X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEmblXmlSource.java;h=fe67b21283031201f83c1212c255489c85534ed1;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;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..fe67b21 100644
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -1,99 +1,162 @@
-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();
-    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 {
-      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);
-    }
-    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;
-  }
-
-}
\ 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;
+  }
+
+}