X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDiscoverer.java;h=4a83ba79a5782c57d04e810fbd8678e28d6a99ea;hb=d545553b53ac1bd1e29eb72250cdb29745f7292f;hp=66f3f3fb8616162f016ad9ae6e5618cfb64f263a;hpb=284164b7a6ed5ed6744f9127b44c3be24230c0d9;p=jalview.git diff --git a/src/jalview/ws/Discoverer.java b/src/jalview/ws/Discoverer.java index 66f3f3f..4a83ba7 100755 --- a/src/jalview/ws/Discoverer.java +++ b/src/jalview/ws/Discoverer.java @@ -1,3 +1,21 @@ +/* +* Jalview - A Sequence Alignment Editor and Viewer +* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle +* +* This program 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 2 +* of the License, or (at your option) any later version. +* +* This program 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 this program; if not, write to the Free Software +* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA +*/ package jalview.ws; /** @@ -15,8 +33,8 @@ package jalview.ws; import ext.vamsas.*; import java.util.Vector; import java.util.Hashtable; -import java.util.ArrayList; import java.util.StringTokenizer; +import javax.swing.JOptionPane; public class Discoverer extends Thread implements Runnable @@ -75,7 +93,7 @@ public class Discoverer } catch (Exception ex) { - jalview.bin.Jalview.log.error( + jalview.bin.Cache.log.error( "Serious! Service location failed\nfor URL :" + WsURL + "\n", ex); @@ -109,27 +127,31 @@ public class Discoverer if (!urls.contains(u)) urls.add(u); else - jalview.bin.Jalview.log.info("Ignoring duplicate url in DISCOVERY_URLS list"); + jalview.bin.Cache.log.info("Ignoring duplicate url in DISCOVERY_URLS list"); } catch (Exception ex) { - jalview.bin.Jalview.log.warn( + jalview.bin.Cache.log.warn( "Problem whilst trying to make a URL from '" + ( (url != null) ? url : "")+"'"); - jalview.bin.Jalview.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.Jalview.log.debug("Exception was ",ex); + jalview.bin.Cache.log.debug("Exception was ",ex); } } }catch(Exception ex) - {jalview.bin.Jalview.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) return urls; return null; } - static - { + /** + * fetch new services or reset to hardwired defaults depending on preferences. + */ + static public void doDiscovery() + { + jalview.bin.Cache.log.debug("(Re)-Initialising the discovery URL list."); try { reallyDiscoverServices = jalview.bin.Cache.getDefault("DISCOVERY_START", false); @@ -139,7 +161,7 @@ public class Discoverer } else { - jalview.bin.Jalview.log.debug("Setting default services"); + jalview.bin.Cache.log.debug("Setting default services"); services = new Hashtable(); // Muscle, Clustal and JPred. ServiceHandle[] defServices = { @@ -152,6 +174,13 @@ public class Discoverer ), 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", + "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", @@ -159,7 +188,7 @@ public class Discoverer "ClustalW Multiple Sequence Alignment"), new ServiceHandle( "SecStrPred", - "Cuff J. A and Barton G.J (1999) Application of enhanced " + + "Cuff J. A and Barton G.J (2000) Application of " + "multiple sequence alignment profiles to improve protein secondary structure prediction, " + "Proteins 40:502-511", "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred","JNet Secondary Structure Prediction" @@ -186,15 +215,26 @@ public class Discoverer ServiceHandles shs = null; try { - jalview.bin.Jalview.log.debug("Discovering services using " + location); + jalview.bin.Cache.log.debug("Discovering services using " + location); shs = locateWebService(location).getServices(); } - catch (Exception e) - { - jalview.bin.Jalview.log.debug("No Discovery service at " + - location); - jalview.bin.Jalview.log.debug(e); - + catch (org.apache.axis.AxisFault f) { + // JBPNote - should do this a better way! + if (f.getFaultReason().indexOf("(407)")>-1) { + if (jalview.gui.Desktop.desktop!=null) + JOptionPane.showMessageDialog(jalview.gui.Desktop.desktop, "Please set up your proxy settings in the 'Connections' tab of the Preferences window", + "Proxy Authorization Failed", + JOptionPane.WARNING_MESSAGE); + } else { + jalview.bin.Cache.log.warn("No Discovery service at " + + location); + jalview.bin.Cache.log.debug("Axis Fault", f); + } + } + catch (Exception e) { + jalview.bin.Cache.log.warn("No Discovery service at " + + location); + jalview.bin.Cache.log.debug("Discovery Service General Exception", e); } if ( (shs != null) && shs.getServices().length > 0) { @@ -219,7 +259,7 @@ public class Discoverer { if (!cat.contains(sh[i])) { - jalview.bin.Jalview.log.debug("A " + sh[i].getAbstractName() + + jalview.bin.Cache.log.debug("A " + sh[i].getAbstractName() + " service called " + sh[i].getName() + " exists at " + sh[i].getEndpointURL() + "\n"); @@ -242,7 +282,7 @@ public class Discoverer disc_serv = new java.net.URL(sh[i].getEndpointURL()); if (!ServiceURLList.contains(disc_serv)) { - jalview.bin.Jalview.log.debug( + jalview.bin.Cache.log.debug( "Adding new discovery service at " + disc_serv); ServiceURLList.add(disc_serv); seenNewDiscovery = true; @@ -250,7 +290,7 @@ public class Discoverer } catch (Exception e) { - jalview.bin.Jalview.log.debug( + jalview.bin.Cache.log.debug( "Ignoring bad discovery service URL " + sh[i].getEndpointURL(), e); } @@ -269,7 +309,7 @@ public class Discoverer int s_url = 0; if (ServiceURLList==null) { - jalview.bin.Jalview.log.debug("No service endpoints to use for service discovery."); + jalview.bin.Cache.log.debug("No service endpoints to use for service discovery."); return; } while (s_url < ServiceURLList.size()) @@ -279,7 +319,7 @@ public class Discoverer buildServiceLists(sh, cat, sscat); } else { - jalview.bin.Jalview.log.warn( + jalview.bin.Cache.log.warn( "No services at " +((java.net.URL) ServiceURLList.get(s_url)) +" - check DISCOVERY_URLS property in .jalview_properties"); @@ -291,14 +331,24 @@ public class Discoverer // so no need to access original discovery thread. // Curent decision is to change properties then notify listeners with old and new values. Hashtable oldServices = services; - Vector oldServicelist = serviceList; + //Vector oldServicelist = serviceList; services = sscat; serviceList = cat; firePropertyChange("services", oldServices, services); } + /** + * creates a new thread to call discoverServices() + */ public void run() { - discoverServices(); + final Discoverer discoverer = this; + Thread discoverThread = new Thread() { + public void run() { + discoverer.doDiscovery(); + discoverer.discoverServices(); + } + }; + discoverThread.start(); } }