+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\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
+ * 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
+ * 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
import jalview.datamodel.Alignment;\r
{\r
super();\r
}\r
+\r
/**\r
* retrieve and parse an emblxml file\r
- * @param emprefx either EMBL or EMBLCDS strings are allowed - anything else will not retrieve emblxml\r
+ * \r
+ * @param emprefx\r
+ * either EMBL or EMBLCDS strings are allowed - anything else will\r
+ * not retrieve emblxml\r
* @param query\r
* @return\r
* @throws Exception\r
*/\r
- public AlignmentI getEmblSequenceRecords(String emprefx, String query) throws Exception\r
+ public AlignmentI getEmblSequenceRecords(String emprefx, String query)\r
+ throws Exception\r
{\r
startQuery();\r
- SequenceI seqs[] = null;\r
- Vector alseq = new Vector(); // the sequences that will actually be presented in the alignment\r
- StringBuffer result = new StringBuffer();\r
EBIFetchClient dbFetch = new EBIFetchClient();\r
- File reply; \r
- try {\r
+ File reply;\r
+ try\r
+ {\r
reply = dbFetch.fetchDataAsFile(\r
- emprefx.toLowerCase() + ":" + query.trim(),\r
- "emblxml",null);\r
- }\r
- catch (Exception e)\r
+ emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null);\r
+ } catch (Exception e)\r
{\r
stopQuery();\r
- throw new Exception("EBI EMBL XML retrieval failed on "+emprefx.toLowerCase()+":"+query.trim(),e);\r
+ throw new Exception("EBI EMBL XML retrieval failed on "\r
+ + emprefx.toLowerCase() + ":" + query.trim(), e);\r
}\r
+ return getEmblSequenceRecords(emprefx, query, reply);\r
+ }\r
+\r
+ /**\r
+ * parse an emblxml file stored locally\r
+ * \r
+ * @param emprefx\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
+ * @return\r
+ * @throws Exception\r
+ */\r
+ public AlignmentI getEmblSequenceRecords(String emprefx, String query,\r
+ File reply) throws Exception\r
+ {\r
+ SequenceI seqs[] = null;\r
+ StringBuffer result = new StringBuffer();\r
if (reply != null && reply.exists())\r
+ {\r
+ efile = null;\r
+ file = reply.getAbsolutePath();\r
+ if (reply.length() > 25)\r
{\r
- efile=null;\r
- file = reply.getAbsolutePath();\r
- if (reply.length()>25)\r
- {\r
- efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);\r
- } else {\r
- result.append("# No EMBL record retrieved for "+emprefx.toLowerCase()+":"+query.trim());\r
- }\r
+ efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);\r
}\r
- if (efile!=null) {\r
- for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {\r
- EmblEntry entry = (EmblEntry) i.next();\r
- SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO: use !fetchNa,!fetchPeptide here instead - see todo in emblEntry\r
- if (seqparts!=null) {\r
- SequenceI[] newseqs = null;\r
- int si=0;\r
- if (seqs==null) {\r
- newseqs = new SequenceI[seqparts.length];\r
- } else {\r
- newseqs = new SequenceI[seqs.length+seqparts.length];\r
- \r
- for (;si<seqs.length; si++) {\r
- newseqs[si] = seqs[si];\r
- seqs[si] = null;\r
- }\r
- }\r
- for (int j=0;j<seqparts.length; si++, j++) {\r
- newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on dataset and refer\r
+ else\r
+ {\r
+ result.append("# No EMBL record retrieved for "\r
+ + emprefx.toLowerCase() + ":" + query.trim());\r
+ }\r
+ }\r
+ if (efile != null)\r
+ {\r
+ for (Iterator i = efile.getEntries().iterator(); i.hasNext();)\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
+ if (seqparts != null)\r
+ {\r
+ SequenceI[] newseqs = null;\r
+ int si = 0;\r
+ if (seqs == null)\r
+ {\r
+ newseqs = new SequenceI[seqparts.length];\r
+ }\r
+ else\r
+ {\r
+ newseqs = new SequenceI[seqs.length + seqparts.length];\r
+\r
+ for (; si < seqs.length; si++)\r
+ {\r
+ newseqs[si] = seqs[si];\r
+ seqs[si] = null;\r
}\r
- seqs=newseqs;\r
- \r
}\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
+ }\r
+ seqs = newseqs;\r
+\r
}\r
- } else {\r
- result=null;\r
}\r
- AlignmentI al =null;\r
- if (seqs!=null && seqs.length>0)\r
+ }\r
+ else\r
+ {\r
+ result = null;\r
+ }\r
+ AlignmentI al = null;\r
+ if (seqs != null && seqs.length > 0)\r
{\r
al = new Alignment(seqs);\r
- result.append("# Successfully parsed the "+emprefx+" queries into an Alignment");\r
+ result.append("# Successfully parsed the " + emprefx\r
+ + " queries into an Alignment");\r
results = result;\r
}\r
stopQuery();\r
return al;\r
}\r
\r
-}
\ No newline at end of file
+}\r
git://source.jalview.org / jalview.git / blobdiff