/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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.
*
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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/>.
*/
package jalview.appletgui;
this.protocol = protocol;
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
- if (jalview.bin.JalviewLite.debug)
+ if (protocol.equals(AppletFormatAdapter.PASTE))
{
- System.err.println("Setting PDB id for file " + pdbentry.getFile());
- if (protocol.equals(AppletFormatAdapter.PASTE))
- {
- pdbentry.setId("PASTED PDB"
- + (chains == null ? "_" : chains.toString()));
- }
- else
- {
- pdbentry.setId(pdbentry.getFile());
- }
+ pdbentry.setId("PASTED PDB"
+ + (chains == null ? "_" : chains.toString()));
+ }
+ else
+ {
+ pdbentry.setId(pdbentry.getFile());
}
}
+
if (jalview.bin.JalviewLite.debug)
{
System.err
resetLastRes.setLength(0);
resetLastRes.append("select " + pdbResNum);
+ eval.append(":");
+ resetLastRes.append(":");
if (!chain.equals(" "))
{
- eval.append(":" + chain);
- resetLastRes.append(":" + chain);
+ eval.append(chain);
+ resetLastRes.append(chain);
}
- eval.append(";wireframe 100;" + eval.toString() + ".*;");
+ eval.append(";wireframe 100;" + eval.toString() + " and not hetero;");
resetLastRes.append(";wireframe 0;" + resetLastRes.toString()
- + ".*;spacefill 0;");
+ + " and not hetero; spacefill 0;");
eval.append("spacefill 200;select none");