X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=webservices%2Fcompbio%2Fws%2Fclient%2FServices.java;h=42d282eb372f4720dabd5354bec4836d28712c42;hb=b2a2fdc2bd95a64b3908d8ea2f31270b6c7199d3;hp=a4e101de9879841e880add22e47ef8fa383857da;hpb=4b647613e686c4edffd44702d86662c6facb2d5a;p=jabaws.git

diff --git a/webservices/compbio/ws/client/Services.java b/webservices/compbio/ws/client/Services.java
index a4e101d..42d282e 100644
--- a/webservices/compbio/ws/client/Services.java
+++ b/webservices/compbio/ws/client/Services.java
@@ -58,14 +58,16 @@ public enum Services {
 
 	public static String toString(Set<Services> services) {
 		if (services == null || services.isEmpty()) {
-			return "";
+			return "No known services...\n";
 		}
 		String value = "";
-		String delim = ", ";
 		for (Services serv : services) {
-			value += serv.toString() + delim;
+			if (null != serv) {
+				value += serv + "\n";
+			} else {
+				value += "Unknown Service\n";
+			}
 		}
-		value = value.substring(0, value.length() - delim.length());
 		return value;
 	}
 
@@ -125,111 +127,205 @@ public enum Services {
 	public String getServiceInfo() {
 		switch (this) {
 			case AAConWS :
-				return AACON_INFO;
+				return AACON_INFO.toString();
+			case JpredWS :
+				return JPRED_INFO.toString();
+			case ClustalOWS :
+				return CLUSTAL_OMEGA_INFO.toString();
+			case ClustalWS :
+				return CLUSTAL_INFO.toString();
+			case DisemblWS :
+				return DISEMBL_INFO.toString();
+			case GlobPlotWS :
+				return GLOBPLOT_INFO.toString();
+			case IUPredWS :
+				return IUPRED_INFO.toString();
+			case JronnWS :
+				return JRONN_INFO.toString();
+			case MafftWS :
+				return MAFFT_INFO.toString();
+			case MuscleWS :
+				return MUSCLE_INFO.toString();
+			case ProbconsWS :
+				return PROBCONS_INFO.toString();
+			case TcoffeeWS :
+				return TCOFFEE_INFO.toString();
+			case RNAalifoldWS :
+				return RNAALIFOLD_INFO.toString();
+			default :
+				throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");
+		}
+	}
+
+	public String getServiceReference() {
+		switch (this) {
+			case AAConWS :
+				return AACON_INFO.getReference();
+			case JpredWS :
+				return JPRED_INFO.getReference();
+			case ClustalOWS :
+				return CLUSTAL_OMEGA_INFO.getReference();
+			case ClustalWS :
+				return CLUSTAL_INFO.getReference();
+			case DisemblWS :
+				return DISEMBL_INFO.getReference();
+			case GlobPlotWS :
+				return GLOBPLOT_INFO.getReference();
+			case IUPredWS :
+				return IUPRED_INFO.getReference();
+			case JronnWS :
+				return JRONN_INFO.getReference();
+			case MafftWS :
+				return MAFFT_INFO.getReference();
+			case MuscleWS :
+				return MUSCLE_INFO.getReference();
+			case ProbconsWS :
+				return PROBCONS_INFO.getReference();
+			case TcoffeeWS :
+				return TCOFFEE_INFO.getReference();
+			case RNAalifoldWS :
+				return RNAALIFOLD_INFO.getReference();
+			default :
+				throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");
+		}
+	}
+
+	public String getServiceVersion() {
+		switch (this) {
+			case AAConWS :
+				return AACON_INFO.getVersion();
 			case JpredWS :
-				return JPRED_INFO;
+				return JPRED_INFO.getVersion();
 			case ClustalOWS :
-				return CLUSTAL_OMEGA_INFO;
+				return CLUSTAL_OMEGA_INFO.getVersion();
 			case ClustalWS :
-				return CLUSTAL_INFO;
+				return CLUSTAL_INFO.getVersion();
 			case DisemblWS :
-				return DISEMBL_INFO;
+				return DISEMBL_INFO.getVersion();
 			case GlobPlotWS :
-				return GLOBPLOT_INFO;
+				return GLOBPLOT_INFO.getVersion();
 			case IUPredWS :
-				return IUPRED_INFO;
+				return IUPRED_INFO.getVersion();
 			case JronnWS :
-				return JRONN_INFO;
+				return JRONN_INFO.getVersion();
 			case MafftWS :
-				return MAFFT_INFO;
+				return MAFFT_INFO.getVersion();
 			case MuscleWS :
-				return MUSCLE_INFO;
+				return MUSCLE_INFO.getVersion();
 			case ProbconsWS :
-				return PROBCONS_INFO;
+				return PROBCONS_INFO.getVersion();
 			case TcoffeeWS :
-				return TCOFFEE_INFO;
+				return TCOFFEE_INFO.getVersion();
 			case RNAalifoldWS :
-				return RNAALIFOLD_INFO;
+				return RNAALIFOLD_INFO.getVersion();
 			default :
 				throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");
 		}
 	}
 
-	public static final String AACON_INFO = new ServiceInfo(AAConWS,
-			"in preparation", "1.0", "http://www.compbio.dundee.ac.uk/aacon").toString();
+	public String getServiceGroup() {
+		switch (this) {
+			case AAConWS :
+				return "annotation";
+			case JpredWS :
+				return "annotation";
+			case ClustalOWS :
+				return "alignment";
+			case ClustalWS :
+				return "alignment";
+			case DisemblWS :
+				return "disorder";
+			case GlobPlotWS :
+				return "disorder";
+			case IUPredWS :
+				return "disorder";
+			case JronnWS :
+				return "disorder";
+			case MafftWS :
+				return "alignment";
+			case MuscleWS :
+				return "alignment";
+			case ProbconsWS :
+				return "alignment";
+			case TcoffeeWS :
+				return "alignment";
+			case RNAalifoldWS :
+				return "annotation";
+			default :
+				throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");
+		}
+	}
+	
+	static ServiceInfo AACON_INFO = new ServiceInfo(AAConWS,
+			"in preparation", "1.0", "http://www.compbio.dundee.ac.uk/aacon");
 
-	public static final String JPRED_INFO = new ServiceInfo(JpredWS,
+	static ServiceInfo JPRED_INFO = new ServiceInfo(JpredWS,
 			"Cole C, Barber JD, Barton GJ.reparation" + 
 			"The Jpred 3 secondary structure prediction server\n" +
 			"Nucl. Acids Res. (2008) 36 (suppl 2): W197-W201., doi: 10.1093/nar/gkn238", 
-			"3.0", "http://www.compbio.dundee.ac.uk/www-jpred").toString();
+			"3.0.3", "http://www.compbio.dundee.ac.uk/www-jpred");
 	
-	public static final String CLUSTAL_INFO = new ServiceInfo(ClustalWS,
+	static ServiceInfo CLUSTAL_INFO = new ServiceInfo(ClustalWS,
 			"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.\n" +
 			"(2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.",
-			"2.0.12", "http://www.clustal.org/clustal2/").toString();
+			"2.0.12", "http://www.clustal.org/clustal2/");
 
-	public static final String CLUSTAL_OMEGA_INFO = new ServiceInfo(ClustalOWS,
+	static ServiceInfo CLUSTAL_OMEGA_INFO = new ServiceInfo(ClustalOWS,
 			"Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega\r\n"
 			+ "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",
-			"1.0.2", "http://www.clustal.org/omega").toString();
+			"1.0.2", "http://www.clustal.org/omega");
 
-	public static final String DISEMBL_INFO = new ServiceInfo(DisemblWS,
+	static ServiceInfo DISEMBL_INFO = new ServiceInfo(DisemblWS,
 			"R. Linding, L.J. Jensen, F. Diella, P. Bork, T.J. Gibson and R.B. Russell\r\n"
 			+ "Protein disorder prediction: implications for structural proteomics\r\n"
 			+ "Structure Vol 11, Issue 11, 4 November 2003", "1.5",
-			"http://dis.embl.de/").toString();
+			"http://dis.embl.de/");
 
-	public static final String GLOBPLOT_INFO = new ServiceInfo(GlobPlotWS,
+	static ServiceInfo GLOBPLOT_INFO = new ServiceInfo(GlobPlotWS,
 			"Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson " +
 			"'GlobPlot: exploring protein sequences for globularity and disorder.' " + 
 			"Nucl. Acids Res. (2003) 31 (13): 3701-3708. doi: 10.1093/nar/gkg519\r\n",
-			"2.3", "http://globplot.embl.de/").toString();
+			"2.3", "http://globplot.embl.de/");
 
-	public static final String IUPRED_INFO = new ServiceInfo(IUPredWS,
+	static ServiceInfo IUPRED_INFO = new ServiceInfo(IUPredWS,
 			"The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins\r\n"
 			+ "Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon\r\n"
 			+ "J. Mol. Biol. (2005) 347, 827-839.", "1.0",
-			"http://iupred.enzim.hu/").toString();
+			"http://iupred.enzim.hu/");
 
-	public static final String TCOFFEE_INFO = new ServiceInfo(TcoffeeWS,
+	static ServiceInfo TCOFFEE_INFO = new ServiceInfo(TcoffeeWS,
 			"T-Coffee: A novel method for multiple sequence alignments  "
 			+ "Notredame, Higgins, Heringa, JMB, 302 (205-217) 2000",
-			"8.99", "http://tcoffee.crg.cat/apps/tcoffee/index.html").toString();
+			"8.99", "http://tcoffee.crg.cat/apps/tcoffee/index.html");
 
-	public static final String MUSCLE_INFO = new ServiceInfo(
-			MuscleWS,
+	static ServiceInfo MUSCLE_INFO = new ServiceInfo(MuscleWS,
 			"Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.\r\n"
 			+ "doi:10.1093/nar/gkh340", "3.8.31",
-			"http://www.drive5.com/muscle/").toString();
+			"http://www.drive5.com/muscle/");
 
-	public static final String PROBCONS_INFO = new ServiceInfo(
-			ProbconsWS,
+	static ServiceInfo PROBCONS_INFO = new ServiceInfo(ProbconsWS,
 			"Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: "
 			+ "Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. ",
-			"1.12", "http://probcons.stanford.edu/").toString();
+			"1.12", "http://probcons.stanford.edu/");
 
-	public static final String JRONN_INFO = new ServiceInfo(
-			JronnWS,
+	static ServiceInfo JRONN_INFO = new ServiceInfo(JronnWS,
 			"unpublished, original algorithm Yang,Z.R., Thomson,R., McMeil,P. and Esnouf,R.M. (2005) "
 					+ "RONN: the bio-basis function neural network technique applied to the "
 					+ "dectection of natively disordered regions in proteins Bioinformatics 21: 3369-3376\r\n",
-			"1.0", "http://www.compbio.dundee.ac.uk/jabaws/").toString();
+			"1.0", "http://www.compbio.dundee.ac.uk/jabaws/");
 
-	public static final String MAFFT_INFO = new ServiceInfo(
-			MafftWS,
+	static ServiceInfo MAFFT_INFO = new ServiceInfo(MafftWS,
 			"Katoh, Toh 2010 (Bioinformatics 26:1899-1900)\r\n"
 					+ "Parallelization of the MAFFT multiple sequence alignment program. ",
-			"6.8.57", "http://mafft.cbrc.jp/alignment/software/").toString();
+			"6.8.57", "http://mafft.cbrc.jp/alignment/software/");
 
-	public static final String RNAALIFOLD_INFO = new ServiceInfo(
-			RNAalifoldWS,
+	static ServiceInfo RNAALIFOLD_INFO = new ServiceInfo(RNAalifoldWS,
 			"Ivo L. Hofacker, Martin Fekete, and Peter F. Stadler 'Secondary Structure Prediction"
 			+ " for Aligned RNA Sequences'. J.Mol.Biol. 319: 1059-1066, 2002. Stephan H. Bernhart,"
 			+ " Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, and Peter F. Stadler. "
 			+ "'RNAalifold: Improved consensus structure prediction for RNA alignments'. BMC Bioinformatics, 9:474, 2008.\r\n",
-			"2.1.2", "http://www.tbi.univie.ac.at/RNA/").toString();
+			"2.1.2", "http://www.tbi.univie.ac.at/RNA/");
 
 	@XmlAccessorType(XmlAccessType.FIELD)
 	static class ServiceInfo {
@@ -253,12 +349,20 @@ public enum Services {
 
 		@Override
 		public String toString() {
-			String value = "SERVICE: " + service + " version " + version + line_delimiter;
+			String value = "SERVICE: " + service + " version " + version + line_delimiter + "\n";
 			value += "JABAWS v. " + jabaws_version + line_delimiter;
-			value += "REFERENCES: " + reference + line_delimiter;
+			value += "REFERENCE: " + reference + line_delimiter + "\n";
 			value += "MORE INFORMATION: " + moreinfo + line_delimiter;
 			return value;
 		}
+
+		public String getReference() {
+			return "REFERENCE: " + reference + line_delimiter + "<br>MORE INFORMATION: " + moreinfo + line_delimiter;
+		}
+
+		public String getVersion() {
+			return version;
+		}
 	}
 
 	public static void main(String[] args) {