X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;h=80206c09a64a1c6b02694e70da891d7fb6c2932c;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=68fa87c6483f0fca0acf0dd7570e836fc1069d9c;hpb=0eda2ac2f334f55f6e5f137789453a9f4dfe4d73;p=jalview.git
diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 68fa87c..80206c0 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -1,3 +1,20 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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 .
+ */
package jalview.ws.dbsources;
import jalview.datamodel.Alignment;
@@ -22,78 +39,124 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
{
super();
}
+
/**
* retrieve and parse an emblxml file
- * @param emprefx either EMBL or EMBLCDS strings are allowed - anything else will not retrieve emblxml
+ *
+ * @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
+ public AlignmentI getEmblSequenceRecords(String emprefx, String query)
+ throws Exception
{
startQuery();
- SequenceI seqs[] = null;
- Vector alseq = new Vector(); // the sequences that will actually be presented in the alignment
- StringBuffer result = new StringBuffer();
EBIFetchClient dbFetch = new EBIFetchClient();
- File reply;
- try {
+ File reply;
+ try
+ {
reply = dbFetch.fetchDataAsFile(
- emprefx.toLowerCase() + ":" + query.trim(),
- "emblxml",null);
- }
- catch (Exception e)
+ emprefx.toLowerCase() + ":" + query.trim(), "emblxml", null);
+ } catch (Exception e)
{
stopQuery();
- throw new Exception("EBI EMBL XML retrieval failed on "+emprefx.toLowerCase()+":"+query.trim(),e);
+ 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=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());
- }
+ efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
}
- 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 (;si0)
+ }
+ 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");
+ result.append("# Successfully parsed the " + emprefx
+ + " queries into an Alignment");
results = result;
}
stopQuery();
return al;
}
-}
\ No newline at end of file
+}