X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;h=e99206ff663305e079d3d66d1e922a16cd224643;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=80206c09a64a1c6b02694e70da891d7fb6c2932c;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 80206c0..e99206f 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -1,162 +1,158 @@
-/*
- * 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 <http://www.gnu.org/licenses/>.
- */
-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 2.9.0b2)
+ * Copyright (C) 2015 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;
+
+public abstract class EmblXmlSource extends EbiFileRetrievedProxy
+{
+
+  /**
+   * Last properly parsed embl file.
+   */
+  public 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(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
+  {
+    SequenceI seqs[] = null;
+    StringBuffer result = new StringBuffer();
+    if (reply != null && reply.exists())
+    {
+      efile = null;
+      file = reply.getAbsolutePath();
+      if (reply.length() > 25)
+      {
+        efile = EmblFile.getEmblFile(reply);
+      }
+      else
+      {
+        result.append(MessageManager.formatMessage(
+                "label.no_embl_record_found",
+                new String[] { emprefx.toLowerCase(), query.trim() }));
+      }
+    }
+    if (efile != null)
+    {
+      for (EmblEntry entry : efile.getEntries())
+      {
+        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(MessageManager.formatMessage(
+              "label.embl_successfully_parsed", new String[] { emprefx }));
+      results = result;
+    }
+    stopQuery();
+    return al;
+  }
+
+}