name="getResult">
+ <part name="parameters" element="tns:getResult"/>
+ </message>
+ <message name="getResultResponse">
+ <part name="parameters" element="tns:getResultResponse"/>
+ </message>
+ <message name="ResultNotAvailableException">
+ <part name="fault" element="tns:ResultNotAvailableException"/>
+ </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="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
+ </message>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ </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="getPresets">
+ <part name="parameters" element="tns:getPresets"/>
+ </message>
+ <message name="getPresetsResponse">
+ <part name="parameters" element="tns:getPresetsResponse"/>
+ </message>
+ <portType name="MsaWS">
+ <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="presetAlign">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignRequest" message="tns:presetAlign"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignResponse" message="tns:presetAlignResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/LimitExceededException"/>
+ <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/JobSubmissionException"/>
+ <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/WrongParameterException"/>
+ </operation>
+ <operation name="customAlign">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignRequest" message="tns:customAlign"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignResponse" message="tns:customAlignResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/LimitExceededException"/>
+ <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="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="cancelJob">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobResponse" message="tns:cancelJobResponse"/>
+ </operation>
+ <operation name="getJobStatus">
+ <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>
+ <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="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="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>
+ </portType>
+ <binding name="MSAprobsWSPortBinding" type="tns:MsaWS">
+ <soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
+ <operation name="align">
+ <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="presetAlign">
+ <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="customAlign">
+ <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="getResult">
+ <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="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="pullExecStatistics">
+ <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>
+ <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="getPresets">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ </binding>
+ <service name="MSAprobsWS">
+ <port name="MSAprobsWSPort" binding="tns:MSAprobsWSPortBinding">
+ <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/01/01/2010/" xmlns:tns="http://msa.data.compbio/01/01/2010/" 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="align" type="tns:align"/>
+
+ <xs:element name="alignResponse" type="tns:alignResponse"/>
+
+ <xs:element name="cancelJob" type="tns:cancelJob"/>
+
+ <xs:element name="cancelJobResponse" type="tns:cancelJobResponse"/>
+
+ <xs:element name="customAlign" type="tns:customAlign"/>
+
+ <xs:element name="customAlignResponse" type="tns:customAlignResponse"/>
+
+ <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="getResult" type="tns:getResult"/>
+
+ <xs:element name="getResultResponse" type="tns:getResultResponse"/>
+
+ <xs:element name="getRunnerOptions" type="tns:getRunnerOptions"/>
+
+ <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="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"/>
+ </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:string" minOccurs="0"/>
+ <xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
+ </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="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"/>
+ <xs:element name="max" type="xs:string" minOccurs="0"/>
+ <xs:element name="min" 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">
+ <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="jpredAlignment">
+ <xs:complexContent>
+ <xs:extension base="tns:alignment">
+ <xs:sequence/>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+
+ <xs:complexType name="ResultNotAvailableException">
+ <xs:sequence>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <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="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:element name="chunk" type="xs:string" minOccurs="0"/>
+ <xs:element name="position" type="xs:long"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="customAlign">
+ <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="customAlignResponse">
+ <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="WrongParameterException">
+ <xs:sequence>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="align">
+ <xs:sequence>
+ <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="alignResponse">
+ <xs:sequence>
+ <xs:element name="return" type="xs:string" minOccurs="0"/>
+ </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="runnerClassName" type="xs:string"/>
+ <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
+ </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="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: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: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="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="presetAlign">
+ <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="presetAlignResponse">
+ <xs:sequence>
+ <xs:element name="return" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:simpleType name="type">
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="Integer"/>
+ <xs:enumeration value="Float"/>
+ </xs:restriction>
+ </xs:simpleType>
+
+ <xs:simpleType name="program">
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="CLUSTAL"/>
+ <xs:enumeration value="ClustalO"/>
+ <xs:enumeration value="Mafft"/>
+ <xs:enumeration value="Muscle"/>
+ <xs:enumeration value="Tcoffee"/>
+ <xs:enumeration value="Probcons"/>
+ <xs:enumeration value="MSAprobs"/>
+ <xs:enumeration value="GLprobs"/>
+ <xs:enumeration value="Jpred"/>
+ </xs:restriction>
+ </xs:simpleType>
+
+ <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:schema>
+
<xs:enumeration value="Muscle"/>
<xs:enumeration value="Tcoffee"/>
<xs:enumeration value="Probcons"/>
+ <xs:enumeration value="MSAprobs"/>
+ <xs:enumeration value="GLprobs"/>
<xs:enumeration value="Jpred"/>
</xs:restriction>
</xs:simpleType>
<xs:enumeration value="Muscle"/>
<xs:enumeration value="Tcoffee"/>
<xs:enumeration value="Probcons"/>
+ <xs:enumeration value="MSAprobs"/>
+ <xs:enumeration value="GLprobs"/>
<xs:enumeration value="Jpred"/>
</xs:restriction>
</xs:simpleType>
<xs:enumeration value="ClustalOWS"/>
<xs:enumeration value="TcoffeeWS"/>
<xs:enumeration value="ProbconsWS"/>
+ <xs:enumeration value="MSAprobsWS"/>
+ <xs:enumeration value="GLprobsWS"/>
<xs:enumeration value="AAConWS"/>
<xs:enumeration value="JronnWS"/>
<xs:enumeration value="DisemblWS"/>
<xs:enumeration value="Muscle"/>
<xs:enumeration value="Tcoffee"/>
<xs:enumeration value="Probcons"/>
+ <xs:enumeration value="MSAprobs"/>
+ <xs:enumeration value="GLprobs"/>
<xs:enumeration value="Jpred"/>
</xs:restriction>
</xs:simpleType>
--- /dev/null
+************************************************************************
+ MSAPROBS is a open-source protein multiple sequence alignment algorithm
+ based on pair hidden markov model and partition function postirior
+ probabilities. If any comments or problems, please contact
+ Liu Yongchao(liuy0039@ntu.edu.sg or nkcslyc@hotmail.com)
+*************************************************************************
+Usage:
+ msaprobs [OPTION]... [infile]...
+
+Description:
+ Align sequences in multi-FASTA format
+
+ -o, --outfile <string>
+ specify the output file name (STDOUT by default)
+ -num_threads <integer>
+ specify the number of threads used, and otherwise detect automatically
+ -clustalw
+ use CLUSTALW output format instead of FASTA format
+
+ -c, --consistency REPS
+ use 0 <= REPS <= 5 (default: 2) passes of consistency transformation
+
+ -ir, --iterative-refinement REPS
+ use 0 <= REPS <= 1000 (default: 100) passes of iterative-refinement
+
+ -v, --verbose
+ report progress while aligning (default: off)
+
+ -annot FILENAME
+ write annotation for multiple alignment to FILENAME
+
+ -a, --alignment-order
+ print sequences in alignment order rather than input order (default: off)
+ -version
+ print out version of MSAPROBS
+
--- /dev/null
+************************************************************************
+ MSAPROBS is a open-source protein multiple sequence alignment algorithm
+ based on pair hidden markov model and partition function postirior
+ probabilities. If any comments or problems, please contact
+ Liu Yongchao(liuy0039@ntu.edu.sg or nkcslyc@hotmail.com)
+*************************************************************************
+Usage:
+ msaprobs [OPTION]... [infile]...
+
+Description:
+ Align sequences in multi-FASTA format
+
+ -o, --outfile <string>
+ specify the output file name (STDOUT by default)
+ -num_threads <integer>
+ specify the number of threads used, and otherwise detect automatically
+ -clustalw
+ use CLUSTALW output format instead of FASTA format
+
+ -c, --consistency REPS
+ use 0 <= REPS <= 5 (default: 2) passes of consistency transformation
+
+ -ir, --iterative-refinement REPS
+ use 0 <= REPS <= 1000 (default: 10) passes of iterative-refinement
+
+ -v, --verbose
+ report progress while aligning (default: off)
+
+ -annot FILENAME
+ write annotation for multiple alignment to FILENAME
+
+ -a, --alignment-order
+ print sequences in alignment order rather than input order (default: off)
+ -version
+ print out version of MSAPROBS
+
build-server:
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/AAConWS.wsdl
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/ClustalWS.wsdl
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/DisemblWS.wsdl
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/GlobPlotWS.wsdl
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/IUPredWS.wsdl
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/IUPredWS_schema1.xsd
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/JpredWS.wsdl
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/JronnWS.wsdl
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MafftWS.wsdl
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MuscleWS.wsdl
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/RNAalifoldWS.wsdl
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/RNAalifoldWS_schema1.xsd
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/RegistryWS.wsdl
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/RegistryWS_schema1.xsd
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/TcoffeeWS.wsdl
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd
[wsgen] command line: wsgen -classpath /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/classes:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-beanutils-1.7.0.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-collections-3.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-lang-2.3.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-logging-1.1.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-annotations-1.0.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-ga-1.1.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-util-1.4.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/derby-10.8.2.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/displaytag-1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/displaytag-export-poi-1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/drmaa.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/itext-1.4.7.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/jstl-1.1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/log4j-1.2.15.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/poi-3.2-FINAL-20081019.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/standard-1.1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-api.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-rt.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-tools.jar -d /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/classes -Xendorsed -keep -wsdl -r /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource -s /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices -verbose compbio.ws.server.JpredWS
[wsgen] Note: ap round: 1
[wsgen] [ProcessedMethods Interface: compbio.data.msa.MsaWS<T>]
[wsgen] compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java
[wsgen] compbio/data/msa/jaxws/WrongParameterExceptionBean.java
[wsgen] Note: ap round: 2
+ [wsgen] command line: wsgen -classpath /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/classes:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-beanutils-1.7.0.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-collections-3.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-lang-2.3.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-logging-1.1.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-annotations-1.0.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-ga-1.1.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-util-1.4.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/derby-10.8.2.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/displaytag-1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/displaytag-export-poi-1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/drmaa.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/itext-1.4.7.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/jstl-1.1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/log4j-1.2.15.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/poi-3.2-FINAL-20081019.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/standard-1.1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-api.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-rt.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-tools.jar -d /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/classes -Xendorsed -keep -wsdl -r /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource -s /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices -verbose compbio.ws.server.MSAprobsWS
+ [wsgen] Note: ap round: 1
+ [wsgen] [ProcessedMethods Interface: compbio.data.msa.MsaWS<T>]
+ [wsgen] [should process method: align hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: true]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: align(java.util.List<compbio.data.sequence.FastaSequence>)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.Align]
+ [wsgen] [should process method: customAlign hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: true]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: customAlign(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAlign]
+ [wsgen] [should process method: presetAlign hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: true]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: presetAlign(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAlign]
+ [wsgen] [should process method: getResult hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: true]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: getResult(java.lang.String)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetResult]
+ [wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService]
+ [wsgen] [ProcessedMethods Interface: compbio.data.msa.JManagement]
+ [wsgen] [should process method: cancelJob hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: cancelJob(java.lang.String)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.CancelJob]
+ [wsgen] [should process method: getJobStatus hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: getJobStatus(java.lang.String)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetJobStatus]
+ [wsgen] [should process method: pullExecStatistics hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: pullExecStatistics(java.lang.String,long)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.PullExecStatistics]
+ [wsgen] [ProcessedMethods Interface: compbio.data.msa.Metadata<T>]
+ [wsgen] [should process method: getRunnerOptions hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: getRunnerOptions()]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetRunnerOptions]
+ [wsgen] [should process method: getPresets hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: getPresets()]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetPresets]
+ [wsgen] [should process method: getLimit hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: getLimit(java.lang.String)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimit]
+ [wsgen] [should process method: getLimits hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: getLimits()]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimits]
+ [wsgen] compbio/data/msa/jaxws/Align.java
+ [wsgen] compbio/data/msa/jaxws/AlignResponse.java
+ [wsgen] compbio/data/msa/jaxws/CancelJob.java
+ [wsgen] compbio/data/msa/jaxws/CancelJobResponse.java
+ [wsgen] compbio/data/msa/jaxws/CustomAlign.java
+ [wsgen] compbio/data/msa/jaxws/CustomAlignResponse.java
+ [wsgen] compbio/data/msa/jaxws/GetJobStatus.java
+ [wsgen] compbio/data/msa/jaxws/GetJobStatusResponse.java
+ [wsgen] compbio/data/msa/jaxws/GetLimit.java
+ [wsgen] compbio/data/msa/jaxws/GetLimitResponse.java
+ [wsgen] compbio/data/msa/jaxws/GetLimits.java
+ [wsgen] compbio/data/msa/jaxws/GetLimitsResponse.java
+ [wsgen] compbio/data/msa/jaxws/GetPresets.java
+ [wsgen] compbio/data/msa/jaxws/GetPresetsResponse.java
+ [wsgen] compbio/data/msa/jaxws/GetResult.java
+ [wsgen] compbio/data/msa/jaxws/GetResultResponse.java
+ [wsgen] compbio/data/msa/jaxws/GetRunnerOptions.java
+ [wsgen] compbio/data/msa/jaxws/GetRunnerOptionsResponse.java
+ [wsgen] compbio/data/msa/jaxws/JobSubmissionExceptionBean.java
+ [wsgen] compbio/data/msa/jaxws/LimitExceededExceptionBean.java
+ [wsgen] compbio/data/msa/jaxws/PresetAlign.java
+ [wsgen] compbio/data/msa/jaxws/PresetAlignResponse.java
+ [wsgen] compbio/data/msa/jaxws/PullExecStatistics.java
+ [wsgen] compbio/data/msa/jaxws/PullExecStatisticsResponse.java
+ [wsgen] compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java
+ [wsgen] compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java
+ [wsgen] compbio/data/msa/jaxws/WrongParameterExceptionBean.java
+ [wsgen] Note: ap round: 2
+ [wsgen] command line: wsgen -classpath /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/classes:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-beanutils-1.7.0.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-collections-3.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-lang-2.3.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-logging-1.1.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-annotations-1.0.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-ga-1.1.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-util-1.4.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/derby-10.8.2.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/displaytag-1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/displaytag-export-poi-1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/drmaa.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/itext-1.4.7.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/jstl-1.1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/log4j-1.2.15.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/poi-3.2-FINAL-20081019.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/standard-1.1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-api.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-rt.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-tools.jar -d /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/classes -Xendorsed -keep -wsdl -r /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource -s /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices -verbose compbio.ws.server.GLprobsWS
+ [wsgen] Note: ap round: 1
+ [wsgen] [ProcessedMethods Interface: compbio.data.msa.MsaWS<T>]
+ [wsgen] [should process method: align hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: true]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: align(java.util.List<compbio.data.sequence.FastaSequence>)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.Align]
+ [wsgen] [should process method: customAlign hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: true]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: customAlign(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAlign]
+ [wsgen] [should process method: presetAlign hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: true]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: presetAlign(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAlign]
+ [wsgen] [should process method: getResult hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: true]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: getResult(java.lang.String)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetResult]
+ [wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService]
+ [wsgen] [ProcessedMethods Interface: compbio.data.msa.JManagement]
+ [wsgen] [should process method: cancelJob hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: cancelJob(java.lang.String)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.CancelJob]
+ [wsgen] [should process method: getJobStatus hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: getJobStatus(java.lang.String)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetJobStatus]
+ [wsgen] [should process method: pullExecStatistics hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: pullExecStatistics(java.lang.String,long)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.PullExecStatistics]
+ [wsgen] [ProcessedMethods Interface: compbio.data.msa.Metadata<T>]
+ [wsgen] [should process method: getRunnerOptions hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: getRunnerOptions()]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetRunnerOptions]
+ [wsgen] [should process method: getPresets hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: getPresets()]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetPresets]
+ [wsgen] [should process method: getLimit hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: getLimit(java.lang.String)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimit]
+ [wsgen] [should process method: getLimits hasWebMethods: false ]
+ [wsgen] [endpointReferencesInterface: true]
+ [wsgen] [declaring class has WebSevice: false]
+ [wsgen] [returning: true]
+ [wsgen] [WrapperGen - method: getLimits()]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimits]
+ [wsgen] compbio/data/msa/jaxws/Align.java
+ [wsgen] compbio/data/msa/jaxws/AlignResponse.java
+ [wsgen] compbio/data/msa/jaxws/CancelJob.java
+ [wsgen] compbio/data/msa/jaxws/CancelJobResponse.java
+ [wsgen] compbio/data/msa/jaxws/CustomAlign.java
+ [wsgen] compbio/data/msa/jaxws/CustomAlignResponse.java
+ [wsgen] compbio/data/msa/jaxws/GetJobStatus.java
+ [wsgen] compbio/data/msa/jaxws/GetJobStatusResponse.java
+ [wsgen] compbio/data/msa/jaxws/GetLimit.java
+ [wsgen] compbio/data/msa/jaxws/GetLimitResponse.java
+ [wsgen] compbio/data/msa/jaxws/GetLimits.java
+ [wsgen] compbio/data/msa/jaxws/GetLimitsResponse.java
+ [wsgen] compbio/data/msa/jaxws/GetPresets.java
+ [wsgen] compbio/data/msa/jaxws/GetPresetsResponse.java
+ [wsgen] compbio/data/msa/jaxws/GetResult.java
+ [wsgen] compbio/data/msa/jaxws/GetResultResponse.java
+ [wsgen] compbio/data/msa/jaxws/GetRunnerOptions.java
+ [wsgen] compbio/data/msa/jaxws/GetRunnerOptionsResponse.java
+ [wsgen] compbio/data/msa/jaxws/JobSubmissionExceptionBean.java
+ [wsgen] compbio/data/msa/jaxws/LimitExceededExceptionBean.java
+ [wsgen] compbio/data/msa/jaxws/PresetAlign.java
+ [wsgen] compbio/data/msa/jaxws/PresetAlignResponse.java
+ [wsgen] compbio/data/msa/jaxws/PullExecStatistics.java
+ [wsgen] compbio/data/msa/jaxws/PullExecStatisticsResponse.java
+ [wsgen] compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java
+ [wsgen] compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java
+ [wsgen] compbio/data/msa/jaxws/WrongParameterExceptionBean.java
+ [wsgen] Note: ap round: 2
[wsgen] command line: wsgen -classpath /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/classes:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-beanutils-1.7.0.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-collections-3.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-lang-2.3.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-logging-1.1.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-annotations-1.0.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-ga-1.1.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-util-1.4.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/derby-10.8.2.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/displaytag-1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/displaytag-export-poi-1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/drmaa.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/itext-1.4.7.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/jstl-1.1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/log4j-1.2.15.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/poi-3.2-FINAL-20081019.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/standard-1.1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-api.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-rt.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-tools.jar -d /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/classes -Xendorsed -keep -wsdl -r /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource -s /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices -verbose compbio.ws.server.ClustalWS
[wsgen] Note: ap round: 1
[wsgen] [ProcessedMethods Interface: compbio.data.msa.MsaWS<T>]
[wsgen] Note: ap round: 2
BUILD SUCCESSFUL
-Total time: 8 seconds
+Total time: 10 seconds
<property name="muscle.wsdl" location="${wsdl.dir}/MuscleWS.wsdl" />\r
<property name="tcoffee.wsdl" location="${wsdl.dir}/TcoffeeWS.wsdl" />\r
<property name="mafft.wsdl" location="${wsdl.dir}/MafftWS.wsdl" />\r
+ <property name="glprobs.wsdl" location="${wsdl.dir}/GLprobsWS.wsdl" />\r
+ <property name="msaprobs.wsdl" location="${wsdl.dir}/MSAprobsWS.wsdl" />\r
+\r
<property name="disembl.wsdl" location="${wsdl.dir}/DisemblWS.wsdl" />\r
<property name="globplot.wsdl" location="${wsdl.dir}/GlobPlotWS.wsdl" />\r
<property name="iupred.wsdl" location="${wsdl.dir}/IUPredWS.wsdl" />\r
<property name="jronn.wsdl" location="${wsdl.dir}/JronnWS.wsdl" />\r
+\r
<property name="registry.wsdl" location="${wsdl.dir}/RegistryWS.wsdl" />\r
- <property name="rnaalifold.wsdl" location="${wsdl.dir}/RNAalifold.wsdl" /> \r
+ <property name="rnaalifold.wsdl" location="${wsdl.dir}/RNAalifold.wsdl" />\r
\r
<taskdef name="wsgen" onerror="report" classname="com.sun.tools.ws.ant.WsGen">\r
<classpath refid="project.classpath" />\r
<classpath refid="classes.path" />\r
<classpath refid="project.classpath" />\r
</wsgen>\r
+ <wsgen sei="compbio.ws.server.MSAprobsWS"\r
+ sourcedestdir="${basedir}/webservices"\r
+ destdir="${classes}"\r
+ resourcedestdir="${wsdl.dir}"\r
+ keep="true"\r
+ genwsdl="true"\r
+ extension="false"\r
+ xendorsed="true"\r
+ verbose="true">\r
+ <classpath refid="classes.path" />\r
+ <classpath refid="project.classpath" />\r
+ </wsgen>\r
+ <wsgen sei="compbio.ws.server.GLprobsWS"\r
+ sourcedestdir="${basedir}/webservices"\r
+ destdir="${classes}"\r
+ resourcedestdir="${wsdl.dir}"\r
+ keep="true"\r
+ genwsdl="true"\r
+ extension="false"\r
+ xendorsed="true"\r
+ verbose="true">\r
+ <classpath refid="classes.path" />\r
+ <classpath refid="project.classpath" />\r
+ </wsgen>\r
<wsgen sei="compbio.ws.server.ClustalWS"\r
sourcedestdir="${basedir}/webservices"\r
destdir="${classes}"\r
<include name="*.java" />\r
</fileset>\r
</delete>\r
+\r
<wsimport wsdl="${clustal.wsdl}"\r
sourcedestdir="${basedir}/webservices/"\r
keep="true" extension="false"\r
package="compbio.ws.client.stub" target="2.1"\r
quiet="false">\r
</wsimport>\r
+\r
<wsimport wsdl="${muscle.wsdl}"\r
sourcedestdir="${basedir}/webservices/"\r
keep="true" extension="false"\r
package="compbio.ws.client.stub" target="2.1"\r
quiet="false">\r
</wsimport>\r
+\r
<wsimport wsdl="${mafft.wsdl}"\r
sourcedestdir="${basedir}/webservices/"\r
keep="true" extension="false"\r
package="compbio.ws.client.stub" target="2.1"\r
quiet="false">\r
</wsimport>\r
+\r
<wsimport wsdl="${tcoffee.wsdl}"\r
sourcedestdir="${basedir}/webservices/"\r
keep="true" extension="false"\r
package="compbio.ws.client.stub" target="2.1"\r
quiet="false">\r
</wsimport>\r
+\r
<wsimport wsdl="${iupred.wsdl}"\r
sourcedestdir="${basedir}/webservices/"\r
keep="true" extension="false"\r
package="compbio.ws.client.stub" target="2.1"\r
quiet="false">\r
</wsimport>\r
+\r
<wsimport wsdl="${registry.wsdl}"\r
sourcedestdir="${basedir}/webservices/"\r
keep="true" extension="false"\r
package="compbio.ws.client.stub" target="2.1"\r
quiet="false">\r
</wsimport>\r
+\r
<wsimport wsdl="${rnaalifold.wsdl}"\r
sourcedestdir="${basedir}/webservices/"\r
keep="true" extension="false"\r
package="compbio.ws.client.stub" target="2.1"\r
quiet="false">\r
</wsimport>\r
- \r
+\r
</target>\r
\r
<!-- \r
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