JAL-1432 updated copyright notices

[jalview.git] / src / jalview / ws / dbsources / das / datamodel / DasSourceRegistry.java

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
index 6d62d97..52e8db5 100644 (file)
--- a/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSourceRegistry.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.
+ *  
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.dbsources.das.datamodel;
 
@@ -7,20 +22,12 @@ import java.net.HttpURLConnection;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Enumeration;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.List;
-import java.util.Map;
-import java.util.Set;
 import java.util.StringTokenizer;
-import java.util.Vector;
 
-import javax.swing.JOptionPane;
-
-import org.apache.http.auth.InvalidCredentialsException;
 import org.biodas.jdas.client.ConnectionPropertyProviderI;
 import org.biodas.jdas.client.SourcesClient;
 import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;
@@ -47,7 +54,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
 
   private Hashtable<String, jalviewSourceI> localSources = null;
 
-  public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das/sources";
+  public static String DEFAULT_REGISTRY = "http://www.dasregistry.org/das/";
 
   /**
    * true if thread is running and we are talking to DAS registry service
@@ -70,6 +77,14 @@ public class DasSourceRegistry implements DasSourceRegistryI,
               DEFAULT_REGISTRY);
       registry = DEFAULT_REGISTRY;
     }
+    if (registry.lastIndexOf("sources.xml") == registry.length() - 11)
+    {
+      // no trailing sources.xml document for registry in JDAS
+      jalview.bin.Cache.setProperty(
+              jalview.bin.Cache.DAS_REGISTRY_URL,
+              registry = registry.substring(0,
+                      registry.lastIndexOf("sources.xml")));
+    }
     return registry;
   }
 
@@ -83,7 +98,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
   private List<jalviewSourceI> getDASSources()
   {
 
-    return getDASSources(getDasRegistryURL());
+    return getDASSources(getDasRegistryURL(), this);
   }
 
   /**
@@ -92,7 +107,8 @@ public class DasSourceRegistry implements DasSourceRegistryI,
    * @param registryURL
    *          return sources from registryURL
    */
-  private static List<jalviewSourceI> getDASSources(String registryURL)
+  private static List<jalviewSourceI> getDASSources(String registryURL,
+          MultipleConnectionPropertyProviderI registry)
   {
     try
     {
@@ -104,21 +120,26 @@ public class DasSourceRegistry implements DasSourceRegistryI,
 
       List<SOURCE> dassources = sources.getSOURCE();
       ArrayList<jalviewSourceI> dsrc = new ArrayList<jalviewSourceI>();
-      HashMap<String,Integer> latests=new HashMap<String, Integer>();
+      HashMap<String, Integer> latests = new HashMap<String, Integer>();
       Integer latest;
       for (SOURCE src : dassources)
       {
-        JalviewSource jsrc=new JalviewSource(src, false);
-        latest=latests.get(jsrc.getSourceURL());
-        if (latest!=null)
+        JalviewSource jsrc = new JalviewSource(src, registry, false);
+        latest = latests.get(jsrc.getSourceURL());
+        if (latest != null)
         {
           if (jsrc.isNewerThan(dsrc.get(latest.intValue())))
           {
             dsrc.set(latest.intValue(), jsrc);
-          } else {
-            System.out.println("Debug: Ingored older source "+jsrc.getTitle());
           }
-        } else {
+          else
+          {
+            System.out.println("Debug: Ignored older source "
+                    + jsrc.getTitle());
+          }
+        }
+        else
+        {
           latests.put(jsrc.getSourceURL(), Integer.valueOf(dsrc.size()));
           dsrc.add(jsrc);
         }
@@ -147,7 +168,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
     }
     return appendLocalSources();
   }
-  
+
   /**
    * generate Sources from the local das source list
    * 
@@ -158,13 +179,21 @@ public class DasSourceRegistry implements DasSourceRegistryI,
     {
       // get local sources from properties and initialise the local source list
       String local = jalview.bin.Cache.getProperty("DAS_LOCAL_SOURCE");
+
       if (local != null)
       {
+        int n = 1;
         StringTokenizer st = new StringTokenizer(local, "\t");
         while (st.hasMoreTokens())
         {
           String token = st.nextToken();
           int bar = token.indexOf("|");
+          if (bar == -1)
+          {
+            System.err
+                    .println("Warning: DAS user local source appears to have no nickname (expected a '|' followed by nickname)\nOffending definition: '"
+                            + token + "'");
+          }
           String url = token.substring(bar + 1);
           boolean features = true, sequence = false;
           if (url.startsWith("sequence:"))
@@ -173,8 +202,25 @@ public class DasSourceRegistry implements DasSourceRegistryI,
             // this source also serves sequences as well as features
             sequence = true;
           }
-          createLocalSource(url, token.substring(0, bar), sequence,
-                  features);
+          try
+          {
+            if (bar > -1)
+            {
+              createLocalSource(url, token.substring(0, bar), sequence,
+                      features);
+            }
+            else
+            {
+              createLocalSource(url, "User Source" + n, sequence, features);
+            }
+          } catch (Exception q)
+          {
+            System.err
+                    .println("Unexpected exception when creating local source from '"
+                            + token + "'");
+            q.printStackTrace();
+          }
+          n++;
         }
       }
     }
@@ -223,7 +269,7 @@ public class DasSourceRegistry implements DasSourceRegistryI,
     {
       localSources = new Hashtable<String, jalviewSourceI>();
     }
-    jalviewSourceI src = new JalviewSource(local, true);
+    jalviewSourceI src = new JalviewSource(local, this, true);
     localSources.put(local.getTitle(), src);
     return src;
   }