applied copyright 2008

[jalview.git] / src / jalview / ws / dbsources / EmblXmlSource.java

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 1300c65..a98e7e2 100644 (file)
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -1,10 +1,28 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
+ * Copyright (C) 2008 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.EBIFetchClient;\r
+import jalview.ws.ebi.EBIFetchClient;\r
 \r
 import java.io.File;\r
 import java.util.Iterator;\r
@@ -23,10 +41,6 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     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
@@ -36,9 +50,6 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
   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
@@ -51,15 +62,35 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
       stopQuery();\r
       throw new Exception("EBI EMBL XML retrieval failed on "+emprefx.toLowerCase()+":"+query.trim(),e);\r
     }\r
+    return getEmblSequenceRecords(emprefx, query, reply);\r
+  }\r
+  /**\r
+   * parse an emblxml file stored locally\r
+   * @param emprefx either EMBL or EMBLCDS strings are allowed - anything else will not retrieve emblxml\r
+   * @param query\r
+   * @param file the EMBL XML file containing the results of a query\r
+   * @return\r
+   * @throws Exception\r
+   */\r
+  public AlignmentI getEmblSequenceRecords(String emprefx, String query, 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
-        efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);\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,!getProteinProducts, emprefx);\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
@@ -94,4 +125,4 @@ public abstract class EmblXmlSource extends EbiFileRetrievedProxy
     return al;\r
   }\r
 \r
-}
\ No newline at end of file
+}\r