/*\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.ws;\r
\r
* MsaWSJob\r
* \r
* @param jobNum\r
- * int\r
+ * int\r
* @param jobId\r
- * String\r
+ * String\r
*/\r
public SeqSearchWSJob(int jobNum, SequenceI[] inSeqs)\r
{\r
* prepare input sequences for service\r
* \r
* @param seqs\r
- * jalview sequences to be prepared\r
+ * jalview sequences to be prepared\r
* @param minlen\r
- * minimum number of residues required for this MsaWS service\r
+ * minimum number of residues required for this MsaWS service\r
* @return true if seqs contains sequences to be submitted to service.\r
*/\r
private boolean prepareInput(SequenceI[] seqs, int minlen)\r
}\r
}\r
boolean valid = nseqs >= 1; // need at least one sequence for valid input\r
- // TODO: generalise\r
+ // TODO: generalise\r
vamsas.objects.simple.Sequence[] seqarray = (valid) ? new vamsas.objects.simple.Sequence[nseqs]\r
: null;\r
boolean submitGaps = (nseqs == 1) ? false : true; // profile is submitted\r
- // with gaps\r
+ // with gaps\r
for (int i = 0, n = 0; i < seqs.length; i++)\r
{\r
\r
* set basic options for this (group) of Msa jobs\r
* \r
* @param subgaps\r
- * boolean\r
+ * boolean\r
* @param presorder\r
- * boolean\r
+ * boolean\r
*/\r
SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,\r
WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
* create one or more Msa jobs to align visible seuqences in _msa\r
* \r
* @param title\r
- * String\r
+ * String\r
* @param _msa\r
- * AlignmentView\r
+ * AlignmentView\r
* @param subgaps\r
- * boolean\r
+ * boolean\r
* @param presorder\r
- * boolean\r
+ * boolean\r
* @param seqset\r
- * Alignment\r
+ * Alignment\r
*/\r
SeqSearchWSThread(ext.vamsas.SeqSearchI server, String wsUrl,\r
WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,\r
* like this: 1. Merge each domain hit back onto the visible segments in\r
* the same way as a Jnet prediction is mapped back\r
* \r
- * Object[] newview = input.getUpdatedView(results, orders, getGapChar()); //\r
- * trash references to original result data for (int j = 0; j <\r
+ * Object[] newview = input.getUpdatedView(results, orders, getGapChar());\r
+ * // trash references to original result data for (int j = 0; j <\r
* jobs.length; j++) { results[j] = null; orders[j] = null; } SequenceI[]\r
* alignment = (SequenceI[]) newview[0]; ColumnSelection columnselection =\r
* (ColumnSelection) newview[1]; Alignment al = new Alignment(alignment);\r