+/*
+ * 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.gui;
import java.util.ArrayList;
{
// todo promote to StructureCommandsI.showLabel()
String modelId = getModelIdForFile(atom.getPdbFile());
- sb.append(String.format(" %s//%s/%d/*", modelId,
- atom.getChain(),
+ sb.append(String.format(" %s//%s/%d/*", modelId, atom.getChain(),
atom.getPdbResNum()));
}
String labelSpec = sb.toString();
@Override
public boolean isViewerRunning()
{
- return pymolManager !=null && pymolManager.isPymolLaunched();
+ return pymolManager != null && pymolManager.isPymolLaunched();
}
@Override
* a second parameter sets the pdbid as the loaded PyMOL object name
*/
String pdbId = pe.getId();
- try {
- String safePDBId = java.net.URLEncoder.encode(pdbId,"UTF-8");
+ try
+ {
+ String safePDBId = java.net.URLEncoder.encode(pdbId, "UTF-8");
pdbId = safePDBId.replace('%', '_');
pdbId = pdbId.replace("-", "__");
char fc = pdbId.charAt(0);
// put an 's' before any numerics
- if (fc>='0' && fc<='9')
+ if (fc >= '0' && fc <= '9')
{
- pdbId = 's'+pdbId;
+ pdbId = 's' + pdbId;
}
-// pdbId.replace('-', 0)
+ // pdbId.replace('-', 0)
} catch (Exception x)
{
- Console.error("Unxpected encoding exception for '"+pdbId+"'",x);
+ Console.error("Unxpected encoding exception for '" + pdbId + "'", x);
}
cmd.addParameter(pdbId);