X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2Fdatamodel%2FJalviewSource.java;h=07ba027c2c14dd4a4502298f6076f4b38e1586e3;hb=1c52130ad032d77caac874c3a8be23a399a3ec93;hp=eb9d8071d3cb7f8ae3cd9836aa10a2622402a4ea;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git

diff --git a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
index eb9d807..07ba027 100644
--- a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
@@ -1,22 +1,29 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ * 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/>.
+ * 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;
 
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
 import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.Date;
@@ -34,9 +41,6 @@ import org.biodas.jdas.schema.sources.PROP;
 import org.biodas.jdas.schema.sources.SOURCE;
 import org.biodas.jdas.schema.sources.VERSION;
 
-import jalview.ws.dbsources.das.api.jalviewSourceI;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
 public class JalviewSource implements jalviewSourceI
 {
   SOURCE source;
@@ -212,9 +216,8 @@ public class JalviewSource implements jalviewSourceI
   {
     for (CAPABILITY p : getVersion().getCAPABILITY())
     {
-      if (p.getType().equalsIgnoreCase(capability.getName())
-              || p.getType().equalsIgnoreCase(
-                      "das1:" + capability.getName()))
+      if (p.getType().equalsIgnoreCase(capability.getName()) || p.getType()
+              .equalsIgnoreCase("das1:" + capability.getName()))
       {
         return p;
       }
@@ -254,10 +257,9 @@ public class JalviewSource implements jalviewSourceI
       for (COORDINATES cs : v.getCOORDINATES())
       {
         COORDINATES ltst = latestc.get(cs.getUri());
-        if (ltst == null
-                || ltst.getVersion() == null
-                || (ltst.getVersion() != null && cs.getVersion() != null && isLaterThan(
-                        ltst.getVersion(), cs.getVersion())))
+        if (ltst == null || ltst.getVersion() == null
+                || (ltst.getVersion() != null && cs.getVersion() != null
+                        && isLaterThan(ltst.getVersion(), cs.getVersion())))
         {
           latestc.put(cs.getUri(), cs);
         }
@@ -275,10 +277,13 @@ public class JalviewSource implements jalviewSourceI
          */
         try
         {
-          seqsources.add(ds = new DasSequenceSource(getTitle() + " ("
-                  + cs.getAuthority() + " " + cs.getSource()
-                  + (cs.getVersion() != null ? " " + cs.getVersion() : "")
-                  + ")", cs.getAuthority(), source, v, cs, connprov));
+          seqsources.add(ds = new DasSequenceSource(
+                  getTitle() + " (" + cs.getAuthority() + " "
+                          + cs.getSource()
+                          + (cs.getVersion() != null ? " " + cs.getVersion()
+                                  : "")
+                          + ")",
+                  cs.getAuthority(), source, v, cs, connprov));
           if (seqsources.size() > 1)
           {
             System.err.println("Added another sequence DB source for "
@@ -297,8 +302,8 @@ public class JalviewSource implements jalviewSourceI
     {
       try
       {
-        seqsources.add(new DasSequenceSource(getTitle(), getTitle(),
-                source, getVersion(), null, connprov));
+        seqsources.add(new DasSequenceSource(getTitle(), getTitle(), source,
+                getVersion(), null, connprov));
       } catch (Exception e)
       {
         // TODO Auto-generated catch block
@@ -338,12 +343,14 @@ public class JalviewSource implements jalviewSourceI
 
       for (CAPABILITY cap : getVersion().getCAPABILITY())
       {
-        String capname = cap.getType().substring(
-                cap.getType().indexOf(":") + 1);
+        String capname = cap.getType()
+                .substring(cap.getType().indexOf(":") + 1);
         int p = cap.getQueryUri().lastIndexOf(capname);
         if (p < -1)
         {
-          throw new Exception("Invalid das source: " + source.getUri());
+          throw new Exception(MessageManager.formatMessage(
+                  "exception.invalid_das_source", new String[]
+                  { source.getUri() }));
         }
         if (cap.getQueryUri().charAt(p) == '/')
         {
@@ -363,7 +370,15 @@ public class JalviewSource implements jalviewSourceI
   @Override
   public boolean isNewerThan(jalviewSourceI other)
   {
-    return isLaterThan(getVersion().getCreated(), other.getVersion()
-            .getCreated());
+    return isLaterThan(getVersion().getCreated(),
+            other.getVersion().getCreated());
+  }
+
+  @Override
+  public boolean isReferenceSource()
+  {
+    // TODO check source object for indication that we are the primary for a DAS
+    // coordinate system
+    return false;
   }
 }