/*
- * 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.gui;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasListener;
import jalview.structure.VamsasSource;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.io.File;
import java.io.IOException;
-import java.util.Enumeration;
import java.util.Hashtable;
import java.util.IdentityHashMap;
import java.util.Iterator;
{
if (sess != null)
{
- throw new Error(
- "Implementation Error - cannot import existing vamsas document into an existing session, Yet!");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_import_vamsas_doc"));
}
try
{
.showInternalMessageDialog(
Desktop.desktop,
- "VAMSAS Document could not be opened as a new session - please choose another",
- "VAMSAS Document Import Failed",
+ MessageManager.getString("label.vamsas_doc_couldnt_be_opened_as_new_session"),
+ MessageManager.getString("label.vamsas_document_import_failed"),
JOptionPane.ERROR_MESSAGE);
}
{
if (!inSession())
{
- throw new Error(
- "Impementation error! Vamsas Operations when client not initialised and connected.");
+ throw new Error(MessageManager.getString("error.implementation_error_vamsas_operation_not_init"));
}
addDocumentUpdateHandler();
addStoreDocumentHandler();
public void end_session(boolean promptUser)
{
if (!inSession())
- throw new Error("Jalview not connected to Vamsas session.");
+ {
+ throw new Error(MessageManager.getString("error.jalview_no_connected_vamsas_session"));
+ }
Cache.log.info("Jalview disconnecting from the Vamsas Session.");
try
{
return;
}
- throw new Error(
- "IMPLEMENTATION ERROR: Cannot recover vamsas object mappings - no backup was made.");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_recover_vamsas_object_mappings"));
}
jv2vobj.clear();
Iterator el = _backup_jv2vobj.entrySet().iterator();
int i = -1;
- public void mouseOver(SequenceI seq, int index,
+ @Override
+ public void mouseOverSequence(SequenceI seq, int index,
VamsasSource source)
{
if (jv2vobj == null)
+ {
return;
+ }
if (seq != last || i != index)
{
VorbaId v = (VorbaId) jv2vobj.get(seq);
AlignmentI visal = null;
if (source instanceof AlignViewport)
{
- visal = ((AlignViewport) source).getAlignment();
+ visal = ((AlignmentViewport) source).getAlignment();
}
SelectionMessage sm = null;
if ((seqsel == null || seqsel.getSize() == 0)
{
// the empty selection.
sm = new SelectionMessage("jalview", new String[]
- { ((AlignViewport) source).getSequenceSetId() }, null,
+ { ((AlignmentViewport) source).getSequenceSetId() }, null,
true);
}
else
{
// gather selected columns outwith the sequence positions
// too
- Enumeration cols = colsel.getSelected().elements();
- while (cols.hasMoreElements())
+ for (Object obj : colsel.getSelected())
{
- int ival = ((Integer) cols.nextElement()).intValue();
+ int ival = ((Integer) obj).intValue();
Pos p = new Pos();
p.setI(ival + 1);
range.addPos(p);