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\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, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS, JpredWS, RNAalifoldWS;\r
  43 \r
  44         public static Services getService(String servName) {\r
  45                 servName = servName.trim().toLowerCase();\r
  46                 for (Services service : Services.values()) {\r
  47                         if (service.toString().equalsIgnoreCase(servName)) {\r
  48                                 return service;\r
  49                         }\r
  50                 }\r
  51                 return null;\r
  52         }\r
  53 \r
  54         Service getService(URL url, String sqname) {\r
  55                 QName qname = new QName(sqname, this.toString());\r
  56                 return Service.create(url, qname);\r
  57         }\r
  58 \r
  59         public static String toString(Set<Services> services) {\r
  60                 if (services == null || services.isEmpty()) {\r
  61                         return "No known services...\n";\r
  62                 }\r
  63                 String value = "";\r
  64                 for (Services serv : services) {\r
  65                         if (null != serv) {\r
  66                                 value += serv + "\n";\r
  67                         } else {\r
  68                                 value += "Unknown Service\n";\r
  69                         }\r
  70                 }\r
  71                 return value;\r
  72         }\r
  73 \r
  74         Class<? extends JABAService> getServiceType() {\r
  75                 switch (this) {\r
  76                         case AAConWS :\r
  77                         case JronnWS :\r
  78                         case DisemblWS :\r
  79                         case GlobPlotWS :\r
  80                         case IUPredWS :\r
  81                         case RNAalifoldWS :\r
  82                                 return SequenceAnnotation.class;\r
  83                         case JpredWS :\r
  84                         case ClustalWS :\r
  85                         case ClustalOWS :\r
  86                         case MafftWS :\r
  87                         case MuscleWS :\r
  88                         case ProbconsWS :\r
  89                         case TcoffeeWS :\r
  90                                 return MsaWS.class;\r
  91 \r
  92                         default :\r
  93                                 throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
  94                 }\r
  95         }\r
  96 \r
  97         \r
  98         String getServiceNamespace() {\r
  99                 switch (this) {\r
 100                         case RNAalifoldWS :\r
 101                         case AAConWS :\r
 102                         case JronnWS :\r
 103                         case DisemblWS :\r
 104                         case GlobPlotWS :\r
 105                         case IUPredWS :\r
 106                                 return JABAService.V2_SERVICE_NAMESPACE;\r
 107                         case ClustalOWS :\r
 108                         case JpredWS :\r
 109                         case ClustalWS :\r
 110                         case MafftWS :\r
 111                         case MuscleWS :\r
 112                         case ProbconsWS :\r
 113                         case TcoffeeWS :\r
 114                                 return JABAService.SERVICE_NAMESPACE;\r
 115                         default :\r
 116                                 throw new RuntimeException("Unrecognised JABAWS Namespace for service " + this +"!");\r
 117                 }\r
 118         }\r
 119         \r
 120         JABAService getInterface(Service service) {\r
 121                 assert service != null;\r
 122 \r
 123                 QName portName = new QName(service.getServiceName().getNamespaceURI(), this.toString() + "Port");\r
 124                 return service.getPort(portName, this.getServiceType());\r
 125         }\r
 126 \r
 127         public String getServiceInfo() {\r
 128                 switch (this) {\r
 129                         case AAConWS :\r
 130                                 return AACON_INFO.toString();\r
 131                         case JpredWS :\r
 132                                 return JPRED_INFO.toString();\r
 133                         case ClustalOWS :\r
 134                                 return CLUSTAL_OMEGA_INFO.toString();\r
 135                         case ClustalWS :\r
 136                                 return CLUSTAL_INFO.toString();\r
 137                         case DisemblWS :\r
 138                                 return DISEMBL_INFO.toString();\r
 139                         case GlobPlotWS :\r
 140                                 return GLOBPLOT_INFO.toString();\r
 141                         case IUPredWS :\r
 142                                 return IUPRED_INFO.toString();\r
 143                         case JronnWS :\r
 144                                 return JRONN_INFO.toString();\r
 145                         case MafftWS :\r
 146                                 return MAFFT_INFO.toString();\r
 147                         case MuscleWS :\r
 148                                 return MUSCLE_INFO.toString();\r
 149                         case ProbconsWS :\r
 150                                 return PROBCONS_INFO.toString();\r
 151                         case TcoffeeWS :\r
 152                                 return TCOFFEE_INFO.toString();\r
 153                         case RNAalifoldWS :\r
 154                                 return RNAALIFOLD_INFO.toString();\r
 155                         default :\r
 156                                 throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
 157                 }\r
 158         }\r
 159 \r
 160         public String getServiceReference() {\r
 161                 switch (this) {\r
 162                         case AAConWS :\r
 163                                 return AACON_INFO.getReference();\r
 164                         case JpredWS :\r
 165                                 return JPRED_INFO.getReference();\r
 166                         case ClustalOWS :\r
 167                                 return CLUSTAL_OMEGA_INFO.getReference();\r
 168                         case ClustalWS :\r
 169                                 return CLUSTAL_INFO.getReference();\r
 170                         case DisemblWS :\r
 171                                 return DISEMBL_INFO.getReference();\r
 172                         case GlobPlotWS :\r
 173                                 return GLOBPLOT_INFO.getReference();\r
 174                         case IUPredWS :\r
 175                                 return IUPRED_INFO.getReference();\r
 176                         case JronnWS :\r
 177                                 return JRONN_INFO.getReference();\r
 178                         case MafftWS :\r
 179                                 return MAFFT_INFO.getReference();\r
 180                         case MuscleWS :\r
 181                                 return MUSCLE_INFO.getReference();\r
 182                         case ProbconsWS :\r
 183                                 return PROBCONS_INFO.getReference();\r
 184                         case TcoffeeWS :\r
 185                                 return TCOFFEE_INFO.getReference();\r
 186                         case RNAalifoldWS :\r
 187                                 return RNAALIFOLD_INFO.getReference();\r
 188                         default :\r
 189                                 throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
 190                 }\r
 191         }\r
 192 \r
 193         public String getServiceVersion() {\r
 194                 switch (this) {\r
 195                         case AAConWS :\r
 196                                 return AACON_INFO.getVersion();\r
 197                         case JpredWS :\r
 198                                 return JPRED_INFO.getVersion();\r
 199                         case ClustalOWS :\r
 200                                 return CLUSTAL_OMEGA_INFO.getVersion();\r
 201                         case ClustalWS :\r
 202                                 return CLUSTAL_INFO.getVersion();\r
 203                         case DisemblWS :\r
 204                                 return DISEMBL_INFO.getVersion();\r
 205                         case GlobPlotWS :\r
 206                                 return GLOBPLOT_INFO.getVersion();\r
 207                         case IUPredWS :\r
 208                                 return IUPRED_INFO.getVersion();\r
 209                         case JronnWS :\r
 210                                 return JRONN_INFO.getVersion();\r
 211                         case MafftWS :\r
 212                                 return MAFFT_INFO.getVersion();\r
 213                         case MuscleWS :\r
 214                                 return MUSCLE_INFO.getVersion();\r
 215                         case ProbconsWS :\r
 216                                 return PROBCONS_INFO.getVersion();\r
 217                         case TcoffeeWS :\r
 218                                 return TCOFFEE_INFO.getVersion();\r
 219                         case RNAalifoldWS :\r
 220                                 return RNAALIFOLD_INFO.getVersion();\r
 221                         default :\r
 222                                 throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
 223                 }\r
 224         }\r
 225 \r
 226         public String getServiceGroup() {\r
 227                 switch (this) {\r
 228                         case AAConWS :\r
 229                                 return "annotation";\r
 230                         case JpredWS :\r
 231                                 return "annotation";\r
 232                         case ClustalOWS :\r
 233                                 return "alignment";\r
 234                         case ClustalWS :\r
 235                                 return "alignment";\r
 236                         case DisemblWS :\r
 237                                 return "disorder";\r
 238                         case GlobPlotWS :\r
 239                                 return "disorder";\r
 240                         case IUPredWS :\r
 241                                 return "disorder";\r
 242                         case JronnWS :\r
 243                                 return "disorder";\r
 244                         case MafftWS :\r
 245                                 return "alignment";\r
 246                         case MuscleWS :\r
 247                                 return "alignment";\r
 248                         case ProbconsWS :\r
 249                                 return "alignment";\r
 250                         case TcoffeeWS :\r
 251                                 return "alignment";\r
 252                         case RNAalifoldWS :\r
 253                                 return "annotation";\r
 254                         default :\r
 255                                 throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
 256                 }\r
 257         }\r
 258         \r
 259         static ServiceInfo AACON_INFO = new ServiceInfo(AAConWS,\r
 260                         "in preparation", "1.0", "http://www.compbio.dundee.ac.uk/aacon");\r
 261 \r
 262         static ServiceInfo JPRED_INFO = new ServiceInfo(JpredWS,\r
 263                         "Cole C, Barber JD, Barton GJ.reparation" + \r
 264                         "The Jpred 3 secondary structure prediction server\n" +\r
 265                         "Nucl. Acids Res. (2008) 36 (suppl 2): W197-W201., doi: 10.1093/nar/gkn238", \r
 266                         "3.0.3", "http://www.compbio.dundee.ac.uk/www-jpred");\r
 267         \r
 268         static ServiceInfo CLUSTAL_INFO = new ServiceInfo(ClustalWS,\r
 269                         "Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, " + \r
 270                         "Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG.\n" +\r
 271                         "(2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.",\r
 272                         "2.0.12", "http://www.clustal.org/clustal2/");\r
 273 \r
 274         static ServiceInfo CLUSTAL_OMEGA_INFO = new ServiceInfo(ClustalOWS,\r
 275                         "Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega\r\n"\r
 276                         + "Fabian Sievers, Andreas Wilm, David Dineen, Toby J. Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D. Thompson, Desmond G. Higgins",\r
 277                         "1.0.2", "http://www.clustal.org/omega");\r
 278 \r
 279         static ServiceInfo DISEMBL_INFO = new ServiceInfo(DisemblWS,\r
 280                         "R. Linding, L.J. Jensen, F. Diella, P. Bork, T.J. Gibson and R.B. Russell\r\n"\r
 281                         + "Protein disorder prediction: implications for structural proteomics\r\n"\r
 282                         + "Structure Vol 11, Issue 11, 4 November 2003", "1.5",\r
 283                         "http://dis.embl.de/");\r
 284 \r
 285         static ServiceInfo GLOBPLOT_INFO = new ServiceInfo(GlobPlotWS,\r
 286                         "Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson " +\r
 287                         "'GlobPlot: exploring protein sequences for globularity and disorder.' " + \r
 288                         "Nucl. Acids Res. (2003) 31 (13): 3701-3708. doi: 10.1093/nar/gkg519\r\n",\r
 289                         "2.3", "http://globplot.embl.de/");\r
 290 \r
 291         static ServiceInfo IUPRED_INFO = new ServiceInfo(IUPredWS,\r
 292                         "The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins\r\n"\r
 293                         + "Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon\r\n"\r
 294                         + "J. Mol. Biol. (2005) 347, 827-839.", "1.0",\r
 295                         "http://iupred.enzim.hu/");\r
 296 \r
 297         static ServiceInfo TCOFFEE_INFO = new ServiceInfo(TcoffeeWS,\r
 298                         "T-Coffee: A novel method for multiple sequence alignments  "\r
 299                         + "Notredame, Higgins, Heringa, JMB, 302 (205-217) 2000",\r
 300                         "8.99", "http://tcoffee.crg.cat/apps/tcoffee/index.html");\r
 301 \r
 302         static ServiceInfo MUSCLE_INFO = new ServiceInfo(MuscleWS,\r
 303                         "Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.\r\n"\r
 304                         + "doi:10.1093/nar/gkh340", "3.8.31",\r
 305                         "http://www.drive5.com/muscle/");\r
 306 \r
 307         static ServiceInfo PROBCONS_INFO = new ServiceInfo(ProbconsWS,\r
 308                         "Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: "\r
 309                         + "Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. ",\r
 310                         "1.12", "http://probcons.stanford.edu/");\r
 311 \r
 312         static ServiceInfo JRONN_INFO = new ServiceInfo(JronnWS,\r
 313                         "unpublished, original algorithm Yang,Z.R., Thomson,R., McMeil,P. and Esnouf,R.M. (2005) "\r
 314                                         + "RONN: the bio-basis function neural network technique applied to the "\r
 315                                         + "dectection of natively disordered regions in proteins Bioinformatics 21: 3369-3376\r\n",\r
 316                         "1.0", "http://www.compbio.dundee.ac.uk/jabaws/");\r
 317 \r
 318         static ServiceInfo MAFFT_INFO = new ServiceInfo(MafftWS,\r
 319                         "Katoh, Toh 2010 (Bioinformatics 26:1899-1900)\r\n"\r
 320                                         + "Parallelization of the MAFFT multiple sequence alignment program. ",\r
 321                         "6.8.57", "http://mafft.cbrc.jp/alignment/software/");\r
 322 \r
 323         static ServiceInfo RNAALIFOLD_INFO = new ServiceInfo(RNAalifoldWS,\r
 324                         "Ivo L. Hofacker, Martin Fekete, and Peter F. Stadler 'Secondary Structure Prediction"\r
 325                         + " for Aligned RNA Sequences'. J.Mol.Biol. 319: 1059-1066, 2002. Stephan H. Bernhart,"\r
 326                         + " Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, and Peter F. Stadler. "\r
 327                         + "'RNAalifold: Improved consensus structure prediction for RNA alignments'. BMC Bioinformatics, 9:474, 2008.\r\n",\r
 328                         "2.1.2", "http://www.tbi.univie.ac.at/RNA/");\r
 329 \r
 330         @XmlAccessorType(XmlAccessType.FIELD)\r
 331         static class ServiceInfo {\r
 332                 Services service;\r
 333                 String reference;\r
 334                 String version;\r
 335                 String moreinfo;\r
 336                 final static String jabaws_version = "2.5";\r
 337                 final static String line_delimiter = "\n";\r
 338 \r
 339                 private ServiceInfo() {\r
 340                         // Default constructor for JAXB\r
 341                 }\r
 342                 private ServiceInfo(Services service, String reference, String version,\r
 343                                 String moreinfo) {\r
 344                         this.service = service;\r
 345                         this.reference = reference;\r
 346                         this.version = version;\r
 347                         this.moreinfo = moreinfo;\r
 348                 }\r
 349 \r
 350                 @Override\r
 351                 public String toString() {\r
 352                         String value = "SERVICE: " + service + " version " + version + line_delimiter + "\n";\r
 353                         value += "JABAWS v. " + jabaws_version + line_delimiter;\r
 354                         value += "REFERENCE: " + reference + line_delimiter + "\n";\r
 355                         value += "MORE INFORMATION: " + moreinfo + line_delimiter;\r
 356                         return value;\r
 357                 }\r
 358 \r
 359                 public String getReference() {\r
 360                         return "REFERENCE: " + reference + line_delimiter + "<br>MORE INFORMATION: " + moreinfo + line_delimiter;\r
 361                 }\r
 362 \r
 363                 public String getVersion() {\r
 364                         return version;\r
 365                 }\r
 366         }\r
 367 \r
 368         public static void main(String[] args) {\r
 369                 System.out.println(MUSCLE_INFO);\r
 370         }\r
 371 }\r