+ \r
+ static ServiceInfo AACON_INFO = new ServiceInfo(AAConWS,\r
+ "in preparation", "1.0", "http://www.compbio.dundee.ac.uk/aacon");\r
+\r
+ static ServiceInfo JPRED_INFO = new ServiceInfo(JpredWS,\r
+ "Cole C, Barber JD, Barton GJ.reparation" + \r
+ "The Jpred 3 secondary structure prediction server\n" +\r
+ "Nucl. Acids Res. (2008) 36 (suppl 2): W197-W201., doi: 10.1093/nar/gkn238", \r
+ "3.0.3", "http://www.compbio.dundee.ac.uk/www-jpred");\r
+ \r
+ static ServiceInfo CLUSTAL_INFO = new ServiceInfo(ClustalWS,\r
+ "Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, " + \r
+ "Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG.\n" +\r
+ "(2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.",\r
+ "2.0.12", "http://www.clustal.org/clustal2/");\r
+\r
+ static ServiceInfo CLUSTAL_OMEGA_INFO = new ServiceInfo(ClustalOWS,\r
+ "Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega\r\n"\r
+ + "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
+ "1.0.2", "http://www.clustal.org/omega");\r
+\r
+ static ServiceInfo DISEMBL_INFO = new ServiceInfo(DisemblWS,\r
+ "R. Linding, L.J. Jensen, F. Diella, P. Bork, T.J. Gibson and R.B. Russell\r\n"\r
+ + "Protein disorder prediction: implications for structural proteomics\r\n"\r
+ + "Structure Vol 11, Issue 11, 4 November 2003", "1.5",\r
+ "http://dis.embl.de/");\r
+\r
+ static ServiceInfo GLOBPLOT_INFO = new ServiceInfo(GlobPlotWS,\r
+ "Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson " +\r
+ "'GlobPlot: exploring protein sequences for globularity and disorder.' " + \r
+ "Nucl. Acids Res. (2003) 31 (13): 3701-3708. doi: 10.1093/nar/gkg519\r\n",\r
+ "2.3", "http://globplot.embl.de/");\r
+\r
+ static ServiceInfo IUPRED_INFO = new ServiceInfo(IUPredWS,\r
+ "The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins\r\n"\r
+ + "Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon\r\n"\r
+ + "J. Mol. Biol. (2005) 347, 827-839.", "1.0",\r
+ "http://iupred.enzim.hu/");\r
+\r
+ static ServiceInfo TCOFFEE_INFO = new ServiceInfo(TcoffeeWS,\r
+ "T-Coffee: A novel method for multiple sequence alignments "\r
+ + "Notredame, Higgins, Heringa, JMB, 302 (205-217) 2000",\r
+ "8.99", "http://tcoffee.crg.cat/apps/tcoffee/index.html");\r
+\r
+ static ServiceInfo MUSCLE_INFO = new ServiceInfo(MuscleWS,\r
+ "Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.\r\n"\r
+ + "doi:10.1093/nar/gkh340", "3.8.31",\r
+ "http://www.drive5.com/muscle/");\r
+\r
+ static ServiceInfo PROBCONS_INFO = new ServiceInfo(ProbconsWS,\r
+ "Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: "\r
+ + "Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. ",\r
+ "1.12", "http://probcons.stanford.edu/");\r
+\r
+ static ServiceInfo JRONN_INFO = new ServiceInfo(JronnWS,\r
+ "unpublished, original algorithm Yang,Z.R., Thomson,R., McMeil,P. and Esnouf,R.M. (2005) "\r
+ + "RONN: the bio-basis function neural network technique applied to the "\r
+ + "dectection of natively disordered regions in proteins Bioinformatics 21: 3369-3376\r\n",\r
+ "1.0", "http://www.compbio.dundee.ac.uk/jabaws/");\r
+\r
+ static ServiceInfo MAFFT_INFO = new ServiceInfo(MafftWS,\r
+ "Katoh, Toh 2010 (Bioinformatics 26:1899-1900)\r\n"\r
+ + "Parallelization of the MAFFT multiple sequence alignment program. ",\r
+ "6.8.57", "http://mafft.cbrc.jp/alignment/software/");\r
+\r
+ static ServiceInfo RNAALIFOLD_INFO = new ServiceInfo(RNAalifoldWS,\r
+ "Ivo L. Hofacker, Martin Fekete, and Peter F. Stadler 'Secondary Structure Prediction"\r
+ + " for Aligned RNA Sequences'. J.Mol.Biol. 319: 1059-1066, 2002. Stephan H. Bernhart,"\r
+ + " Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, and Peter F. Stadler. "\r
+ + "'RNAalifold: Improved consensus structure prediction for RNA alignments'. BMC Bioinformatics, 9:474, 2008.\r\n",\r
+ "2.1.2", "http://www.tbi.univie.ac.at/RNA/");\r
+\r
+ @XmlAccessorType(XmlAccessType.FIELD)\r
+ static class ServiceInfo {\r
+ Services service;\r
+ String reference;\r
+ String version;\r
+ String moreinfo;\r
+ final static String jabaws_version = "2.5";\r
+ final static String line_delimiter = "\n";\r
+\r
+ private ServiceInfo() {\r
+ // Default constructor for JAXB\r
+ }\r
+ private ServiceInfo(Services service, String reference, String version,\r
+ String moreinfo) {\r
+ this.service = service;\r
+ this.reference = reference;\r
+ this.version = version;\r
+ this.moreinfo = moreinfo;\r
+ }\r
+\r
+ @Override\r
+ public String toString() {\r
+ String value = "SERVICE: " + service + " version " + version + line_delimiter + "\n";\r
+ value += "JABAWS v. " + jabaws_version + line_delimiter;\r
+ value += "REFERENCE: " + reference + line_delimiter + "\n";\r
+ value += "MORE INFORMATION: " + moreinfo + line_delimiter;\r
+ return value;\r
+ }\r
+\r
+ public String getReference() {\r
+ return "REFERENCE: " + reference + line_delimiter + "<br>MORE INFORMATION: " + moreinfo + line_delimiter;\r
+ }\r
+\r
+ public String getVersion() {\r
+ return version;\r
+ }\r
+ }\r
+\r
+ public static void main(String[] args) {\r
+ System.out.println(MUSCLE_INFO);\r
+ }\r
+}\r