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