X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FJabaParamStore.java;h=baa1d9d9c5e4ba428963ddb2dea21d12205b8de6;hb=f59ae49cdd2bb8f6721424ea6ce167e8245e7d15;hp=b9f6066a8ff5702aacc4f7b8c3e6eb61dc3fb1f5;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git diff --git a/src/jalview/ws/jws2/JabaParamStore.java b/src/jalview/ws/jws2/JabaParamStore.java index b9f6066..baa1d9d 100644 --- a/src/jalview/ws/jws2/JabaParamStore.java +++ b/src/jalview/ws/jws2/JabaParamStore.java @@ -1,27 +1,28 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.ws.jws2; -import java.io.BufferedReader; import java.io.IOException; -import java.io.Reader; -import java.io.Writer; import java.util.ArrayList; +import java.util.Arrays; import java.util.Hashtable; import java.util.List; import java.util.StringTokenizer; @@ -33,10 +34,11 @@ import compbio.metadata.Preset; import compbio.metadata.PresetManager; import compbio.metadata.RunnerConfig; -import jalview.ws.jws2.Jws2Discoverer.Jws2Instance; +import jalview.util.MessageManager; import jalview.ws.jws2.dm.JabaOption; import jalview.ws.jws2.dm.JabaParameter; import jalview.ws.jws2.dm.JabaWsParamSet; +import jalview.ws.jws2.jabaws2.Jws2Instance; import jalview.ws.params.ArgumentI; import jalview.ws.params.ParamDatastoreI; import jalview.ws.params.ParamManager; @@ -140,24 +142,54 @@ public class JabaParamStore implements ParamDatastoreI public static List getJwsArgsfromJaba(List jabargs) { + return getJwsArgsfromJaba(jabargs, true); + } + + public static List getJwsArgsfromJaba(List jabargs, + boolean sortByOpt) + { List rgs = new ArrayList(); + List rgnames = new ArrayList(); for (Object rg : jabargs) { - ArgumentI narg = (rg instanceof Parameter) ? new JabaParameter( - (Parameter) rg) : (rg instanceof Option) ? new JabaOption( - (Option) rg) : null; + ArgumentI narg = null; + String nargstring = null; + if (rg instanceof Parameter) + { + narg = new JabaParameter((Parameter) rg); + nargstring = narg.getName(); // just sort by name for this + } + else if (rg instanceof Option) + { + narg = new JabaOption((Option) rg); + nargstring = (String) ((Option) rg).getOptionNames().get(0); + } if (narg == null) { - throw new Error( - "Implementation Error: Cannot handle Jaba parameter object " - + rg.getClass()); + throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_handle_jaba_param", new String[]{rg.getClass().toString()})); } else { rgs.add(narg); + rgnames.add(nargstring); } } - return rgs; + if (!sortByOpt) + { + return rgs; + } + ArgumentI[] rgssort = rgs.toArray(new ArgumentI[rgs.size()]); + String[] rgssorton = rgnames.toArray(new String[rgs.size()]); + jalview.util.QuickSort.sort(rgssorton, rgssort); + ArgumentI tmp1; + int i = 0; + while (rgssort.length - i > i) + { + tmp1 = rgssort[rgssort.length - i - 1]; + rgssort[rgssort.length - i - 1] = rgssort[i]; + rgssort[i++] = tmp1; + } + return Arrays.asList(rgssort); } public static List getJabafromJwsArgs(List jwsargs) @@ -169,9 +201,7 @@ public class JabaParamStore implements ParamDatastoreI .getOption() : null; if (narg == null) { - throw new Error( - "Implementation Error: Cannot handle Jaba parameter object " - + rg.getClass()); + throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_handle_jaba_param", new String[]{rg.getClass().toString()})); } else { @@ -209,8 +239,7 @@ public class JabaParamStore implements ParamDatastoreI } if (servicePresets.containsKey(name)) { - throw new Error( - "Implementation error: Attempt to delete a service preset!"); + throw new Error(MessageManager.getString("error.implementation_error_attempt_to_delete_service_preset")); } } @@ -236,9 +265,7 @@ public class JabaParamStore implements ParamDatastoreI : getPreset(presetName)); if (jps == null) { - throw new Error("Implementation error: Can't locate either oldname (" - + oldName + ") or presetName (" + presetName - + "in the datastore!"); + throw new Error(MessageManager.formatMessage("error.implementation_error_cannot_locate_oldname_presetname", new String[]{oldName,presetName})); } jps.setName(presetName); jps.setDescription(text); @@ -272,7 +299,8 @@ public class JabaParamStore implements ParamDatastoreI boolean found = false; for (String url : urls) { - if (service.getUri().equalsIgnoreCase(url)) + if (service.getServiceTypeURI().equals(url) + || service.getUri().equalsIgnoreCase(url)) { found = true; break; @@ -287,8 +315,7 @@ public class JabaParamStore implements ParamDatastoreI { if (!involves(urls)) { - throw new IOException( - "Implementation error: Cannot find service url in the given url set!"); + throw new IOException(MessageManager.getString("error.implementation_error_cannot_find_service_url_in_given_set")); } JabaWsParamSet wsp = new JabaWsParamSet(); @@ -313,15 +340,11 @@ public class JabaParamStore implements ParamDatastoreI { if (!involves(pset.getApplicableUrls())) { - throw new IOException( - "Implementation error: Cannot find service url in the given url set for this service parameter store (" - + service.getUri() + ") !"); - + throw new IOException(MessageManager.formatMessage("error.implementation_error_cannot_find_service_url_in_given_set_param_store", new String[]{service.getUri()})); } if (!(pset instanceof JabaWsParamSet)) { - throw new Error( - "Implementation error: JabaWsParamSets can only be handled by JabaParamStore"); + throw new Error(MessageManager.getString("error.implementation_error_jabaws_param_set_only_handled_by")); } StringBuffer rslt = new StringBuffer();