-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
- * 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
- 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
- }\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
- }\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 2.8.0b1)
+ * Copyright (C) 2014 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.ws.ebi.EBIFetchClient;
+
+import java.io.File;
+import java.util.Iterator;
+
+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;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff