-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.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
- * set this to false to *not* add protein products to alignment dataset.\r
- */\r
- public boolean getProteinProducts=false;\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
- * @param query\r
- * @return\r
- * @throws Exception\r
- */\r
- public AlignmentI getEmblSequenceRecords(String emprefx, String query) 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
- reply = dbFetch.fetchDataAsFile(\r
- emprefx.toLowerCase() + ":" + query.trim(),\r
- "emblxml",null);\r
- }\r
- catch (Exception e)\r
- {\r
- stopQuery();\r
- throw new Exception("EBI EMBL XML retrieval failed on "+emprefx.toLowerCase()+":"+query.trim(),e);\r
- }\r
- if (reply != null && reply.exists())\r
- {\r
- file = reply.getAbsolutePath();\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,!getProteinProducts, emprefx);\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
- }\r
- seqs=newseqs;\r
- \r
- }\r
- }\r
- } else {\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
- results = result;\r
- }\r
- stopQuery();\r
- return al;\r
- }\r
-\r
-}
\ No newline at end of file
+/*
+ * 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