/*
- * 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 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* 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.ext.jmol;
return;
}
StringBuffer selectioncom = new StringBuffer();
-
-
+ // In principle - nSeconds specifies the speed of animation for each
+ // superposition - but is seems to behave weirdly, so we don't specify it.
+ String nSeconds = " ";
+ if (files.length > 10)
+ {
+ nSeconds = " 0.00001 ";
+ }
+ else
+ {
+ nSeconds = " " + (2.0 / files.length) + " ";
+ // if (nSeconds).substring(0,5)+" ";
+ }
+ // see JAL-1345 - should really automatically turn off the animation for
+ // large numbers of structures, but Jmol doesn't seem to allow that.
+ nSeconds = " ";
// union of all aligned positions are collected together.
for (int a = 0; a < _alignment.length; a++)
{
command.append(chainNames[pdbfnum]);
command.append(") against reference (");
command.append(chainNames[refStructure]);
- command.append(")\";\ncompare ");
+ command.append(")\";\ncompare "+nSeconds);
command.append("{");
command.append(1 + pdbfnum);
command.append(".1} {");