-/*\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
- * \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
- * \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
- * \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
- */\r
-package jalview.ws.dbsources;\r
-\r
-import jalview.datamodel.Alignment;\r
-import jalview.datamodel.AlignmentI;\r
-import jalview.datamodel.SequenceI;\r
-import jalview.datamodel.xdb.embl.EmblEntry;\r
-import jalview.ws.ebi.EBIFetchClient;\r
-\r
-import java.io.File;\r
-import java.util.Iterator;\r
-import java.util.Vector;\r
-\r
-public abstract class EmblXmlSource extends EbiFileRetrievedProxy\r
-{\r
-\r
- /**\r
- * Last properly parsed embl file.\r
- */\r
- public jalview.datamodel.xdb.embl.EmblFile efile = null;\r
-\r
- public EmblXmlSource()\r
- {\r
- super();\r
- }\r
-\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
- * @param query\r
- * @return\r
- * @throws Exception\r
- */\r
- public AlignmentI getEmblSequenceRecords(String emprefx, String query)\r
- throws Exception\r
- {\r
- startQuery();\r
- EBIFetchClient dbFetch = new EBIFetchClient();\r
- File reply;\r
- try\r
- {\r
- reply = dbFetch.fetchDataAsFile(emprefx.toLowerCase() + ":"\r
- + query.trim(), "emblxml", null);\r
- } catch (Exception e)\r
- {\r
- stopQuery();\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\r
- * will 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 = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);\r
- }\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
- }\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
- }\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\r
- + " queries into an Alignment");\r
- results = result;\r
- }\r
- stopQuery();\r
- return al;\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ws.dbsources;
+
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.xdb.embl.EmblEntry;
+import jalview.datamodel.xdb.embl.EmblFile;
+import jalview.util.MessageManager;
+import jalview.ws.ebi.EBIFetchClient;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+public abstract class EmblXmlSource extends EbiFileRetrievedProxy
+{
+ /*
+ * JAL-1856 Embl returns this text for query not found
+ */
+ private static final String EMBL_NOT_FOUND_REPLY = "ERROR 12 No entries found.";
+
+ public EmblXmlSource()
+ {
+ super();
+ }
+
+ /**
+ * retrieve and parse an emblxml file
+ *
+ * @param emprefx
+ * either EMBL or EMBLCDS strings are allowed - anything else will
+ * not retrieve emblxml
+ * @param query
+ * @return
+ * @throws Exception
+ */
+ public AlignmentI getEmblSequenceRecords(String emprefx, String query)
+ throws Exception
+ {
+ startQuery();
+ EBIFetchClient dbFetch = new EBIFetchClient();
+ File reply;
+ try
+ {
+ reply = dbFetch.fetchDataAsFile(
+ emprefx.toLowerCase() + ":" + query.trim(), "display=xml",
+ ".xml");
+ } catch (Exception e)
+ {
+ stopQuery();
+ throw new Exception(MessageManager.formatMessage(
+ "exception.ebiembl_retrieval_failed_on", new String[] {
+ emprefx.toLowerCase(), query.trim() }), e);
+ }
+ return getEmblSequenceRecords(emprefx, query, reply);
+ }
+
+ /**
+ * parse an emblxml file stored locally
+ *
+ * @param emprefx
+ * either EMBL or EMBLCDS strings are allowed - anything else will
+ * not retrieve emblxml
+ * @param query
+ * @param file
+ * the EMBL XML file containing the results of a query
+ * @return
+ * @throws Exception
+ */
+ public AlignmentI getEmblSequenceRecords(String emprefx, String query,
+ File reply) throws Exception
+ {
+ EmblFile efile = null;
+ List<SequenceI> seqs = new ArrayList<SequenceI>();
+
+ if (reply != null && reply.exists())
+ {
+ file = reply.getAbsolutePath();
+ if (reply.length() > EMBL_NOT_FOUND_REPLY.length())
+ {
+ efile = EmblFile.getEmblFile(reply);
+ }
+ }
+
+ /*
+ * invalid accession gets a reply with no <entry> elements, text content of
+ * EmbFile reads something like (e.g.) this ungrammatical phrase
+ * Entry: <acc> display type is either not supported or entry is not found.
+ */
+ List<SequenceI> peptides = new ArrayList<SequenceI>();
+ if (efile != null && efile.getEntries() != null)
+ {
+ for (EmblEntry entry : efile.getEntries())
+ {
+ SequenceI seq = entry.getSequence(emprefx, peptides);
+ if (seq != null)
+ {
+ seqs.add(seq.deriveSequence());
+ // place DBReferences on dataset and refer
+ }
+ }
+ }
+
+ AlignmentI al = null;
+ if (!seqs.isEmpty())
+ {
+ al = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
+ }
+ stopQuery();
+ return al;
+ }
+
+ @Override
+ public boolean isDnaCoding()
+ {
+ return true;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff