/*\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
+ * 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.ws;\r
\r
// TODO: make JPredJob deal only with what was sent to and received from a\r
// JNet service\r
int[] predMap = null; // mapping from sequence(i) to the original\r
- // sequence(predMap[i]) being predicted on\r
+\r
+ // sequence(predMap[i]) being predicted on\r
\r
vamsas.objects.simple.Sequence sequence;\r
\r
java.util.Hashtable SequenceInfo = null;\r
\r
int msaIndex = 0; // the position of the original sequence in the array of\r
- // Sequences in the input object that this job holds a\r
- // prediction for\r
+\r
+ // Sequences in the input object that this job holds a\r
+ // prediction for\r
\r
/**\r
* \r
nview.pruneDeletions(ShiftList\r
.parseMap((origseq = ((SequenceI[]) alandcolsel[0])[0])\r
.gapMap())); // recover original prediction sequence's\r
- // mapping to view.\r
+ // mapping to view.\r
int[] viscontigs = nview.getVisibleContigs(0, profileseq.getLength());\r
int spos = 0;\r
int offset = 0;\r
else if (job.sequence != null)\r
{\r
job.jobId = server.predict(job.sequence); // debug like : job.jobId =\r
- // "/jobs/www-jpred/jp_Yatat29";//\r
+ // "/jobs/www-jpred/jp_Yatat29";//\r
}\r
\r
if (job.jobId != null)\r
{\r
/*\r
* java.lang.Object[] alandcolsel =\r
- * input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());\r
- * if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {\r
+ * input.getAlignmentAndColumnSelection\r
+ * (alignFrame.getViewport().getGapCharacter()); if\r
+ * (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {\r
* if (msa) { throw new Error("Implementation Error! ColumnSelection\r
* from input alignment will not map to result alignment!"); } } if\r
* (!msa) { // update hidden regions to account for loss of gaps in\r