import compbio.data.msa.SequenceAnnotation;\r
\r
/**\r
- * List of web services currently supported by JABAWS version 2\r
+ * List of web services currently supported by JABAWS version 2.1\r
* \r
*/\r
public enum Services {\r
* Make sure this class has NO references to runners or engines as it is a\r
* part of minimal client package. Such things should go into ServicesUtil\r
*/\r
- MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS, JpredWS, RNAalifoldWS;\r
+ MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, MSAprobsWS, GLprobsWS,\r
+ AAConWS, \r
+ JronnWS, DisemblWS, GlobPlotWS, IUPredWS, \r
+ JpredWS, \r
+ RNAalifoldWS;\r
\r
public static Services getService(String servName) {\r
servName = servName.trim().toLowerCase();\r
case MafftWS :\r
case MuscleWS :\r
case ProbconsWS :\r
+ case MSAprobsWS :\r
+ case GLprobsWS :\r
case TcoffeeWS :\r
return MsaWS.class;\r
-\r
default :\r
throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
}\r
case MafftWS :\r
case MuscleWS :\r
case ProbconsWS :\r
+ case MSAprobsWS :\r
+ case GLprobsWS :\r
case TcoffeeWS :\r
return JABAService.SERVICE_NAMESPACE;\r
default :\r
return MUSCLE_INFO.toString();\r
case ProbconsWS :\r
return PROBCONS_INFO.toString();\r
+ case MSAprobsWS :\r
+ return MSAPROBS_INFO.toString();\r
+ case GLprobsWS :\r
+ return GLPROBS_INFO.toString();\r
case TcoffeeWS :\r
return TCOFFEE_INFO.toString();\r
case RNAalifoldWS :\r
return MUSCLE_INFO.getReference();\r
case ProbconsWS :\r
return PROBCONS_INFO.getReference();\r
+ case MSAprobsWS :\r
+ return MSAPROBS_INFO.getReference();\r
+ case GLprobsWS :\r
+ return GLPROBS_INFO.getReference();\r
case TcoffeeWS :\r
return TCOFFEE_INFO.getReference();\r
case RNAalifoldWS :\r
return MUSCLE_INFO.getVersion();\r
case ProbconsWS :\r
return PROBCONS_INFO.getVersion();\r
+ case MSAprobsWS :\r
+ return MSAPROBS_INFO.getVersion();\r
+ case GLprobsWS :\r
+ return GLPROBS_INFO.getVersion();\r
case TcoffeeWS :\r
return TCOFFEE_INFO.getVersion();\r
case RNAalifoldWS :\r
return "alignment";\r
case ProbconsWS :\r
return "alignment";\r
+ case GLprobsWS :\r
+ return "alignment";\r
+ case MSAprobsWS :\r
+ return "alignment";\r
case TcoffeeWS :\r
return "alignment";\r
case RNAalifoldWS :\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
+ "Cole C, Barber JD, Barton GJ,\r\n" + \r
+ "\"The Jpred 3 secondary structure prediction server\"\r\n" +\r
+ "Nucl. Acids Res. 36 (suppl 2):W197 (2008)", \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
+ "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
+ "\"Clustal W and Clustal X version 2.0\"\r\n" + \r
+ "Bioinformatics, 23: 2947 (2007)",\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
+ "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
+ "\"Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega\"\r\n" +\r
+ "Mol Syst Biol. 7:539 (2011)",\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
+ "Linding R, Jensen LJ, Diella F, Bork P, Gibson TJ, and Russell RB,\r\n" +\r
+ "\"Protein disorder prediction: implications for structural proteomics\"\r\n" +\r
+ "Structure 11(11):1453 (2003)", \r
+ "1.5", "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
+ "Linding R, Russell RB, Neduva V and Gibson TJ,\r\n" +\r
+ "GlobPlot: exploring protein sequences for globularity and disorder\r\n" + \r
+ "Nucl. Acids Res. 31 (13):3701 (2003)",\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
+ "Dosztányi Z, Csizmók V, Tompa P, and Simon I,\r\n" +\r
+ "\"The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins\"\r\n" +\r
+ "J. Mol. Biol. 347:827 (2005)", \r
+ "1.0", "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
+ "Notredame C, Higgins DG, Heringa L,\r\n" +\r
+ "\"T-Coffee: A novel method for multiple sequence alignments\"\r\n" + \r
+ "JMB, 302(1):205 (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
+ "Edgar RC,\r\n"+ \r
+ "\"MUSCLE: multiple sequence alignment with high accuracy and high throughput\"\r\n" + \r
+ "Nucleic Acids Res. 32(5):1792 (2004)", \r
+ "3.8.31", "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
+ "Do CB, Mahabhashyam MSP, Brudno M, and Batzoglou S,\r\n" +\r
+ "\"PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment\"\r\n" + \r
+ "Genome Research 15:330 (2005)",\r
"1.12", "http://probcons.stanford.edu/");\r
\r
+ static ServiceInfo MSAPROBS_INFO = new ServiceInfo(MSAprobsWS,\r
+ "Liu Y, Schmidt B, and Maskell DL,\r\n" + \r
+ "\"MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities\"\r\n" +\r
+ "Bioinformatics, 26 (16):1958 (2010)",\r
+ "0.9.7", "http://msaprobs.sourceforge.net/");\r
+\r
+ static ServiceInfo GLPROBS_INFO = new ServiceInfo(GLprobsWS,\r
+ "Yongtao Ye, Siu-Ming Yiu, David W. Cheung, Qing Zhan, Hing-Fung Ting, Yadong Wang, Tak-Wah Lam,\r\n" +\r
+ "\"GLProbs: Aligning multiple sequences adaptively\"\r\n" + \r
+ "in progress (2013)",\r
+ "1.0", "http://sourceforge.net/projects/glprobs/");\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
+ "unpublished, original algorithm Yang ZR, Thomson R, McMeil P, and Esnouf RM,\r\n" + \r
+ "\"RONN: the bio-basis function neural network technique applied to the dectection of natively disordered regions in proteins\"\r\n" +\r
+ "Bioinformatics 21:3369 (2005)\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
+ "Katoh K, Toh H,\r\n" +\r
+ "\"Parallelization of the MAFFT multiple sequence alignment program\"\r\n" + \r
+ "Bioinformatics 26:1899 (2010)",\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
+ "Hofacker IL, Fekete M, and Stadler PV,\r\n"+ \r
+ "\"Secondary Structure Prediction for Aligned RNA Sequences\"\r\n" + \r
+ "J.Mol.Biol. 319:1059 (2002) and\r\n " + \r
+ "Bernhart SH, Hofacker IL Will S, Gruber AR, and Stadler PF,\r\n" + \r
+ "\"RNAalifold: Improved consensus structure prediction for RNA alignments\"\r\n" +\r
+ "BMC Bioinformatics, 9:474 (2008)\r\n",\r
"2.1.2", "http://www.tbi.univie.ac.at/RNA/");\r
\r
@XmlAccessorType(XmlAccessType.FIELD)\r
String reference;\r
String version;\r
String moreinfo;\r
- final static String jabaws_version = "2.5";\r
+ final static String jabaws_version = "2.1";\r
final static String line_delimiter = "\n";\r
\r
private ServiceInfo() {\r
git://source.jalview.org / jabaws.git / blobdiff