/*\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
+ *\r
* This file is part of Jalview.\r
- * \r
+ *\r
* Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \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
- * 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
+ *\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
+ *\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.analysis;\r
/**\r
* Functions for cross-referencing sequence databases. user must first specify\r
* if cross-referencing from protein or dna (set dna==true)\r
- * \r
+ *\r
* @author JimP\r
- * \r
+ *\r
*/\r
public class CrossRef\r
{\r
/**\r
* get the DNA or protein references for a protein or dna sequence\r
- * \r
+ *\r
* @param dna\r
* @param rfs\r
* @return\r
/**\r
* Indirect references are references from other sequences from the dataset to\r
* any of the direct DBRefEntrys on the given sequences.\r
- * \r
+ *\r
* @param dna\r
* true if seqs are DNA seqs\r
* @param seqs\r
}\r
\r
/**\r
- * \r
+ *\r
* @param dna\r
* @param seqs\r
* @return\r
}\r
\r
/**\r
- * \r
+ *\r
* @param seqs\r
* @param dna\r
* @param source\r
* find references to lrfs in the cross-reference set of each sequence in\r
* dataset (that is not equal to sequenceI) Identifies matching DBRefEntry\r
* based on source and accession string only - Map and Version are nulled.\r
- * \r
+ *\r
* @param sequenceI\r
* @param lrfs\r
* @param dataset\r
/**\r
* search a given sequence dataset for references matching cross-references to\r
* the given sequence\r
- * \r
+ *\r
* @param sequenceI\r
* @param xrf\r
* @param dataset\r
* TODO: generalise to different protein classifications Search dataset for\r
* DBRefEntrys matching the given one (xrf) and add the associated sequence to\r
* rseq.\r
- * \r
+ *\r
* @param sequenceI\r
* @param xrf\r
* @param dataset\r
/**\r
* precalculate different products that can be found for seqs in dataset and\r
* return them.\r
- * \r
+ *\r
* @param dna\r
* @param seqs\r
* @param dataset\r