X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws1%2FDiscoverer.java;h=ea883c86c48cea4512bd850119550a880971fc9e;hb=fc7f615a5a4d53b9d71f43dcf02c7a77d9ab41e8;hp=629b3d602d285f32d8180a3ab4e78f5b7cade6de;hpb=2b34ad8d6c224117ca2a3199c237fd74d8137da6;p=jalview.git diff --git a/src/jalview/ws/jws1/Discoverer.java b/src/jalview/ws/jws1/Discoverer.java index 629b3d6..ea883c8 100644 --- a/src/jalview/ws/jws1/Discoverer.java +++ b/src/jalview/ws/jws1/Discoverer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,13 +20,18 @@ */ package jalview.ws.jws1; +import jalview.gui.JvOptionPane; import jalview.util.MessageManager; -import java.util.*; +import java.util.Hashtable; +import java.util.StringTokenizer; +import java.util.Vector; -import javax.swing.*; - -import ext.vamsas.*; +import ext.vamsas.IRegistry; +import ext.vamsas.IRegistryServiceLocator; +import ext.vamsas.RegistryServiceSoapBindingStub; +import ext.vamsas.ServiceHandle; +import ext.vamsas.ServiceHandles; public class Discoverer implements Runnable { @@ -92,9 +97,9 @@ public class Discoverer implements Runnable // timeout } catch (Exception ex) { - jalview.bin.Cache.log - .error("Serious! Service location failed\nfor URL :" + WsURL - + "\n", ex); + jalview.bin.Cache.log.error( + "Serious! Service location failed\nfor URL :" + WsURL + "\n", + ex); return null; } @@ -121,9 +126,8 @@ public class Discoverer implements Runnable static private Vector getDiscoveryURLS() { Vector urls = new Vector(); - String RootServiceURLs = jalview.bin.Cache - .getDefault("DISCOVERY_URLS", - "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry"); + String RootServiceURLs = jalview.bin.Cache.getDefault("DISCOVERY_URLS", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/ServiceRegistry"); try { @@ -148,17 +152,17 @@ public class Discoverer implements Runnable jalview.bin.Cache.log .warn("Problem whilst trying to make a URL from '" + ((url != null) ? url : "") + "'"); - jalview.bin.Cache.log - .warn("This was probably due to a malformed comma separated list" + jalview.bin.Cache.log.warn( + "This was probably due to a malformed comma separated list" + " in the DISCOVERY_URLS entry of $(HOME)/.jalview_properties)"); jalview.bin.Cache.log.debug("Exception was ", ex); } } } catch (Exception ex) { - jalview.bin.Cache.log - .warn("Error parsing comma separated list of urls in DISCOVERY_URLS.", - ex); + jalview.bin.Cache.log.warn( + "Error parsing comma separated list of urls in DISCOVERY_URLS.", + ex); } if (urls.size() > 0) { @@ -176,8 +180,8 @@ public class Discoverer implements Runnable .debug("(Re)-Initialising the discovery URL list."); try { - reallyDiscoverServices = jalview.bin.Cache.getDefault( - "DISCOVERY_START", false); + reallyDiscoverServices = jalview.bin.Cache + .getDefault("DISCOVERY_START", false); if (reallyDiscoverServices) { ServiceURLList = getDiscoveryURLS(); @@ -187,35 +191,32 @@ public class Discoverer implements Runnable jalview.bin.Cache.log.debug("Setting default services"); services = new Hashtable(); // Muscle, Clustal and JPred. - ServiceHandle[] defServices = - { - new ServiceHandle( - "MsaWS", - "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " - + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.", - "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS", - MessageManager.getString("label.muscle_multiple_protein_sequence_alignment")), - new ServiceHandle( - "MsaWS", + ServiceHandle[] defServices = { new ServiceHandle("MsaWS", + "Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment " + + "with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.", + "http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS", + MessageManager.getString( + "label.muscle_multiple_protein_sequence_alignment")), + new ServiceHandle("MsaWS", "Katoh, K., K. Kuma, K., Toh, H., and Miyata, T. (2005) " + "\"MAFFT version 5: improvement in accuracy of multiple sequence alignment.\"" + " Nucleic Acids Research, 33 511-518", "http://www.compbio.dundee.ac.uk/JalviewWS/services/MafftWS", - MessageManager.getString("label.mafft_multiple_sequence_alignment")), - new ServiceHandle( - "MsaWS", + MessageManager.getString( + "label.mafft_multiple_sequence_alignment")), + new ServiceHandle("MsaWS", "Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple" + " sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice." + " Nucleic Acids Research, 22 4673-4680", "http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS", - MessageManager.getString("label.clustalw_multiple_sequence_alignment")), - new ServiceHandle( - "SecStrPred", - "Cole C., Barber J. D., Barton G.J (2008) " - + "The Jpred 3 secondary structure prediction server " - + "Nucleic Acids Research, 36 W197-W201", + MessageManager.getString( + "label.clustalw_multiple_sequence_alignment")), + new ServiceHandle("SecStrPred", + "Drozdetskiy A, Cole C, Procter J & Barton GJ. (2015)\nJPred4: a protein secondary structure prediction server" + + "\nNucleic Acids Research, Web Server issue (first published 15th April 2015)" + + "\ndoi://10.1093/nar/gkv332", "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred", - "JNet Secondary Structure Prediction") }; + "JPred Secondary Structure Prediction") }; services = new Hashtable(); serviceList = new Vector(); buildServiceLists(defServices, serviceList, services); @@ -223,8 +224,8 @@ public class Discoverer implements Runnable } catch (Exception e) { - System.err - .println("jalview.rootRegistry is not a proper url!\nWas set to " + System.err.println( + "jalview.rootRegistry is not a proper url!\nWas set to " + RootServiceURL + "\n" + e); } @@ -247,12 +248,11 @@ public class Discoverer implements Runnable { if (jalview.gui.Desktop.desktop != null) { - JOptionPane - .showMessageDialog( - jalview.gui.Desktop.desktop, - MessageManager.getString("label.set_proxy_settings"), - MessageManager.getString("label.proxy_authorization_failed"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showMessageDialog(jalview.gui.Desktop.desktop, + MessageManager.getString("label.set_proxy_settings"), + MessageManager + .getString("label.proxy_authorization_failed"), + JvOptionPane.WARNING_MESSAGE); } } else @@ -314,16 +314,15 @@ public class Discoverer implements Runnable disc_serv = new java.net.URL(sh[i].getEndpointURL()); if (!ServiceURLList.contains(disc_serv)) { - jalview.bin.Cache.log - .debug("Adding new discovery service at " - + disc_serv); + jalview.bin.Cache.log.debug( + "Adding new discovery service at " + disc_serv); ServiceURLList.add(disc_serv); seenNewDiscovery = true; } } catch (Exception e) { - jalview.bin.Cache.log.debug( - "Ignoring bad discovery service URL " + jalview.bin.Cache.log + .debug("Ignoring bad discovery service URL " + sh[i].getEndpointURL(), e); } } @@ -347,17 +346,17 @@ public class Discoverer implements Runnable } while (s_url < ServiceURLList.size()) { - if ((sh = getServices((java.net.URL) ServiceURLList.get(s_url))) != null) + if ((sh = getServices( + (java.net.URL) ServiceURLList.get(s_url))) != null) { buildServiceLists(sh, cat, sscat); } else { - jalview.bin.Cache.log - .warn("No services at " - + ((java.net.URL) ServiceURLList.get(s_url)) - + " - check DISCOVERY_URLS property in .jalview_properties"); + jalview.bin.Cache.log.warn("No services at " + + (ServiceURLList.get(s_url)) + + " - check DISCOVERY_URLS property in .jalview_properties"); } s_url++; } @@ -376,11 +375,13 @@ public class Discoverer implements Runnable /** * creates a new thread to call discoverServices() */ + @Override public void run() { final Discoverer discoverer = this; Thread discoverThread = new Thread() { + @Override public void run() { discoverer.doDiscovery(); @@ -405,12 +406,12 @@ public class Discoverer implements Runnable serviceClientBindings.put("SecStrPred", new JPredClient()); serviceClientBindings.put("SeqSearch", new SeqSearchWSClient()); } - WS1Client instance = (WS1Client) serviceClientBindings.get(sh - .getAbstractName()); + WS1Client instance = (WS1Client) serviceClientBindings + .get(sh.getAbstractName()); if (instance == null) { - System.err - .println("WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for " + System.err.println( + "WARNING - POSSIBLE IMPLEMENTATION ERROR - cannot find WSClient implementation for " + sh.getAbstractName()); } else