/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)\r
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
* \r
* This file is part of Jalview.\r
* \r
* PURPOSE. See the GNU General Public License for more details.\r
* \r
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/\r
package jalview.ext.varna;\r
\r
import java.util.ArrayList;\r
\r
/**\r
- * Routines for generating Jmol commands for Jalview/Jmol binding\r
- * another cruisecontrol test.\r
+ * Routines for generating Jmol commands for Jalview/Jmol binding another
+ * cruisecontrol test.
* \r
* @author JimP\r
*\r
{\r
\r
/**\r
- * Jmol utility which constructs the commands to colour chains by the given alignment\r
+ * Jmol utility which constructs the commands to colour chains by the given
+ * alignment
* \r
*/\r
- public static String[] getColourBySequenceCommand(StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, AlignmentI alignment)\r
+ public static String[] getColourBySequenceCommand(
+ StructureSelectionManager ssm, String[] files,
+ SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
+ AlignmentI alignment)
{\r
\r
ArrayList<String> str = new ArrayList<String>();\r
+ col.getGreen()\r
+ ","\r
+ col.getBlue() + "]";\r
- if (command.length()>newSelcom.length() && command.substring(command.length()-newSelcom.length()).equals(newSelcom))\r
+ if (command.length() > newSelcom.length()
+ && command.substring(
+ command.length() - newSelcom.length())
+ .equals(newSelcom))
{\r
command = VarnaCommands.condenseCommand(command, pos);\r
continue;\r
\r
// work back to last 'select'\r
int p=command.length(),q=p;\r
- do {\r
+ do
+ {
p-=6;\r
- if (p<1) { p=0; };\r
+ if (p < 1)
+ {
+ p = 0;
+ }
+ ;
} while ((q=command.indexOf("select",p))==-1 && p>0);\r
\r
StringBuffer sb = new StringBuffer(command.substring(0,q+7));\r