/*\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 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.dbsources;\r
\r
* retrieve and parse an emblxml file\r
* \r
* @param emprefx\r
- * either EMBL or EMBLCDS strings are allowed - anything else\r
- * will not retrieve emblxml\r
+ * either EMBL or EMBLCDS strings are allowed - anything else will\r
+ * not retrieve emblxml\r
* @param query\r
* @return\r
* @throws Exception\r
File reply;\r
try\r
{\r
- reply = dbFetch.fetchDataAsFile(emprefx.toLowerCase() + ":"\r
- + query.trim(), "emblxml", null);\r
+ reply = dbFetch.fetchDataAsFile(\r
+ emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null);\r
} catch (Exception e)\r
{\r
stopQuery();\r
* parse an emblxml file stored locally\r
* \r
* @param emprefx\r
- * either EMBL or EMBLCDS strings are allowed - anything else\r
- * will not retrieve emblxml\r
+ * either EMBL or EMBLCDS strings are allowed - anything else will\r
+ * not retrieve emblxml\r
* @param query\r
* @param file\r
- * the EMBL XML file containing the results of a query\r
+ * the EMBL XML file containing the results of a query\r
* @return\r
* @throws Exception\r
*/\r
{\r
EmblEntry entry = (EmblEntry) i.next();\r
SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO:\r
- // use\r
- // !fetchNa,!fetchPeptide\r
- // here\r
- // instead\r
- // -\r
- // see\r
- // todo\r
- // in\r
- // emblEntry\r
+ // use\r
+ // !fetchNa,!fetchPeptide\r
+ // here\r
+ // instead\r
+ // -\r
+ // see\r
+ // todo\r
+ // in\r
+ // emblEntry\r
if (seqparts != null)\r
{\r
SequenceI[] newseqs = null;\r
for (int j = 0; j < seqparts.length; si++, j++)\r
{\r
newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on\r
- // dataset and refer\r
+ // dataset and refer\r
}\r
seqs = newseqs;\r
\r