/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
* \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
+ * This file is part of Jalview.\r
* \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
* \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \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
*/\r
package jalview.io;\r
\r
{\r
if (matched)\r
{\r
- // TODO: specify and implement duplication of alignment annotation for multiple group references.\r
+ // TODO: specify and implement duplication of alignment annotation\r
+ // for multiple group references.\r
System.err\r
.println("Ignoring 1:many group reference mappings for group name '"\r
- + groupRef+"'");\r
+ + groupRef + "'");\r
}\r
else\r
{\r
Annotation parseAnnotation(String string, int graphStyle)\r
{\r
boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't\r
- // do the\r
- // glyph\r
- // test\r
- // if we\r
- // don't\r
- // want\r
- // secondary\r
- // structure\r
+ // do the\r
+ // glyph\r
+ // test\r
+ // if we\r
+ // don't\r
+ // want\r
+ // secondary\r
+ // structure\r
String desc = null, displayChar = null;\r
char ss = ' '; // secondaryStructure\r
float value = 0;\r