+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 AM Waterhouse, J Procter, 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
+ * \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
+ * \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
+ */\r
package jalview.datamodel;\r
\r
import java.util.Enumeration;\r
nlen--;\r
dnaSeqs[nlen] = (dnaseq.getDatasetSequence()==null) ? dnaseq : dnaseq.getDatasetSequence();\r
Mapping mp = new Mapping(map);\r
+ // JBPNote DEBUG! THIS !\r
+ //dnaseq.transferAnnotation(aaseq, mp);\r
+ //aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));\r
mp.to = (aaseq.getDatasetSequence()==null) ? aaseq : aaseq.getDatasetSequence();\r
a_aaSeqs.addElement(aaseq);\r
dnaToProt[nlen] = mp;\r
*/\r
public void markMappedRegion(SequenceI seq, int index, SearchResults results)\r
{\r
+ if (dnaToProt==null)\r
+ {\r
+ return;\r
+ }\r
int[] codon;\r
SequenceI ds = seq.getDatasetSequence();\r
for (int mi = 0; mi<dnaToProt.length; mi++)\r