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;\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 "";\r
  62                 }\r
  63                 String value = "";\r
  64                 String delim = ", ";\r
  65                 for (Services serv : services) {\r
  66                         value += serv.toString() + delim;\r
  67                 }\r
  68                 value = value.substring(0, value.length() - delim.length());\r
  69                 return value;\r
  70         }\r
  71 \r
  72         Class<? extends JABAService> getServiceType() {\r
  73                 switch (this) {\r
  74                         // deliberate leaking\r
  75                         case AAConWS :\r
  76                         case JronnWS :\r
  77                         case DisemblWS :\r
  78                         case GlobPlotWS :\r
  79                         case IUPredWS :\r
  80                                 return SequenceAnnotation.class;\r
  81 \r
  82                                 // deliberate leaking\r
  83                         case ClustalWS :\r
  84                         case ClustalOWS :\r
  85                         case MafftWS :\r
  86                         case MuscleWS :\r
  87                         case ProbconsWS :\r
  88                         case TcoffeeWS :\r
  89 \r
  90                                 return MsaWS.class;\r
  91                         default :\r
  92                                 throw new RuntimeException("Unrecognised Web Service Type "\r
  93                                                 + this + " - Should never happened!");\r
  94                 }\r
  95         }\r
  96 \r
  97         JABAService getInterface(Service service) {\r
  98                 assert service != null;\r
  99 \r
 100                 QName portName = new QName(service.getServiceName().getNamespaceURI(),\r
 101                                 this.toString() + "Port");\r
 102                 return service.getPort(portName, this.getServiceType());\r
 103         }\r
 104 \r
 105         public String getServiceInfo() {\r
 106                 switch (this) {\r
 107                         case AAConWS :\r
 108                                 return AACON_INFO;\r
 109                         case ClustalOWS :\r
 110                                 return CLUSTAL_OMEGA_INFO;\r
 111                         case ClustalWS :\r
 112                                 return CLUSTAL_INFO;\r
 113                         case DisemblWS :\r
 114                                 return DISEMBL_INFO;\r
 115                         case GlobPlotWS :\r
 116                                 return GLOBPLOT_INFO;\r
 117                         case IUPredWS :\r
 118                                 return IUPRED_INFO;\r
 119                         case JronnWS :\r
 120                                 return JRONN_INFO;\r
 121                         case MafftWS :\r
 122                                 return MAFFT_INFO;\r
 123                         case MuscleWS :\r
 124                                 return MUSCLE_INFO;\r
 125                         case ProbconsWS :\r
 126                                 return PROBCONS_INFO;\r
 127                         case TcoffeeWS :\r
 128                                 return TCOFFEE_INFO;\r
 129                         default :\r
 130                                 throw new RuntimeException("Unrecognised Web Service Type "\r
 131                                                 + this + " - Should never happened!");\r
 132                 }\r
 133         }\r
 134 \r
 135         public static final String AACON_INFO = new ServiceInfo(AAConWS,\r
 136                         "in preparation", "1.0", "http://www.compbio.dundee.ac.uk/aacon")\r
 137                         .toString();\r
 138         public static final String CLUSTAL_INFO = new ServiceInfo(\r
 139                         ClustalWS,\r
 140                         "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
 141                                         + "(2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948. ",\r
 142                         "2.0.12", "http://www.clustal.org/clustal2/").toString();\r
 143         public static final String CLUSTAL_OMEGA_INFO = new ServiceInfo(\r
 144                         ClustalOWS,\r
 145                         "Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega\r\n"\r
 146                                         + "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
 147                         "1.0.2", "http://www.clustal.org/omega").toString();\r
 148         public static final String DISEMBL_INFO = new ServiceInfo(\r
 149                         DisemblWS,\r
 150                         "R. Linding, L.J. Jensen, F. Diella, P. Bork, T.J. Gibson and R.B. Russell\r\n"\r
 151                                         + "Protein disorder prediction: implications for structural proteomics\r\n"\r
 152                                         + "Structure Vol 11, Issue 11, 4 November 2003", "1.5",\r
 153                         "http://dis.embl.de/").toString();\r
 154         public static final String GLOBPLOT_INFO = new ServiceInfo(\r
 155                         GlobPlotWS,\r
 156                         "Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson "\r
 157                                         + "'GlobPlot: exploring protein sequences for globularity and disorder.' Nucl. Acids Res. (2003) 31 (13): 3701-3708. doi: 10.1093/nar/gkg519\r\n",\r
 158                         "2.3", "http://globplot.embl.de/").toString();\r
 159         public static final String IUPRED_INFO = new ServiceInfo(\r
 160                         IUPredWS,\r
 161                         "The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins\r\n"\r
 162                                         + "Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon\r\n"\r
 163                                         + "J. Mol. Biol. (2005) 347, 827-839.", "1.0",\r
 164                         "http://iupred.enzim.hu/").toString();\r
 165         public static final String TCOFFEE_INFO = new ServiceInfo(TcoffeeWS,\r
 166                         "T-Coffee: A novel method for multiple sequence alignments  "\r
 167                                         + "Notredame, Higgins, Heringa, JMB, 302 (205-217) 2000",\r
 168                         "8.99", "http://tcoffee.crg.cat/apps/tcoffee/index.html")\r
 169                         .toString();\r
 170         public static final String MUSCLE_INFO = new ServiceInfo(\r
 171                         MuscleWS,\r
 172                         "Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.\r\n"\r
 173                                         + "doi:10.1093/nar/gkh340", "3.8.31",\r
 174                         "http://www.drive5.com/muscle/").toString();\r
 175         public static final String PROBCONS_INFO = new ServiceInfo(\r
 176                         ProbconsWS,\r
 177                         "Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: "\r
 178                                         + "Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. ",\r
 179                         "1.12", "http://probcons.stanford.edu/").toString();;\r
 180         public static final String JRONN_INFO = new ServiceInfo(\r
 181                         JronnWS,\r
 182                         "unpublished, original algorithm Yang,Z.R., Thomson,R., McMeil,P. and Esnouf,R.M. (2005) "\r
 183                                         + "RONN: the bio-basis function neural network technique applied to the "\r
 184                                         + "dectection of natively disordered regions in proteins Bioinformatics 21: 3369-3376\r\n",\r
 185                         "1.0", "http://www.compbio.dundee.ac.uk/jabaws/").toString();;\r
 186         public static final String MAFFT_INFO = new ServiceInfo(\r
 187                         MafftWS,\r
 188                         "Katoh, Toh 2010 (Bioinformatics 26:1899-1900)\r\n"\r
 189                                         + "Parallelization of the MAFFT multiple sequence alignment program. ",\r
 190                         "6.8.57", "http://mafft.cbrc.jp/alignment/software/").toString();;\r
 191 \r
 192         @XmlAccessorType(XmlAccessType.FIELD)\r
 193         static class ServiceInfo {\r
 194                 Services service;\r
 195                 String reference;\r
 196                 String version;\r
 197                 String moreinfo;\r
 198                 final static String jabaws_version = "2.0";\r
 199                 final static String line_delimiter = "\n";\r
 200 \r
 201                 private ServiceInfo() {\r
 202                         // Default constructor for JAXB\r
 203                 }\r
 204                 private ServiceInfo(Services service, String reference, String version,\r
 205                                 String moreinfo) {\r
 206                         this.service = service;\r
 207                         this.reference = reference;\r
 208                         this.version = version;\r
 209                         this.moreinfo = moreinfo;\r
 210                 }\r
 211 \r
 212                 @Override\r
 213                 public String toString() {\r
 214                         String value = "SERVICE: " + service + " version " + version\r
 215                                         + line_delimiter;\r
 216                         value += "JABAWS v. " + jabaws_version + line_delimiter;\r
 217                         value += "REFERENCES: " + reference + line_delimiter;\r
 218                         value += "MORE INFORMATION: " + moreinfo + line_delimiter;\r
 219                         return value;\r
 220                 }\r
 221         }\r
 222 \r
 223         public static void main(String[] args) {\r
 224                 System.out.println(MUSCLE_INFO);\r
 225         }\r
 226 }