JAL-1645 source formatting and organise imports

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

diff --git a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
index 139bafe..9cc4239 100644 (file)
--- a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
@@ -1,5 +1,29 @@
+/*
+ * 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.
+ *  
+ * 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;
 
+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;
@@ -10,7 +34,6 @@ import java.util.Map;
 import org.biodas.jdas.client.threads.MultipleConnectionPropertyProviderI;
 import org.biodas.jdas.dassources.Capabilities;
 import org.biodas.jdas.dassources.utils.DasTimeFormat;
-import org.biodas.jdas.dassources.utils.RegistrySourceAdapter;
 import org.biodas.jdas.schema.sources.CAPABILITY;
 import org.biodas.jdas.schema.sources.COORDINATES;
 import org.biodas.jdas.schema.sources.MAINTAINER;
@@ -18,16 +41,16 @@ 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;
+
   MultipleConnectionPropertyProviderI connprov;
-  public JalviewSource(SOURCE local2, MultipleConnectionPropertyProviderI connprov, boolean local)
+
+  public JalviewSource(SOURCE local2,
+          MultipleConnectionPropertyProviderI connprov, boolean local)
   {
-    this.connprov=connprov;
+    this.connprov = connprov;
     this.local = local;
     source = local2;
   }
@@ -311,22 +334,28 @@ public class JalviewSource implements jalviewSourceI
   {
     try
     {
-      // kind of dumb, since org.biodas.jdas.dassources.utils.VersionAdapter.getSourceUriFromQueryUri() does this,
-      // but this way, we can access non DAS 1.6 compliant sources (which have to have a URL like <sourcename>/das/ and cause a validation exception)
-      
+      // kind of dumb, since
+      // org.biodas.jdas.dassources.utils.VersionAdapter.getSourceUriFromQueryUri()
+      // does this,
+      // but this way, we can access non DAS 1.6 compliant sources (which have
+      // to have a URL like <sourcename>/das/ and cause a validation exception)
+
       for (CAPABILITY cap : getVersion().getCAPABILITY())
       {
         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());
-        } 
-        if (cap.getQueryUri().charAt(p)=='/')
+        int p = cap.getQueryUri().lastIndexOf(capname);
+        if (p < -1)
+        {
+          throw new Exception(MessageManager.formatMessage(
+                  "exception.invalid_das_source",
+                  new String[] { source.getUri() }));
+        }
+        if (cap.getQueryUri().charAt(p) == '/')
         {
           p--;
         }
-        return cap.getQueryUri().substring(0,p);
+        return cap.getQueryUri().substring(0, p);
       }
     } catch (Exception x)
     {
@@ -343,4 +372,12 @@ public class JalviewSource implements jalviewSourceI
     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;
+  }
 }