X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;h=b1395745ccc8539752d2279ce038bf5f89e2ceed;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=01f502b45e7904e26ba055ffb1bb1282a8d46c74;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git
diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 01f502b..b139574 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -1,163 +1,139 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-package jalview.ws.dbsources;
-
-import jalview.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.xdb.embl.EmblEntry;
-import jalview.ws.ebi.EBIFetchClient;
-
-import java.io.File;
-import java.util.Iterator;
-import java.util.Vector;
-
-public abstract class EmblXmlSource extends EbiFileRetrievedProxy
-{
-
- /**
- * Last properly parsed embl file.
- */
- public jalview.datamodel.xdb.embl.EmblFile efile = null;
-
- 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(), "emblxml", null);
- } catch (Exception e)
- {
- stopQuery();
- throw new Exception("EBI EMBL XML retrieval failed on "
- + 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
- {
- SequenceI seqs[] = null;
- StringBuffer result = new StringBuffer();
- if (reply != null && reply.exists())
- {
- efile = null;
- file = reply.getAbsolutePath();
- if (reply.length() > 25)
- {
- efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
- }
- else
- {
- result.append("# No EMBL record retrieved for "
- + emprefx.toLowerCase() + ":" + query.trim());
- }
- }
- if (efile != null)
- {
- for (Iterator i = efile.getEntries().iterator(); i.hasNext();)
- {
- EmblEntry entry = (EmblEntry) i.next();
- SequenceI[] seqparts = entry.getSequences(false, true, emprefx); // TODO:
- // use
- // !fetchNa,!fetchPeptide
- // here
- // instead
- // -
- // see
- // todo
- // in
- // emblEntry
- if (seqparts != null)
- {
- SequenceI[] newseqs = null;
- int si = 0;
- if (seqs == null)
- {
- newseqs = new SequenceI[seqparts.length];
- }
- else
- {
- newseqs = new SequenceI[seqs.length + seqparts.length];
-
- for (; si < seqs.length; si++)
- {
- newseqs[si] = seqs[si];
- seqs[si] = null;
- }
- }
- for (int j = 0; j < seqparts.length; si++, j++)
- {
- newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on
- // dataset and refer
- }
- seqs = newseqs;
-
- }
- }
- }
- else
- {
- result = null;
- }
- AlignmentI al = null;
- if (seqs != null && seqs.length > 0)
- {
- al = new Alignment(seqs);
- result.append("# Successfully parsed the " + emprefx
- + " queries into an Alignment");
- results = result;
- }
- stopQuery();
- return al;
- }
-
-}
+/*
+ * 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 .
+ * 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 seqs = new ArrayList();
+
+ 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 elements, text content of
+ * EmbFile reads something like (e.g.) this ungrammatical phrase
+ * Entry: display type is either not supported or entry is not found.
+ */
+ List peptides = new ArrayList();
+ 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;
+ }
+
+}