/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, 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 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.
- *
+ *
* 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
* if true disable the check for jmol
*/
String chkforJmol = getParameter("nojmol");
- if (chkforJmol!=null)
+ if (chkforJmol != null)
{
checkForJmol = !chkforJmol.equals("true");
}
} catch (java.lang.ClassNotFoundException ex)
{
}
- } else {
- jmolAvailable=false;
+ }
+ else
+ {
+ jmolAvailable = false;
if (debug)
{
- System.err.println("Skipping Jmol check. Will use MCView (probably)");
+ System.err
+ .println("Skipping Jmol check. Will use MCView (probably)");
}
}
}
param, protocol);
JnetAnnotationMaker.add_annotation(predictions,
currentAlignFrame.viewport.getAlignment(), 0, false); // false==do
- // not
- // add
- // sequence
- // profile
- // from
- // concise
- // output
+ // not
+ // add
+ // sequence
+ // profile
+ // from
+ // concise
+ // output
currentAlignFrame.alignPanel.fontChanged();
currentAlignFrame.alignPanel.setScrollValues(0, 0);
} catch (Exception ex)
}
param = setProtocolState(param);
- if (!jmolAvailable
- && protocol == AppletFormatAdapter.CLASSLOADER)
+ if (// !jmolAvailable
+ // &&
+ protocol == AppletFormatAdapter.CLASSLOADER)
{
- // TODO: pass PDB file in classloader on to Jmol
+ // TODO: verify this Re:
+ // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
// This exception preserves the current behaviour where, even if
// the local pdb file was identified in the class loader
protocol = AppletFormatAdapter.URL; // this is probably NOT
- // CORRECT!
+ // CORRECT!
param = addProtocol(param); //
}
* separator used for separatorList
*/
protected String separator = "|"; // this is a safe(ish) separator - tabs
- // don't work for firefox
+
+ // don't work for firefox
/**
* parse the string into a list
boolean state)
{
boolean st = state;// !(state==null || state.equals("") ||
- // state.toLowerCase().equals("false"));
+ // state.toLowerCase().equals("false"));
alf.setFeatureGroupState(separatorListToArray(groups), st);
}