/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * 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;
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;
{
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;
}
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);
}
*/
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 "
{
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
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) == '/')
{
@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
+ // TODO check source object for indication that we are the primary for a DAS
+ // coordinate system
return false;
}
}