From e341b16beaae6c54348381d4a0bc11f094246067 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 20 Jul 2018 14:27:50 +0100 Subject: [PATCH] =?utf8?q?JAL-3070=20core=20service=20descriptors=20for=20JA?= =?utf8?q?BAWS=20services=20abstracted=20to=20jalview.ws.api.UIinfo=20Note:=20?= =?utf8?q?The=20jws2.WSClient=E2=80=99s=20=E2=80=99serviceType=E2=80=99=20is?= =?utf8?q?=20now=20UIinfo.getName()=20-=20reflecting=20that=20serviceType=20?= =?utf8?q?was=20actually=20the=20name=20of=20the=20service?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- src/jalview/gui/AlignFrame.java | 2 +- src/jalview/ws/api/UIinfo.java | 40 ++++++- src/jalview/ws/jws2/AADisorderClient.java | 12 +- src/jalview/ws/jws2/JabaParamStore.java | 12 +- src/jalview/ws/jws2/Jws2Client.java | 12 +- src/jalview/ws/jws2/Jws2Discoverer.java | 121 +++++++++++--------- src/jalview/ws/jws2/MsaWSClient.java | 4 +- src/jalview/ws/jws2/RNAalifoldClient.java | 8 +- .../ws/jws2/SequenceAnnotationWSClient.java | 9 +- src/jalview/ws/jws2/dm/AAConSettings.java | 7 +- src/jalview/ws/jws2/jabaws2/Jws2Instance.java | 26 ++--- src/jalview/ws/rest/RestClient.java | 22 ++-- src/jalview/ws/rest/RestJobThread.java | 25 ++-- src/jalview/ws/rest/RestServiceDescription.java | 4 +- 14 files changed, 171 insertions(+), 133 deletions(-) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 9de9e3b..7b6954f 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -4098,7 +4098,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, jws2servs.attachWSMenuEntry(webService, me); for (Jws2Instance sv : jws2servs.getServices()) { - if (sv.description.toLowerCase().contains("jpred")) + if (sv.getName().toLowerCase().contains("jpred")) { for (JMenuItem jmi : legacyItems) { diff --git a/src/jalview/ws/api/UIinfo.java b/src/jalview/ws/api/UIinfo.java index cd156f2..81c4ff3 100644 --- a/src/jalview/ws/api/UIinfo.java +++ b/src/jalview/ws/api/UIinfo.java @@ -6,13 +6,33 @@ package jalview.ws.api; public class UIinfo { - public UIinfo(String action, String name, String description) + private String ServiceType; + + public UIinfo(String serviceType, String action, String name, + String description) { + this.setServiceType(serviceType == null ? "" : serviceType); this.Action = action == null ? "" : action; this.description = description == null ? "" : description; this.Name = name == null ? "" : name; } + /** + * The type of analysis the service performs + */ + public String getServiceType() + { + return ServiceType; + } + + public void setServiceType(String serviceType) + { + ServiceType = serviceType; + } + + /** + * The action when the service performs the analysis + */ public String getAction() { return Action; @@ -23,6 +43,11 @@ public class UIinfo Action = action; } + /** + * name shown to user + * + * @return + */ public String getName() { return Name; @@ -33,6 +58,11 @@ public class UIinfo Name = name; } + /** + * Detailed description (may include references, URLs, html,etc) + * + * @return + */ public String getDescription() { return description; @@ -52,8 +82,12 @@ public class UIinfo } UIinfo other = (UIinfo) object; - return (Name == null && other.getName() == null || Name != null - && other.getName() != null && Name.equals(other.getName())) + return (ServiceType == null && other.getServiceType() == null + || ServiceType != null && other.getServiceType() != null + && ServiceType.equals(other.getServiceType())) + && (Name == null && other.getName() == null + || Name != null && other.getName() != null + && Name.equals(other.getName())) && (Action == null && other.getAction() == null || Action != null && other.getAction() != null && Action.equals(other.getAction())) diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java index 9a2316c..bd4e0ea 100644 --- a/src/jalview/ws/jws2/AADisorderClient.java +++ b/src/jalview/ws/jws2/AADisorderClient.java @@ -66,8 +66,8 @@ public class AADisorderClient extends JabawsCalcWorker { super(sh, alignFrame, thePreset, paramset); af = alignFrame; - typeName = sh.action; - methodName = sh.serviceType; + typeName = sh.getAction(); + methodName = sh.getName(); submitGaps = false; alignedSeqs = false; @@ -169,9 +169,9 @@ public class AADisorderClient extends JabawsCalcWorker if (immediate || !calcMan.isWorking(this) && scoremanager != null) { Map featureTypeMap = featureMap - .get(service.serviceType); + .get(service.getName()); Map> annotTypeMap = annotMap - .get(service.serviceType); + .get(service.getName()); boolean dispFeatures = false; Map fc = new Hashtable<>(); List ourAnnot = new ArrayList<>(); @@ -265,9 +265,9 @@ public class AADisorderClient extends JabawsCalcWorker String typename, calcName; AlignmentAnnotation annot = createAnnotationRowsForScores( ourAnnot, - typename = service.serviceType + " (" + typename = service.getName() + " (" + scr.getMethod() + ")", - calcName = service.getServiceTypeURI() + "/" + calcName = service.getNameURI() + "/" + scr.getMethod(), aseq, base + 1, scr); annot.graph = AlignmentAnnotation.LINE_GRAPH; diff --git a/src/jalview/ws/jws2/JabaParamStore.java b/src/jalview/ws/jws2/JabaParamStore.java index 10ec812..0257a76 100644 --- a/src/jalview/ws/jws2/JabaParamStore.java +++ b/src/jalview/ws/jws2/JabaParamStore.java @@ -47,7 +47,7 @@ import compbio.metadata.RunnerConfig; public class JabaParamStore implements ParamDatastoreI { - Hashtable editedParams = new Hashtable(); + Hashtable editedParams = new Hashtable<>(); private Jws2Instance service; @@ -101,7 +101,7 @@ public class JabaParamStore implements ParamDatastoreI List prefs = new ArrayList(); if (servicePresets == null) { - servicePresets = new Hashtable(); + servicePresets = new Hashtable<>(); PresetManager prman; if ((prman = service.getPresets()) != null) { @@ -148,8 +148,8 @@ public class JabaParamStore implements ParamDatastoreI public static List getJwsArgsfromJaba(List jabargs, boolean sortByOpt) { - List rgs = new ArrayList(); - List rgnames = new ArrayList(); + List rgs = new ArrayList<>(); + List rgnames = new ArrayList<>(); for (Object rg : jabargs) { ArgumentI narg = null; @@ -309,7 +309,7 @@ public class JabaParamStore implements ParamDatastoreI boolean found = false; for (String url : urls) { - if (service.getServiceTypeURI().equals(url) + if (service.getNameURI().equals(url) || service.getUri().equalsIgnoreCase(url)) { found = true; @@ -334,7 +334,7 @@ public class JabaParamStore implements ParamDatastoreI wsp.setDescription(descr); wsp.setApplicableUrls(urls.clone()); - List lines = new ArrayList(); + List lines = new ArrayList<>(); StringTokenizer st = new StringTokenizer(parameterfile, "\n"); while (st.hasMoreTokens()) { diff --git a/src/jalview/ws/jws2/Jws2Client.java b/src/jalview/ws/jws2/Jws2Client.java index 0f1a25e..4e135d1 100644 --- a/src/jalview/ws/jws2/Jws2Client.java +++ b/src/jalview/ws/jws2/Jws2Client.java @@ -144,9 +144,7 @@ public abstract class Jws2Client extends jalview.ws.WSClient protected WebserviceInfo setWebService(Jws2Instance serv, boolean b) { - // serviceHandle = serv; - String serviceInstance = serv.action; // serv.service.getClass().getName(); - WebServiceName = serv.serviceType; + WebServiceName = serv.getName(); WebServiceJobTitle = serv.getActionText(); WsURL = serv.hosturl; if (!b) @@ -154,7 +152,9 @@ public abstract class Jws2Client extends jalview.ws.WSClient return new WebserviceInfo(WebServiceJobTitle, WebServiceJobTitle + " using service hosted at " + serv.hosturl + "\n" - + (serv.description != null ? serv.description : ""), + + (serv.getDescription() != null + ? serv.getDescription() + : ""), false); } return null; @@ -386,12 +386,12 @@ public abstract class Jws2Client extends jalview.ws.WSClient { if (service != null) { - if (!service.serviceType.toString() + if (!service.getServiceType() .equals(compbio.ws.client.Services.AAConWS.toString())) { Cache.log.warn( "Ignoring invalid preferred service for AACon calculations (service type was " - + service.serviceType + ")"); + + service.getServiceType() + ")"); service = null; } else diff --git a/src/jalview/ws/jws2/Jws2Discoverer.java b/src/jalview/ws/jws2/Jws2Discoverer.java index 5319eab..b6c5473 100644 --- a/src/jalview/ws/jws2/Jws2Discoverer.java +++ b/src/jalview/ws/jws2/Jws2Discoverer.java @@ -178,7 +178,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI running = true; // first set up exclusion list if needed - final Set ignoredServices = new HashSet(); + final Set ignoredServices = new HashSet<>(); for (String ignored : Cache .getDefault("IGNORED_JABAWS_SERVICETYPES", "").split("\\|")) { @@ -217,9 +217,9 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { validServiceUrls.removeAllElements(); } - ArrayList svctypes = new ArrayList(); + ArrayList svctypes = new ArrayList<>(); - List qrys = new ArrayList(); + List qrys = new ArrayList<>(); for (final String jwsserver : getServiceUrls()) { JabaWsServerQuery squery = new JabaWsServerQuery(this, jwsserver); @@ -282,13 +282,13 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { svcs[ipos] = svc; spos[ipos++] = 1000 * svcUrls.indexOf(svc.getHost()) + 1 - + svctypes.indexOf(svc.serviceType); + + svctypes.indexOf(svc.getName()); } jalview.util.QuickSort.sort(spos, svcs); - services = new Vector(); + services = new Vector<>(); for (Jws2Instance svc : svcs) { - if (!ignoredServices.contains(svc.serviceType)) + if (!ignoredServices.contains(svc.getName())) { services.add(svc); } @@ -312,7 +312,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { if (services == null) { - services = new Vector(); + services = new Vector<>(); } System.out.println( "Discovered service: " + jwsservers + " " + service.toString()); @@ -329,7 +329,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI service.hasParameters(); if (validServiceUrls == null) { - validServiceUrls = new Vector(); + validServiceUrls = new Vector<>(); } validServiceUrls.add(jwsservers); } @@ -363,13 +363,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI * for moment we keep them separate. */ JMenu atpoint; - List enumerableServices = new ArrayList(); + List enumerableServices = new ArrayList<>(); // jws2al.removeAll(); - Map preferredHosts = new HashMap(); - Map> alternates = new HashMap>(); + Map preferredHosts = new HashMap<>(); + Map> alternates = new HashMap<>(); for (Jws2Instance service : services.toArray(new Jws2Instance[0])) { - if (!isRecalculable(service.action)) + // TODO: check this behaves with refactored serviceType to getName + if (!isRecalculable(service.getName())) { // add 'one shot' services to be displayed using the classic menu // structure @@ -377,28 +378,28 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } else { - if (!preferredHosts.containsKey(service.serviceType)) + if (!preferredHosts.containsKey(service.getName())) { Jws2Instance preferredInstance = getPreferredServiceFor( - alignFrame, service.serviceType); + alignFrame, service.getName()); if (preferredInstance != null) { - preferredHosts.put(service.serviceType, preferredInstance); + preferredHosts.put(service.getName(), preferredInstance); } else { - preferredHosts.put(service.serviceType, service); + preferredHosts.put(service.getName(), service); } } - List ph = alternates.get(service.serviceType); - if (preferredHosts.get(service.serviceType) != service) + List ph = alternates.get(service.getName()); + if (preferredHosts.get(service.getName()) != service) { if (ph == null) { - ph = new ArrayList(); + ph = new ArrayList<>(); } ph.add(service); - alternates.put(service.serviceType, ph); + alternates.put(service.getName(), ph); } } @@ -409,7 +410,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI // and the instantaneous services for (final Jws2Instance service : preferredHosts.values()) { - atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action); + atpoint = JvSwingUtils.findOrCreateMenu(jws2al, + service.getServiceType()); JMenuItem hitm; if (atpoint.getItemCount() > 1) { @@ -431,13 +433,13 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI MessageManager.getString("label.open_jabaws_web_page"))); service.attachWSMenuEntry(atpoint, alignFrame); - if (alternates.containsKey(service.serviceType)) + if (alternates.containsKey(service.getName())) { atpoint.add(hitm = new JMenu( MessageManager.getString("label.switch_server"))); hitm.setToolTipText(JvSwingUtils.wrapTooltip(false, MessageManager.getString("label.choose_jabaws_server"))); - for (final Jws2Instance sv : alternates.get(service.serviceType)) + for (final Jws2Instance sv : alternates.get(service.getName())) { JMenuItem itm; hitm.add(itm = new JMenuItem(sv.getHost())); @@ -453,8 +455,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI @Override public void run() { - setPreferredServiceFor(alignFrame, sv.serviceType, - sv.action, sv); + setPreferredServiceFor(alignFrame, sv.getName(), + sv.getServiceType(), sv); changeSupport.firePropertyChange("services", new Vector(), services); }; @@ -483,17 +485,17 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI */ JMenu atpoint; - List hostLabels = new ArrayList(); - Hashtable lasthostFor = new Hashtable(); - Hashtable> hosts = new Hashtable>(); - ArrayList hostlist = new ArrayList(); + List hostLabels = new ArrayList<>(); + Hashtable lasthostFor = new Hashtable<>(); + Hashtable> hosts = new Hashtable<>(); + ArrayList hostlist = new ArrayList<>(); for (Jws2Instance service : enumerableServices) { ArrayList hostservices = hosts.get(service.getHost()); if (hostservices == null) { hosts.put(service.getHost(), - hostservices = new ArrayList()); + hostservices = new ArrayList<>()); hostlist.add(service.getHost()); } hostservices.add(service); @@ -506,13 +508,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI String sortbytype[] = new String[orderedsvcs.length]; for (int i = 0; i < sortbytype.length; i++) { - sortbytype[i] = orderedsvcs[i].serviceType; + sortbytype[i] = orderedsvcs[i].getName(); } jalview.util.QuickSort.sort(sortbytype, orderedsvcs); for (final Jws2Instance service : orderedsvcs) { - atpoint = JvSwingUtils.findOrCreateMenu(jws2al, service.action); - String type = service.serviceType; + atpoint = JvSwingUtils.findOrCreateMenu(jws2al, + service.getAction()); + String type = service.getName(); if (byhost) { atpoint = JvSwingUtils.findOrCreateMenu(atpoint, host); @@ -532,7 +535,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } } if (!byhost && !hostLabels.contains( - host + service.serviceType + service.getActionText())) + host + service.getName() + service.getActionText())) // !hostLabels.contains(host + (bytype ? // service.serviceType+service.getActionText() : ""))) { @@ -549,8 +552,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { hostLabels.add(host); } - if (lasthostFor.get(service.action) == null - || !lasthostFor.get(service.action).equals(host)) + if (lasthostFor.get(service.getAction()) == null + || !lasthostFor.get(service.getAction()).equals(host)) { atpoint.add(hitm = new JMenuItem(host)); hitm.setForeground(Color.blue); @@ -566,10 +569,10 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI hitm.setToolTipText( JvSwingUtils.wrapTooltip(true, MessageManager .getString("label.open_jabaws_web_page"))); - lasthostFor.put(service.action, host); + lasthostFor.put(service.getAction(), host); } hostLabels.add( - host + service.serviceType + service.getActionText()); + host + service.getName() + service.getActionText()); } service.attachWSMenuEntry(atpoint, alignFrame); @@ -581,7 +584,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { if (args.length > 0) { - testUrls = new ArrayList(); + testUrls = new ArrayList<>(); for (String url : args) { testUrls.add(url); @@ -685,7 +688,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI // return test urls, if there are any, instead of touching cache return testUrls; } - List urls = new ArrayList(); + List urls = new ArrayList<>(); if (this.preferredUrl != null) { @@ -733,8 +736,8 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI public Vector getServices() { - return (services == null) ? new Vector() - : new Vector(services); + return (services == null) ? new Vector<>() + : new Vector<>(services); } /** @@ -839,7 +842,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { if (urlsWithoutServices == null) { - urlsWithoutServices = new Vector(); + urlsWithoutServices = new Vector<>(); } if ((invalidServiceUrls == null @@ -859,7 +862,7 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI { if (invalidServiceUrls == null) { - invalidServiceUrls = new Vector(); + invalidServiceUrls = new Vector<>(); } if (!invalidServiceUrls.contains(jwsservers)) { @@ -947,14 +950,16 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI */ public Jws2Instance getPreferredServiceFor(String[] serviceURLs) { - HashSet urls = new HashSet(); + HashSet urls = new HashSet<>(); urls.addAll(Arrays.asList(serviceURLs)); Jws2Instance match = null; if (services != null) { for (Jws2Instance svc : services) { - if (urls.contains(svc.getServiceTypeURI())) + // TODO getNameURI Should return a versioned URI for the service, but + // doesn't as of 2.11 + if (urls.contains(svc.getNameURI())) { if (match == null) { @@ -974,20 +979,21 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return match; } - Map> preferredServiceMap = new HashMap>();; + Map> preferredServiceMap = new HashMap<>();; /** - * get current preferred service of the given type, or global default + * get current preferred endpoint of the given Jabaws service, or global + * default * * @param af * null or a specific alignFrame - * @param serviceType - * Jws2Instance.serviceType for service + * @param serviceName + * Jws2Instance.getName() for service * @return null if no service of this type is available, the preferred service * for the serviceType and af if specified and if defined. */ public Jws2Instance getPreferredServiceFor(AlignFrame af, - String serviceType) + String serviceName) { String serviceurl = null; synchronized (preferredServiceMap) @@ -1001,14 +1007,14 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI } if (prefmap != null) { - serviceurl = prefmap.get(serviceType); + serviceurl = prefmap.get(serviceName); } } Jws2Instance response = null; for (Jws2Instance svc : services) { - if (svc.serviceType.equals(serviceType)) + if (svc.getName().equals(serviceName)) { if (serviceurl == null || serviceurl.equals(svc.getHost())) { @@ -1020,21 +1026,22 @@ public class Jws2Discoverer implements Runnable, WSMenuEntryProviderI return response; } - public void setPreferredServiceFor(AlignFrame af, String serviceType, + public void setPreferredServiceFor(AlignFrame af, String serviceName, String serviceAction, Jws2Instance selectedServer) { + // TODO: pull out and generalise for the selectedServer's attributes String afid = (af == null) ? "" : af.getViewport().getSequenceSetId(); if (preferredServiceMap == null) { - preferredServiceMap = new HashMap>(); + preferredServiceMap = new HashMap<>(); } Map prefmap = preferredServiceMap.get(afid); if (prefmap == null) { - prefmap = new HashMap(); + prefmap = new HashMap<>(); preferredServiceMap.put(afid, prefmap); } - prefmap.put(serviceType, selectedServer.getHost()); + prefmap.put(serviceName, selectedServer.getHost()); prefmap.put(serviceAction, selectedServer.getHost()); } diff --git a/src/jalview/ws/jws2/MsaWSClient.java b/src/jalview/ws/jws2/MsaWSClient.java index 7e68d3b..bbeefc6 100644 --- a/src/jalview/ws/jws2/MsaWSClient.java +++ b/src/jalview/ws/jws2/MsaWSClient.java @@ -111,7 +111,7 @@ public class MsaWSClient extends Jws2Client MessageManager.formatMessage( "label.service_called_is_not_msa_service", new String[] - { sh.serviceType }), + { sh.getName() }), MessageManager.getString("label.internal_jalview_error"), JvOptionPane.WARNING_MESSAGE); @@ -122,7 +122,7 @@ public class MsaWSClient extends Jws2Client { JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.msa_service_is_unknown", new String[] - { sh.serviceType }), + { sh.getName() }), MessageManager.getString("label.internal_jalview_error"), JvOptionPane.WARNING_MESSAGE); diff --git a/src/jalview/ws/jws2/RNAalifoldClient.java b/src/jalview/ws/jws2/RNAalifoldClient.java index 80c9ce9..32ae38f 100644 --- a/src/jalview/ws/jws2/RNAalifoldClient.java +++ b/src/jalview/ws/jws2/RNAalifoldClient.java @@ -65,7 +65,7 @@ public class RNAalifoldClient extends JabawsCalcWorker { super(sh, alignFrame, preset, paramset); af = alignFrame; - methodName = sh.serviceType; + methodName = sh.getName(); alignedSeqs = true; submitGaps = true; nucleotidesAllowed = true; @@ -112,7 +112,7 @@ public class RNAalifoldClient extends JabawsCalcWorker if (immediate || !calcMan.isWorking(this) && scoremanager != null) { - List ourAnnot = new ArrayList(); + List ourAnnot = new ArrayList<>(); // Unpack the ScoreManager List structs = ((RNAStructScoreManager) scoremanager) @@ -231,7 +231,7 @@ public class RNAalifoldClient extends JabawsCalcWorker // The base pair probabilities are stored in a set in scoreholder. we want // a map - LinkedHashMap basePairs = new LinkedHashMap(); + LinkedHashMap basePairs = new LinkedHashMap<>(); for (Score score : data) { // The Score objects contain a set of size one containing the range and @@ -377,7 +377,7 @@ public class RNAalifoldClient extends JabawsCalcWorker private LinkedHashMap isContact( LinkedHashMap basePairs, int i) { - LinkedHashMap contacts = new LinkedHashMap(); + LinkedHashMap contacts = new LinkedHashMap<>(); for (Range contact : basePairs.keySet()) { diff --git a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java index 45bddac..8befb2a 100644 --- a/src/jalview/ws/jws2/SequenceAnnotationWSClient.java +++ b/src/jalview/ws/jws2/SequenceAnnotationWSClient.java @@ -128,7 +128,7 @@ public class SequenceAnnotationWSClient extends Jws2Client worker.updateParameters(this.preset, paramset); } } - if (sh.action.toLowerCase().contains("disorder")) + if (sh.getAction().toLowerCase().contains("disorder")) { // build IUPred style client. take sequences, returns annotation per // sequence. @@ -156,6 +156,7 @@ public class SequenceAnnotationWSClient extends Jws2Client * @see jalview.ws.jws2.Jws2Client#attachWSMenuEntry(javax.swing.JMenu, * jalview.ws.jws2.jabaws2.Jws2Instance, jalview.gui.AlignFrame) */ + @Override public void attachWSMenuEntry(JMenu wsmenu, final Jws2Instance service, final AlignFrame alignFrame) { @@ -166,8 +167,8 @@ public class SequenceAnnotationWSClient extends Jws2Client } boolean hasparams = service.hasParameters(); // Assume name ends in WS - String calcName = service.serviceType.substring(0, - service.serviceType.length() - 2); + String calcName = service.getName().substring(0, + service.getName().length() - 2); JMenuItem annotservice = new JMenuItem(MessageManager.formatMessage( "label.calcname_with_default_settings", new String[] @@ -193,6 +194,7 @@ public class SequenceAnnotationWSClient extends Jws2Client annotservice.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { new SequenceAnnotationWSClient(service, alignFrame, null, true); @@ -217,6 +219,7 @@ public class SequenceAnnotationWSClient extends Jws2Client + "
" + preset.getDescription())); methodR.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { new SequenceAnnotationWSClient(service, alignFrame, preset, diff --git a/src/jalview/ws/jws2/dm/AAConSettings.java b/src/jalview/ws/jws2/dm/AAConSettings.java index 708787e..5cc8f66 100644 --- a/src/jalview/ws/jws2/dm/AAConSettings.java +++ b/src/jalview/ws/jws2/dm/AAConSettings.java @@ -76,8 +76,8 @@ public class AAConSettings extends jalview.ws.params.AutoCalcSetting preset = pr; return; } - List oldargs = new ArrayList(), - newargs = new ArrayList(); + List oldargs = new ArrayList<>(), + newargs = new ArrayList<>(); oldargs.addAll(preset.getArguments()); // need to compare parameters for (ArgumentI newparg : pr.getArguments()) @@ -112,6 +112,7 @@ public class AAConSettings extends jalview.ws.params.AutoCalcSetting : JabaParamStore.getJwsArgsfromJaba(jobArgset); } + @Override public String getWsParamFile() { List