X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Frest%2FRestClient.java;h=a71b70d62a72db33a6bdcc4d4be6aed3f24d47a4;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=27f5271097e0645777f97d8aa24e6ce9a4d21936;hpb=7c70cb09e9de68ab567e38520d6d09f0c17a3939;p=jalview.git diff --git a/src/jalview/ws/rest/RestClient.java b/src/jalview/ws/rest/RestClient.java index 27f5271..a71b70d 100644 --- a/src/jalview/ws/rest/RestClient.java +++ b/src/jalview/ws/rest/RestClient.java @@ -48,8 +48,8 @@ import javax.swing.event.MenuListener; * @author JimP * */ -public class RestClient extends WSClient implements WSClientI, - WSMenuEntryProviderI +public class RestClient extends WSClient + implements WSClientI, WSMenuEntryProviderI { RestServiceDescription service; @@ -97,9 +97,9 @@ public class RestClient extends WSClient implements WSClientI, public void setWebserviceInfo(boolean headless) { - WebServiceJobTitle = MessageManager.formatMessage( - "label.webservice_job_title", new String[] { - service.details.Action, service.details.Name }); + WebServiceJobTitle = MessageManager + .formatMessage("label.webservice_job_title", new String[] + { service.details.Action, service.details.Name }); WebServiceName = service.details.Name; WebServiceReference = "No reference - go to url for more info"; if (service.details.description != null) @@ -108,8 +108,8 @@ public class RestClient extends WSClient implements WSClientI, } if (!headless) { - wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceName + "\n" - + WebServiceReference, true); + wsInfo = new WebserviceInfo(WebServiceJobTitle, + WebServiceName + "\n" + WebServiceReference, true); wsInfo.setRenderAsHtml(true); } @@ -142,9 +142,9 @@ public class RestClient extends WSClient implements WSClientI, final AlignFrame alignFrame) { JMenuItem submit = new JMenuItem(service.details.Name); - submit.setToolTipText(MessageManager.formatMessage( - "label.rest_client_submit", new String[] { - service.details.Action, service.details.Name })); + submit.setToolTipText(MessageManager + .formatMessage("label.rest_client_submit", new String[] + { service.details.Action, service.details.Name })); submit.addActionListener(new ActionListener() { @@ -259,43 +259,42 @@ public class RestClient extends WSClient implements WSClientI, { // intersect groups with selected region _input = new AlignmentView(av.getAlignment(), - av.getAlignment() - .getHiddenColumns(), av.getSelectionGroup(), - av.hasHiddenColumns(), true, true); + av.getAlignment().getHiddenColumns(), + av.getSelectionGroup(), av.hasHiddenColumns(), true, + true); viewTitle = MessageManager.formatMessage( - "label.select_visible_region_of", - new String[] { - (av.hasHiddenColumns() ? MessageManager - .getString("label.visible") : ""), + "label.select_visible_region_of", new String[] + { (av.hasHiddenColumns() + ? MessageManager.getString("label.visible") + : ""), af.getTitle() }); } else { // use selected region to partition alignment _input = new AlignmentView(av.getAlignment(), - av.getAlignment() - .getHiddenColumns(), av.getSelectionGroup(), - av.hasHiddenColumns(), false, true); + av.getAlignment().getHiddenColumns(), + av.getSelectionGroup(), av.hasHiddenColumns(), false, + true); } viewTitle = MessageManager.formatMessage( - "label.select_unselect_visible_regions_from", - new String[] { - (av.hasHiddenColumns() ? MessageManager - .getString("label.visible") : ""), + "label.select_unselect_visible_regions_from", new String[] + { (av.hasHiddenColumns() + ? MessageManager.getString("label.visible") + : ""), af.getTitle() }); } else { // just take selected region intersection _input = new AlignmentView(av.getAlignment(), - av.getAlignment() - .getHiddenColumns(), av.getSelectionGroup(), - av.hasHiddenColumns(), true, true); + av.getAlignment().getHiddenColumns(), + av.getSelectionGroup(), av.hasHiddenColumns(), true, true); viewTitle = MessageManager.formatMessage( - "label.select_visible_region_of", - new String[] { - (av.hasHiddenColumns() ? MessageManager - .getString("label.visible") : ""), + "label.select_visible_region_of", new String[] + { (av.hasHiddenColumns() + ? MessageManager.getString("label.visible") + : ""), af.getTitle() }); } } @@ -303,14 +302,16 @@ public class RestClient extends WSClient implements WSClientI, { // standard alignment view without selection present _input = new AlignmentView(av.getAlignment(), - av.getAlignment() - .getHiddenColumns(), null, av.hasHiddenColumns(), false, - true); + av.getAlignment().getHiddenColumns(), null, + av.hasHiddenColumns(), false, true); viewTitle = "" - + (av.hasHiddenColumns() ? (new StringBuffer(" ") - .append(MessageManager - .getString("label.visible_region_of")) - .toString()) : "") + af.getTitle(); + + (av.hasHiddenColumns() + ? (new StringBuffer(" ") + .append(MessageManager + .getString("label.visible_region_of")) + .toString()) + : "") + + af.getTitle(); } RestJobThread jobsthread = new RestJobThread(this); @@ -328,22 +329,21 @@ public class RestClient extends WSClient implements WSClientI, else { // TODO: try to tell the user why the job couldn't be started. - JvOptionPane - .showMessageDialog( - Desktop.desktop, - (jobsthread.hasWarnings() ? jobsthread.getWarnings() - : MessageManager - .getString("label.job_couldnt_be_started_check_input")), - MessageManager - .getString("label.unable_start_web_service_analysis"), - JvOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(Desktop.desktop, + (jobsthread.hasWarnings() ? jobsthread.getWarnings() + : MessageManager.getString( + "label.job_couldnt_be_started_check_input")), + MessageManager + .getString("label.unable_start_web_service_analysis"), + JvOptionPane.WARNING_MESSAGE); } } public static RestClient makeShmmrRestClient() { - String action = "Analysis", description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", name = MessageManager - .getString("label.multiharmony"); + String action = "Analysis", + description = "Sequence Harmony and Multi-Relief (Brandt et al. 2010)", + name = MessageManager.getString("label.multiharmony"); Hashtable iparams = new Hashtable(); jalview.ws.rest.params.JobConstant toolp; // toolp = new jalview.ws.rest.JobConstant("tool","jalview"); @@ -370,11 +370,9 @@ public class RestClient extends WSClient implements WSClientI, iparams.put("groups", sgroups); sgroups.token = "groups"; sgroups.sep = " "; - RestServiceDescription shmrService = new RestServiceDescription( - action, - description, - name, - "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview",// ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1", + RestServiceDescription shmrService = new RestServiceDescription(action, + description, name, + "http://zeus.few.vu.nl/programs/shmrwww/index.php?tool=jalview", // ?tool=jalview&mbjob[method]=shmr&mbjob[description]=step1", "?tool=jalview", iparams, true, false, '-'); // a priori knowledge of the data returned from the service shmrService.addResultDatatype(JvDataType.ANNOTATION); @@ -413,16 +411,16 @@ public class RestClient extends WSClient implements WSClientI, try { for (RestServiceDescription descr : RestServiceDescription - .parseDescriptions(jalview.bin.Cache.getDefault( - RSBS_SERVICES, - makeShmmrRestClient().service.toString()))) + .parseDescriptions( + jalview.bin.Cache.getDefault(RSBS_SERVICES, + makeShmmrRestClient().service.toString()))) { services.add(descr.toString()); } } catch (Exception ex) { - System.err - .println("Serious - RSBS descriptions in user preferences are corrupt!"); + System.err.println( + "Serious - RSBS descriptions in user preferences are corrupt!"); ex.printStackTrace(); }