webservices/compbio/ws/client/Services.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0     \r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 \r
  19 package compbio.ws.client;\r
  20 \r
  21 import java.net.URL;\r
  22 import java.util.Set;\r
  23 \r
  24 import javax.xml.bind.annotation.XmlAccessType;\r
  25 import javax.xml.bind.annotation.XmlAccessorType;\r
  26 import javax.xml.namespace.QName;\r
  27 import javax.xml.ws.Service;\r
  28 \r
  29 import compbio.data.msa.JABAService;\r
  30 import compbio.data.msa.MsaWS;\r
  31 import compbio.data.msa.SequenceAnnotation;\r
  32 \r
  33 /**\r
  34  * List of web services currently supported by JABAWS version 2.1\r
  35  * \r
  36  */\r
  37 public enum Services {\r
  38         /*\r
  39          * Make sure this class has NO references to runners or engines as it is a\r
  40          * part of minimal client package. Such things should go into ServicesUtil\r
  41          */\r
  42         MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, MSAprobsWS, GLprobsWS,\r
  43         AAConWS, \r
  44         JronnWS, DisemblWS, GlobPlotWS, IUPredWS, \r
  45         JpredWS, \r
  46         RNAalifoldWS;\r
  47 \r
  48         public static Services getService(String servName) {\r
  49                 servName = servName.trim().toLowerCase();\r
  50                 for (Services service : Services.values()) {\r
  51                         if (service.toString().equalsIgnoreCase(servName)) {\r
  52                                 return service;\r
  53                         }\r
  54                 }\r
  55                 return null;\r
  56         }\r
  57 \r
  58         Service getService(URL url, String sqname) {\r
  59                 QName qname = new QName(sqname, this.toString());\r
  60                 return Service.create(url, qname);\r
  61         }\r
  62 \r
  63         public static String toString(Set<Services> services) {\r
  64                 if (services == null || services.isEmpty()) {\r
  65                         return "No known services...\n";\r
  66                 }\r
  67                 String value = "";\r
  68                 for (Services serv : services) {\r
  69                         if (null != serv) {\r
  70                                 value += serv + "\n";\r
  71                         } else {\r
  72                                 value += "Unknown Service\n";\r
  73                         }\r
  74                 }\r
  75                 return value;\r
  76         }\r
  77 \r
  78         Class<? extends JABAService> getServiceType() {\r
  79                 switch (this) {\r
  80                         case AAConWS :\r
  81                         case JronnWS :\r
  82                         case DisemblWS :\r
  83                         case GlobPlotWS :\r
  84                         case IUPredWS :\r
  85                         case RNAalifoldWS :\r
  86                                 return SequenceAnnotation.class;\r
  87                         case JpredWS :\r
  88                         case ClustalWS :\r
  89                         case ClustalOWS :\r
  90                         case MafftWS :\r
  91                         case MuscleWS :\r
  92                         case ProbconsWS :\r
  93                         case MSAprobsWS :\r
  94                         case GLprobsWS :\r
  95                         case TcoffeeWS :\r
  96                                 return MsaWS.class;\r
  97                         default :\r
  98                                 throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
  99                 }\r
 100         }\r
 101 \r
 102         \r
 103         String getServiceNamespace() {\r
 104                 switch (this) {\r
 105                         case RNAalifoldWS :\r
 106                         case AAConWS :\r
 107                         case JronnWS :\r
 108                         case DisemblWS :\r
 109                         case GlobPlotWS :\r
 110                         case IUPredWS :\r
 111                         case MSAprobsWS :\r
 112                         case GLprobsWS :\r
 113                         case JpredWS :\r
 114                         case ClustalOWS :\r
 115                                 return JABAService.V2_SERVICE_NAMESPACE;\r
 116                         case ClustalWS :\r
 117                         case MafftWS :\r
 118                         case MuscleWS :\r
 119                         case ProbconsWS :\r
 120                         case TcoffeeWS :\r
 121                                 return JABAService.SERVICE_NAMESPACE;\r
 122                         default :\r
 123                                 throw new RuntimeException("Unrecognised JABAWS Namespace for service " + this +"!");\r
 124                 }\r
 125         }\r
 126         \r
 127         JABAService getInterface(Service service) {\r
 128                 assert service != null;\r
 129 \r
 130                 QName portName = new QName(service.getServiceName().getNamespaceURI(), this.toString() + "Port");\r
 131                 return service.getPort(portName, this.getServiceType());\r
 132         }\r
 133 \r
 134         public String getServiceInfo() {\r
 135                 switch (this) {\r
 136                         case AAConWS :\r
 137                                 return AACON_INFO.toString();\r
 138                         case JpredWS :\r
 139                                 return JPRED_INFO.toString();\r
 140                         case ClustalOWS :\r
 141                                 return CLUSTAL_OMEGA_INFO.toString();\r
 142                         case ClustalWS :\r
 143                                 return CLUSTAL_INFO.toString();\r
 144                         case DisemblWS :\r
 145                                 return DISEMBL_INFO.toString();\r
 146                         case GlobPlotWS :\r
 147                                 return GLOBPLOT_INFO.toString();\r
 148                         case IUPredWS :\r
 149                                 return IUPRED_INFO.toString();\r
 150                         case JronnWS :\r
 151                                 return JRONN_INFO.toString();\r
 152                         case MafftWS :\r
 153                                 return MAFFT_INFO.toString();\r
 154                         case MuscleWS :\r
 155                                 return MUSCLE_INFO.toString();\r
 156                         case ProbconsWS :\r
 157                                 return PROBCONS_INFO.toString();\r
 158                         case MSAprobsWS :\r
 159                                 return MSAPROBS_INFO.toString();\r
 160                         case GLprobsWS :\r
 161                                 return GLPROBS_INFO.toString();\r
 162                         case TcoffeeWS :\r
 163                                 return TCOFFEE_INFO.toString();\r
 164                         case RNAalifoldWS :\r
 165                                 return RNAALIFOLD_INFO.toString();\r
 166                         default :\r
 167                                 throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
 168                 }\r
 169         }\r
 170 \r
 171         public String getServiceReference() {\r
 172                 switch (this) {\r
 173                         case AAConWS :\r
 174                                 return AACON_INFO.getReference();\r
 175                         case JpredWS :\r
 176                                 return JPRED_INFO.getReference();\r
 177                         case ClustalOWS :\r
 178                                 return CLUSTAL_OMEGA_INFO.getReference();\r
 179                         case ClustalWS :\r
 180                                 return CLUSTAL_INFO.getReference();\r
 181                         case DisemblWS :\r
 182                                 return DISEMBL_INFO.getReference();\r
 183                         case GlobPlotWS :\r
 184                                 return GLOBPLOT_INFO.getReference();\r
 185                         case IUPredWS :\r
 186                                 return IUPRED_INFO.getReference();\r
 187                         case JronnWS :\r
 188                                 return JRONN_INFO.getReference();\r
 189                         case MafftWS :\r
 190                                 return MAFFT_INFO.getReference();\r
 191                         case MuscleWS :\r
 192                                 return MUSCLE_INFO.getReference();\r
 193                         case ProbconsWS :\r
 194                                 return PROBCONS_INFO.getReference();\r
 195                         case MSAprobsWS :\r
 196                                 return MSAPROBS_INFO.getReference();\r
 197                         case GLprobsWS :\r
 198                                 return GLPROBS_INFO.getReference();\r
 199                         case TcoffeeWS :\r
 200                                 return TCOFFEE_INFO.getReference();\r
 201                         case RNAalifoldWS :\r
 202                                 return RNAALIFOLD_INFO.getReference();\r
 203                         default :\r
 204                                 throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
 205                 }\r
 206         }\r
 207 \r
 208         public String getServiceVersion() {\r
 209                 switch (this) {\r
 210                         case AAConWS :\r
 211                                 return AACON_INFO.getVersion();\r
 212                         case JpredWS :\r
 213                                 return JPRED_INFO.getVersion();\r
 214                         case ClustalOWS :\r
 215                                 return CLUSTAL_OMEGA_INFO.getVersion();\r
 216                         case ClustalWS :\r
 217                                 return CLUSTAL_INFO.getVersion();\r
 218                         case DisemblWS :\r
 219                                 return DISEMBL_INFO.getVersion();\r
 220                         case GlobPlotWS :\r
 221                                 return GLOBPLOT_INFO.getVersion();\r
 222                         case IUPredWS :\r
 223                                 return IUPRED_INFO.getVersion();\r
 224                         case JronnWS :\r
 225                                 return JRONN_INFO.getVersion();\r
 226                         case MafftWS :\r
 227                                 return MAFFT_INFO.getVersion();\r
 228                         case MuscleWS :\r
 229                                 return MUSCLE_INFO.getVersion();\r
 230                         case ProbconsWS :\r
 231                                 return PROBCONS_INFO.getVersion();\r
 232                         case MSAprobsWS :\r
 233                                 return MSAPROBS_INFO.getVersion();\r
 234                         case GLprobsWS :\r
 235                                 return GLPROBS_INFO.getVersion();\r
 236                         case TcoffeeWS :\r
 237                                 return TCOFFEE_INFO.getVersion();\r
 238                         case RNAalifoldWS :\r
 239                                 return RNAALIFOLD_INFO.getVersion();\r
 240                         default :\r
 241                                 throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
 242                 }\r
 243         }\r
 244 \r
 245         public String getServiceGroup() {\r
 246                 switch (this) {\r
 247                         case AAConWS :\r
 248                                 return "annotation";\r
 249                         case JpredWS :\r
 250                                 return "annotation";\r
 251                         case ClustalOWS :\r
 252                                 return "alignment";\r
 253                         case ClustalWS :\r
 254                                 return "alignment";\r
 255                         case DisemblWS :\r
 256                                 return "disorder";\r
 257                         case GlobPlotWS :\r
 258                                 return "disorder";\r
 259                         case IUPredWS :\r
 260                                 return "disorder";\r
 261                         case JronnWS :\r
 262                                 return "disorder";\r
 263                         case MafftWS :\r
 264                                 return "alignment";\r
 265                         case MuscleWS :\r
 266                                 return "alignment";\r
 267                         case ProbconsWS :\r
 268                                 return "alignment";\r
 269                         case GLprobsWS :\r
 270                                 return "alignment";\r
 271                         case MSAprobsWS :\r
 272                                 return "alignment";\r
 273                         case TcoffeeWS :\r
 274                                 return "alignment";\r
 275                         case RNAalifoldWS :\r
 276                                 return "annotation";\r
 277                         default :\r
 278                                 throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
 279                 }\r
 280         }\r
 281         \r
 282         static ServiceInfo AACON_INFO = new ServiceInfo(AAConWS,\r
 283                         "in preparation", "1.0", "http://www.compbio.dundee.ac.uk/aacon");\r
 284 \r
 285         static ServiceInfo JPRED_INFO = new ServiceInfo(JpredWS,\r
 286                         "Cole C, Barber JD, Barton GJ,\r\n" + \r
 287                         "\"The Jpred 3 secondary structure prediction server\"\r\n" +\r
 288                         "Nucl. Acids Res. 36 (suppl 2):W197 (2008)", \r
 289                         "3.0.3", "http://www.compbio.dundee.ac.uk/www-jpred");\r
 290         \r
 291         static ServiceInfo CLUSTAL_INFO = new ServiceInfo(ClustalWS,\r
 292                         "Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG,\r\n" +\r
 293                         "\"Clustal W and Clustal X version 2.0\"\r\n" + \r
 294                         "Bioinformatics, 23: 2947 (2007)",\r
 295                         "2.0.12", "http://www.clustal.org/clustal2/");\r
 296 \r
 297         static ServiceInfo CLUSTAL_OMEGA_INFO = new ServiceInfo(ClustalOWS,\r
 298                         "Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG,\r\n" +\r
 299                         "\"Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega\"\r\n" +\r
 300                         "Mol Syst Biol. 7:539 (2011)",\r
 301                         "1.0.2", "http://www.clustal.org/omega/");\r
 302 \r
 303         static ServiceInfo DISEMBL_INFO = new ServiceInfo(DisemblWS,\r
 304                         "Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, and Russell RB,\r\n" +\r
 305                         "\"Protein disorder prediction: implications for structural proteomics\"\r\n" +\r
 306                         "Structure 11(11):1453 (2003)", \r
 307                         "1.5", "http://dis.embl.de/");\r
 308 \r
 309         static ServiceInfo GLOBPLOT_INFO = new ServiceInfo(GlobPlotWS,\r
 310                         "Linding R, Russell RB, Neduva V and Gibson TJ,\r\n" +\r
 311                         "GlobPlot: exploring protein sequences for globularity and disorder\r\n" + \r
 312                         "Nucl. Acids Res. 31 (13):3701 (2003)",\r
 313                         "2.3", "http://globplot.embl.de/");\r
 314 \r
 315         static ServiceInfo IUPRED_INFO = new ServiceInfo(IUPredWS,\r
 316                         "Dosztányi Z, Csizmók V, Tompa P, and Simon I,\r\n" +\r
 317                         "\"The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins\"\r\n" +\r
 318                         "J. Mol. Biol. 347:827 (2005)", \r
 319                         "1.0", "http://iupred.enzim.hu/");\r
 320 \r
 321         static ServiceInfo TCOFFEE_INFO = new ServiceInfo(TcoffeeWS,\r
 322                         "Notredame C, Higgins DG, Heringa L,\r\n" +\r
 323                         "\"T-Coffee: A novel method for multiple sequence alignments\"\r\n" + \r
 324                         "JMB, 302(1):205 (2000)",\r
 325                         "8.99", "http://tcoffee.crg.cat/apps/tcoffee/index.html");\r
 326 \r
 327         static ServiceInfo MUSCLE_INFO = new ServiceInfo(MuscleWS,\r
 328                         "Edgar RC,\r\n"+ \r
 329                         "\"MUSCLE: multiple sequence alignment with high accuracy and high throughput\"\r\n" + \r
 330                         "Nucleic Acids Res. 32(5):1792 (2004)", \r
 331                         "3.8.31", "http://www.drive5.com/muscle/");\r
 332 \r
 333         static ServiceInfo PROBCONS_INFO = new ServiceInfo(ProbconsWS,\r
 334                         "Do CB, Mahabhashyam MSP, Brudno M, and Batzoglou S,\r\n" +\r
 335                         "\"PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment\"\r\n" + \r
 336                         "Genome Research 15:330 (2005)",\r
 337                         "1.12", "http://probcons.stanford.edu/");\r
 338 \r
 339         static ServiceInfo MSAPROBS_INFO = new ServiceInfo(MSAprobsWS,\r
 340                         "Liu Y, Schmidt B, and Maskell DL,\r\n" + \r
 341                         "\"MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities\"\r\n" +\r
 342                         "Bioinformatics, 26 (16):1958 (2010)",\r
 343                         "0.9.7", "http://msaprobs.sourceforge.net/");\r
 344 \r
 345         static ServiceInfo GLPROBS_INFO = new ServiceInfo(GLprobsWS,\r
 346                         "Yongtao Ye, Siu-Ming Yiu, David W. Cheung, Qing Zhan, Hing-Fung Ting, Yadong Wang, Tak-Wah Lam,\r\n" +\r
 347                         "\"GLProbs: Aligning multiple sequences adaptively\"\r\n" + \r
 348                         "in progress (2013)",\r
 349                         "1.0", "http://sourceforge.net/projects/glprobs/");\r
 350 \r
 351         static ServiceInfo JRONN_INFO = new ServiceInfo(JronnWS,\r
 352                         "unpublished, original algorithm Yang ZR, Thomson R, McMeil P, and Esnouf RM,\r\n" + \r
 353                         "\"RONN: the bio-basis function neural network technique applied to the dectection of natively disordered regions in proteins\"\r\n" +\r
 354                         "Bioinformatics 21:3369 (2005)\r\n",\r
 355                         "1.0", "http://www.compbio.dundee.ac.uk/jabaws/");\r
 356 \r
 357         static ServiceInfo MAFFT_INFO = new ServiceInfo(MafftWS,\r
 358                         "Katoh K, Toh H,\r\n" +\r
 359                         "\"Parallelization of the MAFFT multiple sequence alignment program\"\r\n" + \r
 360                         "Bioinformatics 26:1899 (2010)",\r
 361                         "6.8.57", "http://mafft.cbrc.jp/alignment/software/");\r
 362 \r
 363         static ServiceInfo RNAALIFOLD_INFO = new ServiceInfo(RNAalifoldWS,\r
 364                         "Hofacker IL, Fekete M, and Stadler PV,\r\n"+ \r
 365                         "\"Secondary Structure Prediction for Aligned RNA Sequences\"\r\n" + \r
 366                         "J.Mol.Biol. 319:1059 (2002) and\r\n " + \r
 367                         "Bernhart SH, Hofacker IL Will S, Gruber AR, and Stadler PF,\r\n" + \r
 368                         "\"RNAalifold: Improved consensus structure prediction for RNA alignments\"\r\n" +\r
 369                         "BMC Bioinformatics, 9:474 (2008)\r\n",\r
 370                         "2.1.2", "http://www.tbi.univie.ac.at/RNA/");\r
 371 \r
 372         @XmlAccessorType(XmlAccessType.FIELD)\r
 373         static class ServiceInfo {\r
 374                 Services service;\r
 375                 String reference;\r
 376                 String version;\r
 377                 String moreinfo;\r
 378                 final static String jabaws_version = "2.1";\r
 379                 final static String line_delimiter = "\n";\r
 380 \r
 381                 private ServiceInfo() {\r
 382                         // Default constructor for JAXB\r
 383                 }\r
 384                 private ServiceInfo(Services service, String reference, String version,\r
 385                                 String moreinfo) {\r
 386                         this.service = service;\r
 387                         this.reference = reference;\r
 388                         this.version = version;\r
 389                         this.moreinfo = moreinfo;\r
 390                 }\r
 391 \r
 392                 @Override\r
 393                 public String toString() {\r
 394                         String value = "SERVICE: " + service + " version " + version + line_delimiter + "\n";\r
 395                         value += "JABAWS v. " + jabaws_version + line_delimiter;\r
 396                         value += "REFERENCE: " + reference + line_delimiter + "\n";\r
 397                         value += "MORE INFORMATION: " + moreinfo + line_delimiter;\r
 398                         return value;\r
 399                 }\r
 400 \r
 401                 public String getReference() {\r
 402                         return "REFERENCE: " + reference + line_delimiter + "<br>MORE INFORMATION: " + moreinfo + line_delimiter;\r
 403                 }\r
 404 \r
 405                 public String getVersion() {\r
 406                         return version;\r
 407                 }\r
 408         }\r
 409 \r
 410         public static void main(String[] args) {\r
 411                 System.out.println(MUSCLE_INFO);\r
 412         }\r
 413 }\r