/*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 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.seqfetcher;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.SequenceI;
import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
import java.util.ArrayList;
import java.util.Enumeration;
public String[] getSupportedDb()
{
if (FETCHABLEDBS == null)
+ {
return null;
+ }
String[] sf = new String[FETCHABLEDBS.size()];
Enumeration e = FETCHABLEDBS.keys();
int i = 0;
{
String db = (String) e.nextElement();
if (source.compareToIgnoreCase(db) == 0)
+ {
return true;
+ }
}
jalview.bin.Cache.log.warn("isFetchable doesn't know about '" + source
+ "'");
*/
System.out.println(hdr);
if (rrb != null)
+ {
System.out.println(rrb);
+ }
System.out.println("# end of " + hdr);
}
DbSourceProxy[] l = dblist.values().toArray(new DbSourceProxy[0]);
int i = 0;
String[] nm = new String[l.length];
- // make sure standard dbs appear first, followed by reference das sources, followed by anything else.
+ // make sure standard dbs appear first, followed by reference das sources,
+ // followed by anything else.
for (DbSourceProxy s : l)
{
- nm[i++] = ""+s.getTier()+s.getDbName().toLowerCase();
+ nm[i++] = "" + s.getTier() + s.getDbName().toLowerCase();
}
jalview.util.QuickSort.sort(nm, l);
dbs = new ArrayList<DbSourceProxy>();
* @param dbSourceProxy
* reference for class implementing
* jalview.ws.seqfetcher.DbSourceProxy
- * @throws java.lang.IllegalArgumentException
- * if class does not implement jalview.ws.seqfetcher.DbSourceProxy
*/
- protected void addDBRefSourceImpl(Class dbSourceProxy)
+ protected void addDBRefSourceImpl(
+ Class<? extends DbSourceProxy> dbSourceProxy)
throws java.lang.IllegalArgumentException
{
DbSourceProxy proxy = null;
try
{
- Object proxyObj = dbSourceProxy.getConstructor(null)
- .newInstance(null);
- if (!DbSourceProxy.class.isInstance(proxyObj))
- {
- throw new IllegalArgumentException(
- dbSourceProxy.toString()
- + " does not implement the jalview.ws.seqfetcher.DbSourceProxy");
- }
- proxy = (DbSourceProxy) proxyObj;
+ DbSourceProxy proxyObj = dbSourceProxy.getConstructor().newInstance();
+ proxy = proxyObj;
} catch (IllegalArgumentException e)
{
throw e;
} catch (Exception e)
{
// Serious problems if this happens.
- throw new Error("DBRefSource Implementation Exception", e);
+ throw new Error(
+ MessageManager
+ .getString("error.dbrefsource_implementation_exception"),
+ e);
}
addDbRefSourceImpl(proxy);
}
if (!jalview.ws.seqfetcher.DbSourceProxy.class.isAssignableFrom(class1))
{
throw new Error(
- "Implmentation Error - getDbInstances must be given a class that implements jalview.ws.seqfetcher.DbSourceProxy (was given '"
- + class1 + "')");
+ MessageManager
+ .formatMessage(
+ "error.implementation_error_dbinstance_must_implement_interface",
+ new String[] { class1.toString() }));
}
if (FETCHABLEDBS == null)
{
{
ArrayList<DbSourceProxy> prlist = new ArrayList<DbSourceProxy>();
for (String fetchable : getSupportedDb())
+ {
for (DbSourceProxy pr : getSourceProxy(fetchable))
{
if (class1.isInstance(pr))
prlist.add(pr);
}
}
+ }
if (prlist.size() == 0)
{
return null;