diff -Nru libjaba-client-java-0+dfsg/META-INF/MANIFEST.MF libjaba-client-java-2.0.1/META-INF/MANIFEST.MF --- libjaba-client-java-0+dfsg/META-INF/MANIFEST.MF 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/META-INF/MANIFEST.MF 2013-07-02 10:38:26.000000000 +0000 @@ -0,0 +1,9 @@ +Manifest-Version: 1.0 +Ant-Version: Apache Ant 1.9.0 +Created-By: 1.6.0_45-b06 (Sun Microsystems Inc.) +Built-By: Peter Troshin +Implementation-Title: Java Bioinformatics Analyses Web Services Client + Source Code +Implementation-Vendor: Peter Troshin +Implementation-URL: http://www.compbio.dundee.ac.uk/jabaws + Binary files /tmp/g3g2TZyGVo/libjaba-client-java-0+dfsg/compbio/data/msa/Category.class and /tmp/4G4zTDPKJm/libjaba-client-java-2.0.1/compbio/data/msa/Category.class differ diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/Category.java libjaba-client-java-2.0.1/compbio/data/msa/Category.java --- libjaba-client-java-0+dfsg/compbio/data/msa/Category.java 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/Category.java 2013-06-14 14:16:52.000000000 +0000 @@ -0,0 +1,114 @@ +package compbio.data.msa; + +import java.util.HashSet; +import java.util.Set; +import java.util.TreeSet; + +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; + +import compbio.ws.client.Services; + +/** + * Class that splits {@link Services} to categories. Services themselves have no + * knowledge which category they belongs to. + * + * This class is responsible for initialization of all the categories (done + * statically) and holds the category names as constrains. + * + * Two categories considered equals if their names are equals. + * + * @author pvtroshin + * @version 1.0 September 2011 + */ +@XmlAccessorType(XmlAccessType.FIELD) +public class Category { + /* + * TODO refactor initialization and constrains into separate classes if + * further complexity is expected. + */ + + /** + * All of the Category names + */ + public static final String CATEGORY_ALIGNMENT = "Alignment"; + public static final String CATEGORY_DISORDER = "Protein Disorder"; + public static final String CATEGORY_CONSERVATION = "Conservation"; + + public String name; + Set services; + + private Category(String name, Set services) { + this.name = name; + this.services = services; + } + + private Category() { + // Default constructor for JAXB + } + + public Set getServices() { + return new TreeSet(services); + } + + public static Set getCategories() { + return init(); + } + + private static Set init() { + Set align_services = new HashSet(); + align_services.add(Services.ClustalOWS); + align_services.add(Services.ClustalWS); + align_services.add(Services.MafftWS); + align_services.add(Services.MuscleWS); + align_services.add(Services.ProbconsWS); + align_services.add(Services.TcoffeeWS); + Category alignment = new Category(CATEGORY_ALIGNMENT, align_services); + + Set disorder_services = new HashSet(); + disorder_services.add(Services.DisemblWS); + disorder_services.add(Services.GlobPlotWS); + disorder_services.add(Services.IUPredWS); + disorder_services.add(Services.JronnWS); + + Category disorder = new Category(CATEGORY_DISORDER, disorder_services); + Set conservation_services = new HashSet(); + conservation_services.add(Services.AAConWS); + + Category conservation = new Category(CATEGORY_CONSERVATION, + conservation_services); + + Set categories = new HashSet(); + categories.add(alignment); + categories.add(disorder); + categories.add(conservation); + + return categories; + } + + @Override + public int hashCode() { + final int prime = 31; + int result = 1; + result = prime * result + ((name == null) ? 0 : name.hashCode()); + return result; + } + + @Override + public boolean equals(Object obj) { + if (this == obj) + return true; + if (obj == null) + return false; + if (getClass() != obj.getClass()) + return false; + Category other = (Category) obj; + if (name == null) { + if (other.name != null) + return false; + } else if (!name.equals(other.name)) + return false; + return true; + } + +} Binary files /tmp/g3g2TZyGVo/libjaba-client-java-0+dfsg/compbio/data/msa/JABAService.class and /tmp/4G4zTDPKJm/libjaba-client-java-2.0.1/compbio/data/msa/JABAService.class differ diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/JABAService.java libjaba-client-java-2.0.1/compbio/data/msa/JABAService.java --- libjaba-client-java-0+dfsg/compbio/data/msa/JABAService.java 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/JABAService.java 2013-06-14 14:16:52.000000000 +0000 @@ -0,0 +1,33 @@ +/* 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.data.msa; + +/** + * This is a marker interface, contains no methods + * + * @author pvtroshin + * + */ +public interface JABAService { + + // JABAWS version 1.0 service name + static final String SERVICE_NAMESPACE = "http://msa.data.compbio/01/01/2010/"; + // JABAWS version 2.0 service name + static final String V2_SERVICE_NAMESPACE = "http://msa.data.compbio/01/12/2010/"; + +} Binary files /tmp/g3g2TZyGVo/libjaba-client-java-0+dfsg/compbio/data/msa/JManagement.class and /tmp/4G4zTDPKJm/libjaba-client-java-2.0.1/compbio/data/msa/JManagement.class differ diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/JManagement.java libjaba-client-java-2.0.1/compbio/data/msa/JManagement.java --- libjaba-client-java-0+dfsg/compbio/data/msa/JManagement.java 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/JManagement.java 2013-06-14 14:16:52.000000000 +0000 @@ -0,0 +1,72 @@ +/* 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.data.msa; + +import java.security.InvalidParameterException; + +import javax.jws.WebParam; + +import compbio.metadata.ChunkHolder; +import compbio.metadata.JobStatus; + +public interface JManagement { + + /** + * Stop running the job jobId but leave its output untouched + * + * @return true if job was cancelled successfully, false otherwise + * @throws InvalidParameterException + * is thrown if jobId is empty or cannot be recognised e.g. in + * invalid format + */ + boolean cancelJob(@WebParam(name = "jobId") String jobId); + + /** + * Return the status of the job. + * + * @param jobId + * - unique job identifier + * @return JobStatus - status of the job + * @throws InvalidParameterException + * is thrown if jobId is empty or cannot be recognised e.g. in + * invalid format + * @see JobStatus + */ + JobStatus getJobStatus(@WebParam(name = "jobId") String jobId); + + /** + * Reads 1kb chunk from the statistics file which is specific to a given web + * service from the position. If in time of a request less then + * 1kb data is available from the position to the end of the file, then it + * returns all the data available from the position to the end of the file. + * + * @param jobId + * - unique job identifier + * @param position + * - next position within the file to read + * @return ChunkHolder - which contains a chunk of data and a next position + * within the file from which no data has been read + * @throws InvalidParameterException + * thrown if jobId is empty or cannot be recognised e.g. in + * invalid format and also if the position value is negative + * @see ChunkHolder + */ + ChunkHolder pullExecStatistics(@WebParam(name = "jobId") String jobId, + @WebParam(name = "position") long position); + +} Binary files /tmp/g3g2TZyGVo/libjaba-client-java-0+dfsg/compbio/data/msa/Metadata.class and /tmp/4G4zTDPKJm/libjaba-client-java-2.0.1/compbio/data/msa/Metadata.class differ diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/Metadata.java libjaba-client-java-2.0.1/compbio/data/msa/Metadata.java --- libjaba-client-java-0+dfsg/compbio/data/msa/Metadata.java 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/Metadata.java 2013-06-14 14:16:52.000000000 +0000 @@ -0,0 +1,63 @@ +/* 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.data.msa; + +import javax.jws.WebParam; + +import compbio.metadata.Limit; +import compbio.metadata.LimitsManager; +import compbio.metadata.PresetManager; +import compbio.metadata.RunnerConfig; + +public interface Metadata { + + /** + * Get options supported by a web service + * + * @return RunnerConfig the list of options and parameters supported by a + * web service. + */ + RunnerConfig getRunnerOptions(); + + /** + * Get presets supported by a web service + * + * @return PresetManager the object contains information about presets + * supported by a web service + */ + PresetManager getPresets(); + + /** + * Get a Limit for a preset. + * + * @param presetName + * the name of the preset. if no name is provided, then the + * default preset is returned. If no limit for a particular + * preset is defined then the default preset is returned + * @return Limit + */ + Limit getLimit(@WebParam(name = "presetName") String presetName); + + /** + * List Limits supported by a web service. + * + * @return LimitManager + */ + LimitsManager getLimits(); + +} Binary files /tmp/g3g2TZyGVo/libjaba-client-java-0+dfsg/compbio/data/msa/MsaWS.class and /tmp/4G4zTDPKJm/libjaba-client-java-2.0.1/compbio/data/msa/MsaWS.class differ diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/MsaWS.java libjaba-client-java-2.0.1/compbio/data/msa/MsaWS.java --- libjaba-client-java-0+dfsg/compbio/data/msa/MsaWS.java 2010-11-17 11:30:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/MsaWS.java 2013-06-28 14:01:28.000000000 +0000 @@ -1,6 +1,6 @@ -/* Copyright (c) 2009 Peter Troshin +/* Copyright (c) 2011 Peter Troshin * - * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0 + * 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 @@ -26,17 +26,11 @@ import compbio.data.sequence.Alignment; import compbio.data.sequence.FastaSequence; -import compbio.metadata.ChunkHolder; -import compbio.metadata.JobStatus; import compbio.metadata.JobSubmissionException; -import compbio.metadata.Limit; import compbio.metadata.LimitExceededException; -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.UnsupportedRuntimeException; import compbio.metadata.WrongParameterException; @@ -45,13 +39,13 @@ * * @author pvtroshin * - * @version 1.0 September 2009 + * Date November 2010 * * @param * executable type / web service type */ @WebService(targetNamespace = "http://msa.data.compbio/01/01/2010/") -public interface MsaWS { +public interface MsaWS extends JABAService, JManagement, Metadata { /** * Align a list of sequences with default settings. @@ -62,7 +56,7 @@ * JobSubmissionException will be thrown. * * @param sequences - * List of FastaSequence objects. The programme does not perform + * List of FastaSequence objects. The program does not perform * any sequence validity checks. Nor does it checks whether the * sequences names are unique. It is responsibility of the caller * to make sure of this @@ -201,87 +195,4 @@ Alignment getResult(@WebParam(name = "jobId") String jobId) throws ResultNotAvailableException; - /** - * Stop running the job jobId but leave its output untouched - * - * @return true if job was cancelled successfully, false otherwise - * @throws InvalidParameterException - * is thrown if jobId is empty or cannot be recognised e.g. in - * invalid format - */ - boolean cancelJob(@WebParam(name = "jobId") String jobId); - - /** - * Return the status of the job. - * - * @param jobId - * - unique job identifier - * @return JobStatus - status of the job - * @throws InvalidParameterException - * is thrown if jobId is empty or cannot be recognised e.g. in - * invalid format - * @see JobStatus - */ - JobStatus getJobStatus(@WebParam(name = "jobId") String jobId); - - /** - * Reads 1kb chunk from the statistics file which is specific to a given web - * service from the position. If in time of a request less then - * 1kb data is available from the position to the end of the file, then it - * returns all the data available from the position to the end of the file. - * - * @param jobId - * - unique job identifier - * @param position - * - next position within the file to read - * @return ChunkHolder - which contains a chunk of data and a next position - * within the file from which no data has been read - * @throws InvalidParameterException - * thrown if jobId is empty or cannot be recognised e.g. in - * invalid format and also if the position value is negative - * @see ChunkHolder - */ - ChunkHolder pullExecStatistics(@WebParam(name = "jobId") String jobId, - @WebParam(name = "position") long position); - - /* - * TODO - * @param jobId - * @return byte getProgress(@WebParam(name = "jobId") String jobId); - */ - - /** - * Get options supported by a web service - * - * @return RunnerConfig the list of options and parameters supported by a - * web service. - */ - RunnerConfig getRunnerOptions(); - - /** - * Get presets supported by a web service - * - * @return PresetManager the object contains information about presets - * supported by a web service - */ - PresetManager getPresets(); - - /** - * Get a Limit for a preset. - * - * @param presetName - * the name of the preset. if no name is provided, then the - * default preset is returned. If no limit for a particular - * preset is defined then the default preset is returned - * @return Limit - */ - Limit getLimit(@WebParam(name = "presetName") String presetName); - - /** - * List Limits supported by a web service. - * - * @return LimitManager - */ - LimitsManager getLimits(); - } diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/RegistryWS.java libjaba-client-java-2.0.1/compbio/data/msa/RegistryWS.java --- libjaba-client-java-0+dfsg/compbio/data/msa/RegistryWS.java 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/RegistryWS.java 2013-06-14 14:16:52.000000000 +0000 @@ -0,0 +1,101 @@ +/* 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.data.msa; + +import java.util.Date; +import java.util.Set; + +import javax.jws.WebService; + +import compbio.ws.client.Services; + +/** + * JABAWS services registry + * + * @author pvtroshin + * @version 1.0 June 2011 + */ +@WebService(targetNamespace = JABAService.V2_SERVICE_NAMESPACE) +public interface RegistryWS extends JABAService { + + /** + * List of services that are functioning on the server. This function + * returns the results of testing performed some time ago by + * {@link #testAllServices} or {@link #testService(Services)} methods. The + * time of last check can be obtained from + * {@link #getLastTestedOn(Services)} method + * + * @return the Set of Services which are functioning on the server + * @see #testAllServices() + */ + Set getSupportedServices(); + /** + * Number of seconds since the last test. Returns 0 if the service was not + * tested or tested less then a one second ago. + * + * @param service + * @return when last time tested + */ + int getLastTested(Services service); + /** + * The date and time the service has been verified to work last time + * + * @param service + * @return the Date and time on which the service was last tested + */ + Date getLastTestedOn(Services service); + /** + * Test all JABAWS services on the server + * + * @return the test log + */ + String testAllServices(); + /** + * Test a particular service + * + * @param service + * @return the testing log + */ + String testService(Services service); + /** + * Check whether a particular web service is working on this server + * + * @param service + * @return true if the service was functioning in time of last testing. + */ + boolean isOperating(Services service); + + /** + * Gives the description of the service. + * + * @param service + * @return String, plain text or html formatted piece, but NOT a full html + * document + */ + String getServiceDescription(Services service); + + /** + * Gets the list of services per category. ServiceClassifier has the method + * that returns Map> + * + * @return ServiceClassifier the object to represent relation between + * Services and Categories + */ + Set getServiceCategories(); + +} Binary files /tmp/g3g2TZyGVo/libjaba-client-java-0+dfsg/compbio/data/msa/SequenceAnnotation.class and /tmp/4G4zTDPKJm/libjaba-client-java-2.0.1/compbio/data/msa/SequenceAnnotation.class differ diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/SequenceAnnotation.java libjaba-client-java-2.0.1/compbio/data/msa/SequenceAnnotation.java --- libjaba-client-java-0+dfsg/compbio/data/msa/SequenceAnnotation.java 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/SequenceAnnotation.java 2013-06-14 14:16:52.000000000 +0000 @@ -0,0 +1,220 @@ +/* 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.data.msa; + +import java.security.InvalidParameterException; +import java.util.List; + +import javax.jws.WebMethod; +import javax.jws.WebParam; +import javax.jws.WebService; + +import compbio.data.sequence.FastaSequence; +import compbio.data.sequence.ScoreManager; +import compbio.metadata.JobSubmissionException; +import compbio.metadata.LimitExceededException; +import compbio.metadata.Option; +import compbio.metadata.Preset; +import compbio.metadata.ResultNotAvailableException; +import compbio.metadata.UnsupportedRuntimeException; +import compbio.metadata.WrongParameterException; + +/** + * Interface for tools that results to one or more annotation to sequence(s) + * + * Single, multiple sequences their groups or alignments can be annotated + * + * @author Peter Troshin + * + * @param + * executable type / web service type + * + * @version 1.0 November 2010 + */ +@WebService(targetNamespace = JABAService.V2_SERVICE_NAMESPACE) +public interface SequenceAnnotation + extends + JABAService, + JManagement, + Metadata { + + /** + * + * Analyse the sequences. The actual analysis algorithm is defined by the + * type T. + * + * Any dataset containing a greater number of sequences or the average + * length of the sequences are greater then defined in the default Limit + * will not be accepted for an alignment operation and + * JobSubmissionException will be thrown. + * + * @param sequences + * List of FastaSequence objects. The programme does not perform + * any sequence validity checks. Nor does it checks whether the + * sequences names are unique. It is responsibility of the caller + * to validate this information + * @return jobId - unique identifier for the job + * @throws JobSubmissionException + * is thrown when the job could not be submitted due to the + * following reasons: 1) The number of sequences in the + * submission or their average length is greater then defined by + * the default Limit. 2) Any problems on the server side e.g. it + * is misconfigured or malfunction, is reported via this + * exception. In the first case the information on the limit + * could be obtained from an exception. + * @throws InvalidParameterException + * thrown if input list of fasta sequence is null or empty + * @throws UnsupportedRuntimeException + * thrown if server OS does not support native executables for a + * given web service, e.g. JABAWS is deployed on Windows and + * Mafft service is called + * @throws LimitExceededException + * is throw if the input sequences number or average length + * exceeds what is defined by the limit + */ + @WebMethod + String analize( + @WebParam(name = "fastaSequences") List sequences) + throws UnsupportedRuntimeException, LimitExceededException, + JobSubmissionException; + + /** + * Analyse the sequences according to custom settings defined in options + * list. The actual analysis algorithm is defined by the type T. Default + * Limit is used to decide whether the calculation will be permitted or + * denied + * + * @param sequences + * List of FastaSequence objects. The programme does not perform + * any sequence validity checks. Nor does it checks whether the + * sequences names are unique. It is responsibility of the caller + * to validate this information + * @param options + * A list of Options + * @return jobId - unique identifier for the job + * @throws JobSubmissionException + * is thrown when the job could not be submitted due to the + * following reasons: 1) The number of sequences in the + * submission or their average length is greater then defined by + * the default Limit. 2) Any problems on the server side e.g. it + * is misconfigured or malfunction, is reported via this + * exception. In the first case the information on the limit + * could be obtained from an exception. + * @throws WrongParameterException + * is throws when 1) One of the Options provided is not + * supported, 2) The value of the option is defined outside the + * boundaries. In both cases exception object contain the + * information on the violating Option. + * @throws InvalidParameterException + * thrown if input list of fasta sequence is null or empty + * @throws UnsupportedRuntimeException + * thrown if server OS does not support native executables for a + * given web service, e.g. JABAWS is deployed on Windows and + * Mafft service is called + * @throws LimitExceededException + * is throw if the input sequences number or average length + * exceeds what is defined by the limit + * @see Option + */ + @WebMethod + String customAnalize( + @WebParam(name = "fastaSequences") List sequences, + @WebParam(name = "options") List> options) + throws UnsupportedRuntimeException, LimitExceededException, + JobSubmissionException, WrongParameterException; + + /** + * Analyse the sequences according to the preset settings. The actual + * analysis algorithm is defined by the type T. + * + * Limit for a presetName is used whether the calculation will be permitted + * or denied. If no Limit was defined for a presetName, than default limit + * is used. + * + * @param sequences + * List of FastaSequence objects. The programme does not perform + * any sequence validity checks. Nor does it checks whether the + * sequences names are unique. It is responsibility of the caller + * to validate this information + * @param preset + * A list of Options + * @return String - jobId - unique identifier for the job + * @throws JobSubmissionException + * is thrown when the job could not be submitted due to the + * following reasons: 1) The number of sequences in the + * submission or their average length is greater then defined by + * the default Limit. 2) Any problems on the server side e.g. it + * is misconfigured or malfunction, is reported via this + * exception. In the first case the information on the limit + * could be obtained from an exception. + * @throws WrongParameterException + * is throws when 1) One of the Options provided is not + * supported, 2) The value of the option is defined outside the + * boundaries. In both cases exception object contain the + * information on the violating Option. + * @throws InvalidParameterException + * thrown if input list of fasta sequence is null or empty + * @throws UnsupportedRuntimeException + * thrown if server OS does not support native executables for a + * given web service, e.g. JABAWS is deployed on Windows and + * Mafft service is called + * @throws LimitExceededException + * is throw if the input sequences number or average length + * exceeds what is defined by the limit + */ + @WebMethod + String presetAnalize( + @WebParam(name = "fastaSequences") List sequences, + @WebParam(name = "preset") Preset preset) + throws UnsupportedRuntimeException, LimitExceededException, + JobSubmissionException, WrongParameterException; + + /** + * Return the result of the job. + * + * @param jobId + * a unique job identifier + * @return the Map with the sequence names, sequence group names or the word + * 'Alignment' in case of alignments and values the represented by a + * Set of Score objects. The alignment can be represented in as + * little as one key->value pair in this map, the list of sequences + * will be represented by multiple key->value mappings. If multiple + * annotations were calculated, then they are represented as a Set + * of Scores. + * @throws ResultNotAvailableException + * this exception is throw if the job execution was not + * successful or the result of the execution could not be found. + * (e.g. removed). Exception could also be thrown is dues to the + * lower level problems on the server i.e. IOException, + * FileNotFoundException problems as well as + * UnknownFileFormatException. + * @throws InvalidParameterException + * thrown if jobId is empty or cannot be recognised e.g. in + * invalid format + * + */ + @WebMethod + ScoreManager getAnnotation(@WebParam(name = "jobId") String jobId) + throws ResultNotAvailableException; + /* + * The method should really return Map and Set, but unfortunately JAXB + * cannot serialize interfaces, has a concrete implementation is used Could + * also specify the generic Set e.g. ? extends Set. But this would require + * the client cast or operate with generic Set. Keep it simple for now. + */ +} diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/Align.java libjaba-client-java-2.0.1/compbio/data/msa/jaxws/Align.java --- libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/Align.java 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/jaxws/Align.java 2013-06-14 14:16:52.000000000 +0000 @@ -0,0 +1,37 @@ + +package compbio.data.msa.jaxws; + +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + +@XmlRootElement(name = "align", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "align", namespace = "http://msa.data.compbio/01/01/2010/") +public class Align { + + @XmlElement(name = "fastaSequences", namespace = "") + private List fastaSequences; + + /** + * + * @return + * returns List + */ + public List getFastaSequences() { + return this.fastaSequences; + } + + /** + * + * @param fastaSequences + * the value for the fastaSequences property + */ + public void setFastaSequences(List fastaSequences) { + this.fastaSequences = fastaSequences; + } + +} diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/AlignResponse.java libjaba-client-java-2.0.1/compbio/data/msa/jaxws/AlignResponse.java --- libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/AlignResponse.java 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/jaxws/AlignResponse.java 2013-06-14 14:16:52.000000000 +0000 @@ -0,0 +1,36 @@ + +package compbio.data.msa.jaxws; + +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + +@XmlRootElement(name = "alignResponse", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "alignResponse", namespace = "http://msa.data.compbio/01/01/2010/") +public class AlignResponse { + + @XmlElement(name = "return", namespace = "") + private String _return; + + /** + * + * @return + * returns String + */ + public String getReturn() { + return this._return; + } + + /** + * + * @param _return + * the value for the _return property + */ + public void setReturn(String _return) { + this._return = _return; + } + +} diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/Analize.java libjaba-client-java-2.0.1/compbio/data/msa/jaxws/Analize.java --- libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/Analize.java 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/jaxws/Analize.java 2013-06-14 14:16:52.000000000 +0000 @@ -0,0 +1,37 @@ + +package compbio.data.msa.jaxws; + +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + +@XmlRootElement(name = "analize", namespace = "http://msa.data.compbio/01/12/2010/") +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "analize", namespace = "http://msa.data.compbio/01/12/2010/") +public class Analize { + + @XmlElement(name = "fastaSequences", namespace = "") + private List fastaSequences; + + /** + * + * @return + * returns List + */ + public List getFastaSequences() { + return this.fastaSequences; + } + + /** + * + * @param fastaSequences + * the value for the fastaSequences property + */ + public void setFastaSequences(List fastaSequences) { + this.fastaSequences = fastaSequences; + } + +} diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/AnalizeResponse.java libjaba-client-java-2.0.1/compbio/data/msa/jaxws/AnalizeResponse.java --- libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/AnalizeResponse.java 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/jaxws/AnalizeResponse.java 2013-06-14 14:16:52.000000000 +0000 @@ -0,0 +1,36 @@ + +package compbio.data.msa.jaxws; + +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + +@XmlRootElement(name = "analizeResponse", namespace = "http://msa.data.compbio/01/12/2010/") +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "analizeResponse", namespace = "http://msa.data.compbio/01/12/2010/") +public class AnalizeResponse { + + @XmlElement(name = "return", namespace = "") + private String _return; + + /** + * + * @return + * returns String + */ + public String getReturn() { + return this._return; + } + + /** + * + * @param _return + * the value for the _return property + */ + public void setReturn(String _return) { + this._return = _return; + } + +} diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/CancelJob.java libjaba-client-java-2.0.1/compbio/data/msa/jaxws/CancelJob.java --- libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/CancelJob.java 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/jaxws/CancelJob.java 2013-06-14 14:16:52.000000000 +0000 @@ -0,0 +1,36 @@ + +package compbio.data.msa.jaxws; + +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + +@XmlRootElement(name = "cancelJob", namespace = "http://msa.data.compbio/01/12/2010/") +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "cancelJob", namespace = "http://msa.data.compbio/01/12/2010/") +public class CancelJob { + + @XmlElement(name = "jobId", namespace = "") + private String jobId; + + /** + * + * @return + * returns String + */ + public String getJobId() { + return this.jobId; + } + + /** + * + * @param jobId + * the value for the jobId property + */ + public void setJobId(String jobId) { + this.jobId = jobId; + } + +} diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/CancelJobResponse.java libjaba-client-java-2.0.1/compbio/data/msa/jaxws/CancelJobResponse.java --- libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/CancelJobResponse.java 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/jaxws/CancelJobResponse.java 2013-06-14 14:16:52.000000000 +0000 @@ -0,0 +1,36 @@ + +package compbio.data.msa.jaxws; + +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + +@XmlRootElement(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/12/2010/") +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/12/2010/") +public class CancelJobResponse { + + @XmlElement(name = "return", namespace = "") + private boolean _return; + + /** + * + * @return + * returns boolean + */ + public boolean isReturn() { + return this._return; + } + + /** + * + * @param _return + * the value for the _return property + */ + public void setReturn(boolean _return) { + this._return = _return; + } + +} diff -Nru libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/CustomAlign.java libjaba-client-java-2.0.1/compbio/data/msa/jaxws/CustomAlign.java --- libjaba-client-java-0+dfsg/compbio/data/msa/jaxws/CustomAlign.java 1970-01-01 00:00:00.000000000 +0000 +++ libjaba-client-java-2.0.1/compbio/data/msa/jaxws/CustomAlign.java 2013-06-14 14:16:52.000000000 +0000 @@ -0,0 +1,60 @@ + +package compbio.data.msa.jaxws; + +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + +@XmlRootElement(name = "customAlign", namespace = "http://msa.data.compbio/01/01/2010/") +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "customAlign", namespace = "http://msa.data.compbio/01/01/2010/", propOrder = { + "fastaSequences", + "options" +}) +public class CustomAlign { + + @XmlElement(name = "fastaSequences", namespace = "") + private List fastaSequences; + @XmlElement(name = "options", namespace = "") + private List options; + + /** + * + * @return + * returns List + */ + public List getFastaSequences() { + return this.fastaSequences; + } + + /** + * + * @param fastaSequences + * the value for the fastaSequences property + */ + public void setFastaSequences(List fastaSequences) { + this.fastaSequences = fastaSequences; + } + + /** + * + * @return + * returns List