From: Sasha Sherstnev Date: Tue, 24 Sep 2013 14:11:53 +0000 (+0100) Subject: Add all needed infrastructure for MSAprobs and GLprobs X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9dc05c5beb667f2cc7dfc11bc0cb013325a92b88;p=jabaws.git Add all needed infrastructure for MSAprobs and GLprobs --- diff --git a/WEB-INF/sun-jaxws.xml b/WEB-INF/sun-jaxws.xml index e8b759b..13d6fac 100644 --- a/WEB-INF/sun-jaxws.xml +++ b/WEB-INF/sun-jaxws.xml @@ -21,6 +21,12 @@ + + diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml index 22df95e..cec1884 100644 --- a/WEB-INF/web.xml +++ b/WEB-INF/web.xml @@ -133,6 +133,18 @@ + MSAprobsWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + + GLprobsWS + com.sun.xml.ws.transport.http.servlet.WSServlet + 1 + + + AAConWS com.sun.xml.ws.transport.http.servlet.WSServlet 1 @@ -250,6 +262,16 @@ + MSAprobsWS + /MSAprobsWS + + + + GLprobsWS + /GLprobsWS + + + AAConWS /AAConWS diff --git a/build.xml b/build.xml index 4fbafe9..af10a7e 100644 --- a/build.xml +++ b/build.xml @@ -19,7 +19,7 @@ - + diff --git a/conf/Executable.properties b/conf/Executable.properties index a592c3a..a4f1aa3 100644 --- a/conf/Executable.properties +++ b/conf/Executable.properties @@ -236,4 +236,20 @@ rnaalifold.parameters.file = conf/settings/RNAalifoldParameters.xml rnaalifold.limits.file = conf/settings/RNAalifoldLimits.xml rnaalifold.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M +########################################################################################### +# MSAProbs CONFIGURATION # +########################################################################################### +local.msaprobs.bin = binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs +cluster.msaprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/MSAProbs-0.9.7/MSAProbs/msaprobs +msaprobs.parameters.file = conf/settings/MSAprobsParameters.xml +msaprobs.limits.file = conf/settings/MSAprobsLimits.xml +msaprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M +########################################################################################### +# GLprobs CONFIGURATION # +########################################################################################### +local.glprobs.bin = binaries/src/GLProbs-1.0/glprobs +cluster.glprobs.bin = /homes/www-jws2/test-servers/tomcat7-jaba3/webapps/jabawsRNA/binaries/src/GLProbs-1.0/glprobs +glprobs.parameters.file = conf/settings/GLprobsParameters.xml +glprobs.limits.file = conf/settings/GLprobsLimits.xml +glprobs.cluster.settings = -P webservices -R y -l h_cpu=24:00:00 -l ram=6000M diff --git a/conf/settings/GLprobsLimits.xml b/conf/settings/GLprobsLimits.xml new file mode 100644 index 0000000..e29585a --- /dev/null +++ b/conf/settings/GLprobsLimits.xml @@ -0,0 +1,13 @@ + + + compbio.runner.msa.MSAprobs + + 2000 + 1000 + + + # LocalEngineExecutionLimit # + 30 + 500 + + diff --git a/conf/settings/GLprobsParameters.xml b/conf/settings/GLprobsParameters.xml new file mode 100644 index 0000000..ee18617 --- /dev/null +++ b/conf/settings/GLprobsParameters.xml @@ -0,0 +1,73 @@ + + + compbio.runner.msa.GLprobs + + + CLUSTAL format for output alignment + + CLUSTAL output format is used instead of the FASTA format + + -clustalw + prog_docs/glprobs.txt + + + + Another order of sequence in output alignment + + print sequences in alignment order rather than input order + + -a + --alignment-order + prog_docs/glprobs.txt + + + + + + passes of consistency transformation + + passes of consistency transformation + + -c + --consistency + prog_docs/glprobs.txt + 2 + + Integer + 0 + 5 + + + + + passes of consistency transformation + + number of passes of iterative-refinement + + -ir + --iterative-refinement + prog_docs/glprobs.txt + 100 + + Integer + 0 + 1000 + + + + + Number of CPUs + + Number of CPU used by msaprobs. + My default the number is equal to the total number of CPU on the system. + + -num_threads + prog_docs/glprobs.txt + 1 + + Integer + 1 + + + + diff --git a/conf/settings/GLprobsPresets.xml b/conf/settings/GLprobsPresets.xml new file mode 100644 index 0000000..c7d44f6 --- /dev/null +++ b/conf/settings/GLprobsPresets.xml @@ -0,0 +1,15 @@ + + + compbio.runner.msa.MSAprobs + + + working + + Working configuration + + + + + + + diff --git a/conf/settings/MSAprobsLimits.xml b/conf/settings/MSAprobsLimits.xml new file mode 100644 index 0000000..e29585a --- /dev/null +++ b/conf/settings/MSAprobsLimits.xml @@ -0,0 +1,13 @@ + + + compbio.runner.msa.MSAprobs + + 2000 + 1000 + + + # LocalEngineExecutionLimit # + 30 + 500 + + diff --git a/conf/settings/MSAprobsParameters.xml b/conf/settings/MSAprobsParameters.xml new file mode 100644 index 0000000..6ace32c --- /dev/null +++ b/conf/settings/MSAprobsParameters.xml @@ -0,0 +1,72 @@ + + + compbio.runner.msa.MSAprobs + + + CLUSTAL format for output alignment + + CLUSTAL output format is used instead of the FASTA format + + -clustalw + prog_docs/msaprobs.txt + + + + Another order of sequence in output alignment + + print sequences in alignment order rather than input order + + -a + --alignment-order + prog_docs/msaprobs.txt + + + + + + passes of consistency transformation + + passes of consistency transformation + + -c + --consistency + prog_docs/msaprobs.txt + 2 + + Integer + 0 + 5 + + + + + passes of consistency transformation + + number of passes of iterative-refinement + + -ir + --iterative-refinement + prog_docs/msaprobs.txt + 10 + + Integer + 0 + 1000 + + + + + Number of CPUs + + Number of CPU used by msaprobs. + My default the number is equal to the total number of CPU on the system. + + -num_threads + prog_docs/msaprobs.txt + 1 + + Integer + 1 + + + diff --git a/conf/settings/MSAprobsPresets.xml b/conf/settings/MSAprobsPresets.xml new file mode 100644 index 0000000..c7d44f6 --- /dev/null +++ b/conf/settings/MSAprobsPresets.xml @@ -0,0 +1,15 @@ + + + compbio.runner.msa.MSAprobs + + + working + + Working configuration + + + + + + + diff --git a/conf/settings/ProbconsParameters.xml b/conf/settings/ProbconsParameters.xml index c66cdcb..10caac1 100644 --- a/conf/settings/ProbconsParameters.xml +++ b/conf/settings/ProbconsParameters.xml @@ -23,85 +23,85 @@ @@ -111,44 +111,50 @@ aligned. This option is used in case the default parameters are not appropriate for the particular sequences being aligned; in general, this option is not recommended as it may lead to unstable alignment parameters. - + -pre prog_docs/probcons.pdf 0 - - Integer + + Integer 0 20 + Passes of iterative refinement - This specifies the number of iterations of iterative refinement to be performed. In each -stage of iterative refinement, the set of sequences in the alignment is randomly -partitioned into two groups. After projecting the alignments to these groups, the two -groups are realigned, resulting in an alignment whose objective score is guaranteed to be -at least that of the original alignment + + This specifies the number of iterations of iterative refinement to be performed. + In each stage of iterative refinement, the set of sequences in the alignment is + randomly partitioned into two groups. After projecting the alignments to these + groups, the two groups are realigned, resulting in an alignment whose objective + score is guaranteed to be at least that of the original alignment + -ir prog_docs/probcons.pdf - 100 - - Integer + 100 + + Integer 0 1000 + Passes of consistency transformation - Each pass applies one round of the consistency transformation on the set of sequences. - The consistency transformation is described in detail in the mentioned papers. In each - round, the aligner computes the consistency transformation for each pair of sequences - using all other sequences. The aligner then updates the posterior probability matrices of - the pairwise alignments. + + Each pass applies one round of the consistency transformation on the set of sequences. + The consistency transformation is described in detail in the mentioned papers. In each + round, the aligner computes the consistency transformation for each pair of sequences + using all other sequences. The aligner then updates the posterior probability matrices of + the pairwise alignments. + -c prog_docs/probcons.pdf 2 - - Integer + + Integer 0 5 diff --git a/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java b/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java index fc44c44..3856a1e 100644 --- a/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java +++ b/datamodel/compbio/data/sequence/ClustalAlignmentUtil.java @@ -104,7 +104,7 @@ public final class ClustalAlignmentUtil { id = str.nextToken(); // PROBCONS output clustal formatted file with not mention // of CLUSTAL (:-)) - if (id.equals("CLUSTAL") || id.equals("PROBCONS")) { + if (id.equals("CLUSTAL") || id.equals("PROBCONS") || id.equals("MSAPROBS")) { flag = true; } else { if (flag) { diff --git a/datamodel/compbio/data/sequence/Program.java b/datamodel/compbio/data/sequence/Program.java index 0a234a3..3c7570a 100644 --- a/datamodel/compbio/data/sequence/Program.java +++ b/datamodel/compbio/data/sequence/Program.java @@ -54,6 +54,17 @@ public enum Program { * Probcons */ Probcons, + + /** + * MSAprobs + */ + MSAprobs, + + /** + * GLprobs + */ + GLprobs, + /** * Jpred */ diff --git a/how_to_add_new_webservice.txt b/how_to_add_new_webservice.txt index 5825767..ebdd382 100644 --- a/how_to_add_new_webservice.txt +++ b/how_to_add_new_webservice.txt @@ -51,7 +51,7 @@ How To add a new executable. implement a web service which confirms to it within a webservices source folder. -12) Register web service in WEB-INF/ web.xml and sun-jaxws.xml +12) Register web service in WEB-INF/web.xml and WEB-INF/sun-jaxws.xml 13) Add generated wsdl to wsbuild.xml ant script to generate the stubs diff --git a/runner/compbio/runner/msa/GLprobs.java b/runner/compbio/runner/msa/GLprobs.java new file mode 100644 index 0000000..949461e --- /dev/null +++ b/runner/compbio/runner/msa/GLprobs.java @@ -0,0 +1,95 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ + +package compbio.runner.msa; + +import java.io.FileNotFoundException; +import java.io.IOException; +import java.util.Arrays; +import java.util.List; + +import org.apache.log4j.Logger; + +import compbio.data.sequence.Alignment; +import compbio.data.sequence.UnknownFileFormatException; +import compbio.engine.client.PipedExecutable; +import compbio.engine.client.SkeletalExecutable; +import compbio.metadata.ResultNotAvailableException; +import compbio.runner.RunnerUtil; + +public class GLprobs extends SkeletalExecutable + implements + PipedExecutable { + + private static Logger log = Logger.getLogger(GLprobs.class); + + private final static String ANNOTATION = "annotation.txt"; + + public static final String KEY_VALUE_SEPARATOR = " "; + + /** + */ + public GLprobs() { + addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION)); + /* + * Could either have probabilities or the alignment, but not both "-t", + * "probabilities" + */ + } + + @SuppressWarnings("unchecked") + @Override + public Alignment getResults(String workDirectory) + throws ResultNotAvailableException { + try { + return RunnerUtil.readClustalFile(workDirectory, getOutput()); + } catch (FileNotFoundException e) { + log.error(e.getMessage(), e.getCause()); + throw new ResultNotAvailableException(e); + } catch (IOException e) { + log.error(e.getMessage(), e.getCause()); + throw new ResultNotAvailableException(e); + } catch (UnknownFileFormatException e) { + log.error(e.getMessage(), e.getCause()); + throw new ResultNotAvailableException(e); + } catch (NullPointerException e) { + log.error(e.getMessage(), e.getCause()); + throw new ResultNotAvailableException(e); + } + } + + @Override + public List getCreatedFiles() { + return Arrays.asList(getOutput(), ANNOTATION, getError()); + } + + @Override + public GLprobs setInput(String inFile) { + String input = getInput(); + super.setInput(inFile); + // TODO replace with setLast + cbuilder.setParam(inFile); + return this; + } + + @SuppressWarnings("unchecked") + @Override + public Class getType() { + return (Class) this.getClass(); + } +} diff --git a/runner/compbio/runner/msa/MSAprobs.java b/runner/compbio/runner/msa/MSAprobs.java new file mode 100644 index 0000000..9264384 --- /dev/null +++ b/runner/compbio/runner/msa/MSAprobs.java @@ -0,0 +1,95 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ + +package compbio.runner.msa; + +import java.io.FileNotFoundException; +import java.io.IOException; +import java.util.Arrays; +import java.util.List; + +import org.apache.log4j.Logger; + +import compbio.data.sequence.Alignment; +import compbio.data.sequence.UnknownFileFormatException; +import compbio.engine.client.PipedExecutable; +import compbio.engine.client.SkeletalExecutable; +import compbio.metadata.ResultNotAvailableException; +import compbio.runner.RunnerUtil; + +public class MSAprobs extends SkeletalExecutable + implements + PipedExecutable { + + private static Logger log = Logger.getLogger(MSAprobs.class); + + private final static String ANNOTATION = "annotation.txt"; + + public static final String KEY_VALUE_SEPARATOR = " "; + + /** + */ + public MSAprobs() { + addParameters(Arrays.asList("-v", "-clustalw", "-annot", ANNOTATION)); + /* + * Could either have probabilities or the alignment, but not both "-t", + * "probabilities" + */ + } + + @SuppressWarnings("unchecked") + @Override + public Alignment getResults(String workDirectory) + throws ResultNotAvailableException { + try { + return RunnerUtil.readClustalFile(workDirectory, getOutput()); + } catch (FileNotFoundException e) { + log.error(e.getMessage(), e.getCause()); + throw new ResultNotAvailableException(e); + } catch (IOException e) { + log.error(e.getMessage(), e.getCause()); + throw new ResultNotAvailableException(e); + } catch (UnknownFileFormatException e) { + log.error(e.getMessage(), e.getCause()); + throw new ResultNotAvailableException(e); + } catch (NullPointerException e) { + log.error(e.getMessage(), e.getCause()); + throw new ResultNotAvailableException(e); + } + } + + @Override + public List getCreatedFiles() { + return Arrays.asList(getOutput(), ANNOTATION, getError()); + } + + @Override + public MSAprobs setInput(String inFile) { + String input = getInput(); + super.setInput(inFile); + // TODO replace with setLast + cbuilder.setParam(inFile); + return this; + } + + @SuppressWarnings("unchecked") + @Override + public Class getType() { + return (Class) this.getClass(); + } +} diff --git a/webservices/compbio/data/msa/Category.java b/webservices/compbio/data/msa/Category.java index fa9968b..8694d16 100644 --- a/webservices/compbio/data/msa/Category.java +++ b/webservices/compbio/data/msa/Category.java @@ -64,6 +64,8 @@ public class Category { align_services.add(Services.MafftWS); align_services.add(Services.MuscleWS); align_services.add(Services.ProbconsWS); + align_services.add(Services.MSAprobsWS); + align_services.add(Services.GLprobsWS); align_services.add(Services.TcoffeeWS); Category alignment = new Category(CATEGORY_ALIGNMENT, align_services); diff --git a/webservices/compbio/ws/client/Services.java b/webservices/compbio/ws/client/Services.java index 42d282e..6815e33 100644 --- a/webservices/compbio/ws/client/Services.java +++ b/webservices/compbio/ws/client/Services.java @@ -31,7 +31,7 @@ import compbio.data.msa.MsaWS; import compbio.data.msa.SequenceAnnotation; /** - * List of web services currently supported by JABAWS version 2 + * List of web services currently supported by JABAWS version 2.1 * */ public enum Services { @@ -39,7 +39,11 @@ public enum Services { * Make sure this class has NO references to runners or engines as it is a * part of minimal client package. Such things should go into ServicesUtil */ - MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS, JpredWS, RNAalifoldWS; + MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, MSAprobsWS, GLprobsWS, + AAConWS, + JronnWS, DisemblWS, GlobPlotWS, IUPredWS, + JpredWS, + RNAalifoldWS; public static Services getService(String servName) { servName = servName.trim().toLowerCase(); @@ -86,9 +90,10 @@ public enum Services { case MafftWS : case MuscleWS : case ProbconsWS : + case MSAprobsWS : + case GLprobsWS : case TcoffeeWS : return MsaWS.class; - default : throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!"); } @@ -110,6 +115,8 @@ public enum Services { case MafftWS : case MuscleWS : case ProbconsWS : + case MSAprobsWS : + case GLprobsWS : case TcoffeeWS : return JABAService.SERVICE_NAMESPACE; default : @@ -148,6 +155,10 @@ public enum Services { return MUSCLE_INFO.toString(); case ProbconsWS : return PROBCONS_INFO.toString(); + case MSAprobsWS : + return MSAPROBS_INFO.toString(); + case GLprobsWS : + return GLPROBS_INFO.toString(); case TcoffeeWS : return TCOFFEE_INFO.toString(); case RNAalifoldWS : @@ -181,6 +192,10 @@ public enum Services { return MUSCLE_INFO.getReference(); case ProbconsWS : return PROBCONS_INFO.getReference(); + case MSAprobsWS : + return MSAPROBS_INFO.getReference(); + case GLprobsWS : + return GLPROBS_INFO.getReference(); case TcoffeeWS : return TCOFFEE_INFO.getReference(); case RNAalifoldWS : @@ -214,6 +229,10 @@ public enum Services { return MUSCLE_INFO.getVersion(); case ProbconsWS : return PROBCONS_INFO.getVersion(); + case MSAprobsWS : + return MSAPROBS_INFO.getVersion(); + case GLprobsWS : + return GLPROBS_INFO.getVersion(); case TcoffeeWS : return TCOFFEE_INFO.getVersion(); case RNAalifoldWS : @@ -247,6 +266,10 @@ public enum Services { return "alignment"; case ProbconsWS : return "alignment"; + case GLprobsWS : + return "alignment"; + case MSAprobsWS : + return "alignment"; case TcoffeeWS : return "alignment"; case RNAalifoldWS : @@ -260,71 +283,90 @@ public enum Services { "in preparation", "1.0", "http://www.compbio.dundee.ac.uk/aacon"); static ServiceInfo JPRED_INFO = new ServiceInfo(JpredWS, - "Cole C, Barber JD, Barton GJ.reparation" + - "The Jpred 3 secondary structure prediction server\n" + - "Nucl. Acids Res. (2008) 36 (suppl 2): W197-W201., doi: 10.1093/nar/gkn238", + "Cole C, Barber JD, Barton GJ,\r\n" + + "\"The Jpred 3 secondary structure prediction server\"\r\n" + + "Nucl. Acids Res. 36 (suppl 2):W197 (2008)", "3.0.3", "http://www.compbio.dundee.ac.uk/www-jpred"); static ServiceInfo CLUSTAL_INFO = new ServiceInfo(ClustalWS, - "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.\n" + - "(2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.", + "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" + + "\"Clustal W and Clustal X version 2.0\"\r\n" + + "Bioinformatics, 23: 2947 (2007)", "2.0.12", "http://www.clustal.org/clustal2/"); static ServiceInfo CLUSTAL_OMEGA_INFO = new ServiceInfo(ClustalOWS, - "Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega\r\n" - + "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", - "1.0.2", "http://www.clustal.org/omega"); + "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" + + "\"Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega\"\r\n" + + "Mol Syst Biol. 7:539 (2011)", + "1.0.2", "http://www.clustal.org/omega/"); static ServiceInfo DISEMBL_INFO = new ServiceInfo(DisemblWS, - "R. Linding, L.J. Jensen, F. Diella, P. Bork, T.J. Gibson and R.B. Russell\r\n" - + "Protein disorder prediction: implications for structural proteomics\r\n" - + "Structure Vol 11, Issue 11, 4 November 2003", "1.5", - "http://dis.embl.de/"); + "Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, and Russell RB,\r\n" + + "\"Protein disorder prediction: implications for structural proteomics\"\r\n" + + "Structure 11(11):1453 (2003)", + "1.5", "http://dis.embl.de/"); static ServiceInfo GLOBPLOT_INFO = new ServiceInfo(GlobPlotWS, - "Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson " + - "'GlobPlot: exploring protein sequences for globularity and disorder.' " + - "Nucl. Acids Res. (2003) 31 (13): 3701-3708. doi: 10.1093/nar/gkg519\r\n", + "Linding R, Russell RB, Neduva V and Gibson TJ,\r\n" + + "GlobPlot: exploring protein sequences for globularity and disorder\r\n" + + "Nucl. Acids Res. 31 (13):3701 (2003)", "2.3", "http://globplot.embl.de/"); static ServiceInfo IUPRED_INFO = new ServiceInfo(IUPredWS, - "The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins\r\n" - + "Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon\r\n" - + "J. Mol. Biol. (2005) 347, 827-839.", "1.0", - "http://iupred.enzim.hu/"); + "Dosztányi Z, Csizmók V, Tompa P, and Simon I,\r\n" + + "\"The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins\"\r\n" + + "J. Mol. Biol. 347:827 (2005)", + "1.0", "http://iupred.enzim.hu/"); static ServiceInfo TCOFFEE_INFO = new ServiceInfo(TcoffeeWS, - "T-Coffee: A novel method for multiple sequence alignments " - + "Notredame, Higgins, Heringa, JMB, 302 (205-217) 2000", + "Notredame C, Higgins DG, Heringa L,\r\n" + + "\"T-Coffee: A novel method for multiple sequence alignments\"\r\n" + + "JMB, 302(1):205 (2000)", "8.99", "http://tcoffee.crg.cat/apps/tcoffee/index.html"); static ServiceInfo MUSCLE_INFO = new ServiceInfo(MuscleWS, - "Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.\r\n" - + "doi:10.1093/nar/gkh340", "3.8.31", - "http://www.drive5.com/muscle/"); + "Edgar RC,\r\n"+ + "\"MUSCLE: multiple sequence alignment with high accuracy and high throughput\"\r\n" + + "Nucleic Acids Res. 32(5):1792 (2004)", + "3.8.31", "http://www.drive5.com/muscle/"); static ServiceInfo PROBCONS_INFO = new ServiceInfo(ProbconsWS, - "Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: " - + "Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. ", + "Do CB, Mahabhashyam MSP, Brudno M, and Batzoglou S,\r\n" + + "\"PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment\"\r\n" + + "Genome Research 15:330 (2005)", "1.12", "http://probcons.stanford.edu/"); + static ServiceInfo MSAPROBS_INFO = new ServiceInfo(MSAprobsWS, + "Liu Y, Schmidt B, and Maskell DL,\r\n" + + "\"MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities\"\r\n" + + "Bioinformatics, 26 (16):1958 (2010)", + "0.9.7", "http://msaprobs.sourceforge.net/"); + + static ServiceInfo GLPROBS_INFO = new ServiceInfo(GLprobsWS, + "Yongtao Ye, Siu-Ming Yiu, David W. Cheung, Qing Zhan, Hing-Fung Ting, Yadong Wang, Tak-Wah Lam,\r\n" + + "\"GLProbs: Aligning multiple sequences adaptively\"\r\n" + + "in progress (2013)", + "1.0", "http://sourceforge.net/projects/glprobs/"); + static ServiceInfo JRONN_INFO = new ServiceInfo(JronnWS, - "unpublished, original algorithm Yang,Z.R., Thomson,R., McMeil,P. and Esnouf,R.M. (2005) " - + "RONN: the bio-basis function neural network technique applied to the " - + "dectection of natively disordered regions in proteins Bioinformatics 21: 3369-3376\r\n", + "unpublished, original algorithm Yang ZR, Thomson R, McMeil P, and Esnouf RM,\r\n" + + "\"RONN: the bio-basis function neural network technique applied to the dectection of natively disordered regions in proteins\"\r\n" + + "Bioinformatics 21:3369 (2005)\r\n", "1.0", "http://www.compbio.dundee.ac.uk/jabaws/"); static ServiceInfo MAFFT_INFO = new ServiceInfo(MafftWS, - "Katoh, Toh 2010 (Bioinformatics 26:1899-1900)\r\n" - + "Parallelization of the MAFFT multiple sequence alignment program. ", + "Katoh K, Toh H,\r\n" + + "\"Parallelization of the MAFFT multiple sequence alignment program\"\r\n" + + "Bioinformatics 26:1899 (2010)", "6.8.57", "http://mafft.cbrc.jp/alignment/software/"); static ServiceInfo RNAALIFOLD_INFO = new ServiceInfo(RNAalifoldWS, - "Ivo L. Hofacker, Martin Fekete, and Peter F. Stadler 'Secondary Structure Prediction" - + " for Aligned RNA Sequences'. J.Mol.Biol. 319: 1059-1066, 2002. Stephan H. Bernhart," - + " Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, and Peter F. Stadler. " - + "'RNAalifold: Improved consensus structure prediction for RNA alignments'. BMC Bioinformatics, 9:474, 2008.\r\n", + "Hofacker IL, Fekete M, and Stadler PV,\r\n"+ + "\"Secondary Structure Prediction for Aligned RNA Sequences\"\r\n" + + "J.Mol.Biol. 319:1059 (2002) and\r\n " + + "Bernhart SH, Hofacker IL Will S, Gruber AR, and Stadler PF,\r\n" + + "\"RNAalifold: Improved consensus structure prediction for RNA alignments\"\r\n" + + "BMC Bioinformatics, 9:474 (2008)\r\n", "2.1.2", "http://www.tbi.univie.ac.at/RNA/"); @XmlAccessorType(XmlAccessType.FIELD) @@ -333,7 +375,7 @@ public enum Services { String reference; String version; String moreinfo; - final static String jabaws_version = "2.5"; + final static String jabaws_version = "2.1"; final static String line_delimiter = "\n"; private ServiceInfo() { diff --git a/webservices/compbio/ws/client/ServicesUtil.java b/webservices/compbio/ws/client/ServicesUtil.java index 7084028..8f9bcdc 100644 --- a/webservices/compbio/ws/client/ServicesUtil.java +++ b/webservices/compbio/ws/client/ServicesUtil.java @@ -15,6 +15,8 @@ import compbio.runner.msa.ClustalW; import compbio.runner.msa.Mafft; import compbio.runner.msa.Muscle; import compbio.runner.msa.Probcons; +import compbio.runner.msa.MSAprobs; +import compbio.runner.msa.GLprobs; import compbio.runner.msa.Tcoffee; import compbio.runner.structure.RNAalifold; @@ -31,7 +33,7 @@ public class ServicesUtil { return null; } - public static Class> getServiceImpl(Services service) { + private static Class> getServiceImpl(Services service) { switch (service) { case AAConWS : return AACon.class; @@ -49,6 +51,10 @@ public class ServicesUtil { return Tcoffee.class; case ProbconsWS : return Probcons.class; + case MSAprobsWS : + return MSAprobs.class; + case GLprobsWS : + return GLprobs.class; case DisemblWS : return Disembl.class; case GlobPlotWS : diff --git a/webservices/compbio/ws/server/GLprobsWS.java b/webservices/compbio/ws/server/GLprobsWS.java new file mode 100644 index 0000000..91b048d --- /dev/null +++ b/webservices/compbio/ws/server/GLprobsWS.java @@ -0,0 +1,157 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ + +package compbio.ws.server; + +import java.io.File; +import java.util.List; + +import javax.jws.WebService; + +import org.apache.log4j.Logger; + +import compbio.data.msa.JABAService; +import compbio.data.msa.MsaWS; +import compbio.data.sequence.Alignment; +import compbio.data.sequence.FastaSequence; +import compbio.data.sequence.Program; +import compbio.engine.AsyncExecutor; +import compbio.engine.Configurator; +import compbio.engine.client.ConfiguredExecutable; +import compbio.engine.client.SkeletalExecutable; +import compbio.engine.client.EngineUtil; +import compbio.metadata.ChunkHolder; +import compbio.metadata.JobStatus; +import compbio.metadata.JobSubmissionException; +import compbio.metadata.Limit; +import compbio.metadata.LimitsManager; +import compbio.metadata.Option; +import compbio.metadata.Preset; +import compbio.metadata.PresetManager; +import compbio.metadata.ResultNotAvailableException; +import compbio.metadata.RunnerConfig; +import compbio.metadata.WrongParameterException; +import compbio.runner.RunnerUtil; +import compbio.runner.msa.GLprobs; + +@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "GLprobsWS") +public class GLprobsWS implements MsaWS { + + private static Logger log = Logger.getLogger(GLprobsWS.class); + + private static final RunnerConfig GLprobsOptions = RunnerUtil.getSupportedOptions(GLprobs.class); + private static final LimitsManager limitMan = EngineUtil.getLimits(new GLprobs().getType()); + + @Override + public String align(List sequences) + throws JobSubmissionException { + WSUtil.validateFastaInput(sequences); + ConfiguredExecutable confGLprobs = init(sequences); + return WSUtil.align(sequences, confGLprobs, log, "align", getLimit("")); + } + + ConfiguredExecutable init(List dataSet) + throws JobSubmissionException { + GLprobs GLprobs = new GLprobs(); + GLprobs.setInput(SkeletalExecutable.INPUT); + GLprobs.setOutput(SkeletalExecutable.OUTPUT); + GLprobs.setError(SkeletalExecutable.ERROR); + return Configurator.configureExecutable(GLprobs, dataSet); + } + + @Override + public String customAlign(List sequences, + List> options) throws JobSubmissionException, + WrongParameterException { + WSUtil.validateFastaInput(sequences); + ConfiguredExecutable confGLprobs = init(sequences); + List params = WSUtil.getCommands(options, GLprobs.KEY_VALUE_SEPARATOR); + log.info("Setting parameters:" + params); + confGLprobs.addParameters(params); + return WSUtil.align(sequences, confGLprobs, log, "customAlign",getLimit("")); + } + + @Override + public String presetAlign(List sequences, + Preset preset) throws JobSubmissionException, + WrongParameterException { + WSUtil.validateFastaInput(sequences); + if (preset == null) { + throw new WrongParameterException("Preset must be provided!"); + } + ConfiguredExecutable confGLprobs = init(sequences); + confGLprobs.addParameters(preset.getOptions()); + Limit limit = getLimit(preset.getName()); + return WSUtil.align(sequences, confGLprobs, log, "presetAlign", limit); + } + + @SuppressWarnings("unchecked") + @Override + public Alignment getResult(String jobId) throws ResultNotAvailableException { + WSUtil.validateJobId(jobId); + AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId); + ConfiguredExecutable GLprobs = (ConfiguredExecutable) asyncEngine.getResults(jobId); + Alignment al = GLprobs.getResults(); + return new Alignment (al.getSequences(), Program.GLprobs, '-'); + } + + @Override + public Limit getLimit(String presetName) { + if (limitMan == null) { + // Limit is not defined + return null; + } + return limitMan.getLimitByName(presetName); + } + + @Override + public LimitsManager getLimits() { + return limitMan; + } + + @Override + public ChunkHolder pullExecStatistics(String jobId, long position) { + WSUtil.validateJobId(jobId); + // TODO check if output is the one to return + String file = Configurator.getWorkDirectory(jobId) + File.separator + new GLprobs().getError(); + return WSUtil.pullFile(file, position); + } + + @Override + public boolean cancelJob(String jobId) { + WSUtil.validateJobId(jobId); + return WSUtil.cancelJob(jobId); + } + + @Override + public JobStatus getJobStatus(String jobId) { + WSUtil.validateJobId(jobId); + return WSUtil.getJobStatus(jobId); + } + + @Override + public PresetManager getPresets() { + return null; + } + + @Override + public RunnerConfig getRunnerOptions() { + return GLprobsOptions; + } + +} diff --git a/webservices/compbio/ws/server/MSAprobsWS.java b/webservices/compbio/ws/server/MSAprobsWS.java new file mode 100644 index 0000000..0f25069 --- /dev/null +++ b/webservices/compbio/ws/server/MSAprobsWS.java @@ -0,0 +1,157 @@ +/* Copyright (c) 2011 Peter Troshin + * + * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ + +package compbio.ws.server; + +import java.io.File; +import java.util.List; + +import javax.jws.WebService; + +import org.apache.log4j.Logger; + +import compbio.data.msa.JABAService; +import compbio.data.msa.MsaWS; +import compbio.data.sequence.Alignment; +import compbio.data.sequence.FastaSequence; +import compbio.data.sequence.Program; +import compbio.engine.AsyncExecutor; +import compbio.engine.Configurator; +import compbio.engine.client.ConfiguredExecutable; +import compbio.engine.client.SkeletalExecutable; +import compbio.engine.client.EngineUtil; +import compbio.metadata.ChunkHolder; +import compbio.metadata.JobStatus; +import compbio.metadata.JobSubmissionException; +import compbio.metadata.Limit; +import compbio.metadata.LimitsManager; +import compbio.metadata.Option; +import compbio.metadata.Preset; +import compbio.metadata.PresetManager; +import compbio.metadata.ResultNotAvailableException; +import compbio.metadata.RunnerConfig; +import compbio.metadata.WrongParameterException; +import compbio.runner.RunnerUtil; +import compbio.runner.msa.MSAprobs; + +@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "MSAprobsWS") +public class MSAprobsWS implements MsaWS { + + private static Logger log = Logger.getLogger(MSAprobsWS.class); + + private static final RunnerConfig MSAprobsOptions = RunnerUtil.getSupportedOptions(MSAprobs.class); + private static final LimitsManager limitMan = EngineUtil.getLimits(new MSAprobs().getType()); + + @Override + public String align(List sequences) + throws JobSubmissionException { + WSUtil.validateFastaInput(sequences); + ConfiguredExecutable confMSAprobs = init(sequences); + return WSUtil.align(sequences, confMSAprobs, log, "align", getLimit("")); + } + + ConfiguredExecutable init(List dataSet) + throws JobSubmissionException { + MSAprobs MSAprobs = new MSAprobs(); + MSAprobs.setInput(SkeletalExecutable.INPUT); + MSAprobs.setOutput(SkeletalExecutable.OUTPUT); + MSAprobs.setError(SkeletalExecutable.ERROR); + return Configurator.configureExecutable(MSAprobs, dataSet); + } + + @Override + public String customAlign(List sequences, + List> options) throws JobSubmissionException, + WrongParameterException { + WSUtil.validateFastaInput(sequences); + ConfiguredExecutable confMSAprobs = init(sequences); + List params = WSUtil.getCommands(options, MSAprobs.KEY_VALUE_SEPARATOR); + log.info("Setting parameters:" + params); + confMSAprobs.addParameters(params); + return WSUtil.align(sequences, confMSAprobs, log, "customAlign",getLimit("")); + } + + @Override + public String presetAlign(List sequences, + Preset preset) throws JobSubmissionException, + WrongParameterException { + WSUtil.validateFastaInput(sequences); + if (preset == null) { + throw new WrongParameterException("Preset must be provided!"); + } + ConfiguredExecutable confMSAprobs = init(sequences); + confMSAprobs.addParameters(preset.getOptions()); + Limit limit = getLimit(preset.getName()); + return WSUtil.align(sequences, confMSAprobs, log, "presetAlign", limit); + } + + @SuppressWarnings("unchecked") + @Override + public Alignment getResult(String jobId) throws ResultNotAvailableException { + WSUtil.validateJobId(jobId); + AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId); + ConfiguredExecutable MSAprobs = (ConfiguredExecutable) asyncEngine.getResults(jobId); + Alignment al = MSAprobs.getResults(); + return new Alignment (al.getSequences(), Program.MSAprobs, '-'); + } + + @Override + public Limit getLimit(String presetName) { + if (limitMan == null) { + // Limit is not defined + return null; + } + return limitMan.getLimitByName(presetName); + } + + @Override + public LimitsManager getLimits() { + return limitMan; + } + + @Override + public ChunkHolder pullExecStatistics(String jobId, long position) { + WSUtil.validateJobId(jobId); + // TODO check if output is the one to return + String file = Configurator.getWorkDirectory(jobId) + File.separator + new MSAprobs().getError(); + return WSUtil.pullFile(file, position); + } + + @Override + public boolean cancelJob(String jobId) { + WSUtil.validateJobId(jobId); + return WSUtil.cancelJob(jobId); + } + + @Override + public JobStatus getJobStatus(String jobId) { + WSUtil.validateJobId(jobId); + return WSUtil.getJobStatus(jobId); + } + + @Override + public PresetManager getPresets() { + return null; + } + + @Override + public RunnerConfig getRunnerOptions() { + return MSAprobsOptions; + } + +} diff --git a/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd b/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd index 7e56e9d..0099b0e 100644 --- a/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd +++ b/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd @@ -365,6 +365,8 @@ + + diff --git a/webservices/compbio/ws/server/resource/GLprobsWS.wsdl b/webservices/compbio/ws/server/resource/GLprobsWS.wsdl new file mode 100644 index 0000000..66288af --- /dev/null +++ b/webservices/compbio/ws/server/resource/GLprobsWS.wsdl @@ -0,0 +1,292 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/GLprobsWS_schema1.xsd b/webservices/compbio/ws/server/resource/GLprobsWS_schema1.xsd new file mode 100644 index 0000000..6af7a92 --- /dev/null +++ b/webservices/compbio/ws/server/resource/GLprobsWS_schema1.xsd @@ -0,0 +1,374 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd b/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd index 41ab3ea..e1e8e5f 100644 --- a/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd +++ b/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd @@ -351,6 +351,8 @@ + + diff --git a/webservices/compbio/ws/server/resource/MSAprobsWS.wsdl b/webservices/compbio/ws/server/resource/MSAprobsWS.wsdl new file mode 100644 index 0000000..a50285c --- /dev/null +++ b/webservices/compbio/ws/server/resource/MSAprobsWS.wsdl @@ -0,0 +1,292 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/MSAprobsWS_schema1.xsd b/webservices/compbio/ws/server/resource/MSAprobsWS_schema1.xsd new file mode 100644 index 0000000..5ab9459 --- /dev/null +++ b/webservices/compbio/ws/server/resource/MSAprobsWS_schema1.xsd @@ -0,0 +1,374 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd b/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd index 7e56e9d..0099b0e 100644 --- a/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd +++ b/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd @@ -365,6 +365,8 @@ + + diff --git a/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd b/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd index 026c65f..30961c2 100644 --- a/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd +++ b/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd @@ -351,6 +351,8 @@ + + diff --git a/webservices/compbio/ws/server/resource/RegistryWS_schema1.xsd b/webservices/compbio/ws/server/resource/RegistryWS_schema1.xsd index 2efa715..d3bda02 100644 --- a/webservices/compbio/ws/server/resource/RegistryWS_schema1.xsd +++ b/webservices/compbio/ws/server/resource/RegistryWS_schema1.xsd @@ -152,6 +152,8 @@ + + diff --git a/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd b/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd index 314111a..c2f11cb 100644 --- a/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd +++ b/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd @@ -351,6 +351,8 @@ + + diff --git a/website/prog_docs/glprobs.txt b/website/prog_docs/glprobs.txt new file mode 100644 index 0000000..8d150b5 --- /dev/null +++ b/website/prog_docs/glprobs.txt @@ -0,0 +1,36 @@ +************************************************************************ + 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 + specify the output file name (STDOUT by default) + -num_threads + 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 + diff --git a/website/prog_docs/msaprobs.txt b/website/prog_docs/msaprobs.txt new file mode 100644 index 0000000..dc8142d --- /dev/null +++ b/website/prog_docs/msaprobs.txt @@ -0,0 +1,36 @@ +************************************************************************ + 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 + specify the output file name (STDOUT by default) + -num_threads + 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 + diff --git a/wsbuild.log b/wsbuild.log index 5b45197..35dff38 100644 --- a/wsbuild.log +++ b/wsbuild.log @@ -2,28 +2,8 @@ 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] @@ -246,6 +226,228 @@ build-server: [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] + [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)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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,java.util.List>)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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.metadata.Preset)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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] + [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] + [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] + [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] + [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] + [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] + [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] + [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)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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,java.util.List>)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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.metadata.Preset)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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] + [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] + [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] + [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] + [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] + [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] + [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] @@ -1333,4 +1535,4 @@ build-server: [wsgen] Note: ap round: 2 BUILD SUCCESSFUL -Total time: 8 seconds +Total time: 10 seconds diff --git a/wsbuild.xml b/wsbuild.xml index b1a56b4..c8aa0e5 100644 --- a/wsbuild.xml +++ b/wsbuild.xml @@ -24,12 +24,16 @@ + + + + - + @@ -76,6 +80,30 @@ + + + + + + + + + + + + + + + - +