X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblFile.java;h=8a32c130c9230c6ac7a4e4e5fa52700200fda18a;hb=88515cdb74e4603a40c8c1dca14107b5ca503e04;hp=3b043962f862aaf36fb66dda5baf1989440b5c61;hpb=732f372a01b4f5706e8cd3250c9b1761f176a853;p=jalview.git

diff --git a/src/jalview/datamodel/xdb/embl/EmblFile.java b/src/jalview/datamodel/xdb/embl/EmblFile.java
index 3b04396..8a32c13 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFile.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFile.java
@@ -1,92 +1,203 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.datamodel.xdb.embl;
 
+import jalview.datamodel.DBRefEntry;
+import jalview.ws.dbsources.Uniprot;
 
 import java.io.File;
 import java.io.FileReader;
+import java.io.PrintWriter;
 import java.io.Reader;
 import java.util.Vector;
 
 import org.exolab.castor.mapping.Mapping;
 import org.exolab.castor.xml.Unmarshaller;
 
-public class EmblFile {
-    Vector entries;
-    Vector errors;
-    /**
-     * @return the entries
-     */
-    public Vector getEntries() {
-        return entries;
-    }
-    /**
-     * @param entries the entries to set
-     */
-    public void setEntries(Vector entries) {
-        this.entries = entries;
-    }
-    /**
-     * @return the errors
-     */
-    public Vector getErrors() {
-        return errors;
+/**
+ * Data model for entries returned from an EMBL query, as marshalled by a Castor
+ * binding file
+ * 
+ * For example: http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/embl/x53828/emblxml
+ * 
+ * @see embl_mapping.xml
+ */
+public class EmblFile
+{
+  Vector<EmblEntry> entries;
+
+  Vector<EmblError> errors;
+
+  String text;
+
+  /**
+   * @return the entries
+   */
+  public Vector<EmblEntry> getEntries()
+  {
+    return entries;
+  }
+
+  /**
+   * @param entries
+   *          the entries to set
+   */
+  public void setEntries(Vector<EmblEntry> entries)
+  {
+    this.entries = entries;
+  }
+
+  /**
+   * @return the errors
+   */
+  public Vector<EmblError> getErrors()
+  {
+    return errors;
+  }
+
+  /**
+   * @param errors
+   *          the errors to set
+   */
+  public void setErrors(Vector<EmblError> errors)
+  {
+    this.errors = errors;
+  }
+
+  /**
+   * Parse an EmblXML file into an EmblFile object
+   * 
+   * @param file
+   * @return parsed EmblXML or null if exceptions were raised
+   */
+  public static EmblFile getEmblFile(File file)
+  {
+    if (file == null)
+    {
+      return null;
     }
-    /**
-     * @param errors the errors to set
-     */
-    public void setErrors(Vector errors) {
-        this.errors = errors;
+    try
+    {
+      return EmblFile.getEmblFile(new FileReader(file));
+    } catch (Exception e)
+    {
+      System.err.println("Exception whilst reading EMBLfile from " + file);
+      e.printStackTrace(System.err);
     }
-    /**
-     * Parse an EmblXML file into an EmblFile object
-     * @param file
-     * @return parsed EmblXML or null if exceptions were raised
-     */
-    public static EmblFile getEmblFile(File file)
+    return null;
+  }
+
+  public static EmblFile getEmblFile(Reader file)
+  {
+    EmblFile record = new EmblFile();
+    try
     {
-        if (file==null)
-            return null;
-        try {
-            return EmblFile.getEmblFile(new FileReader(file));
-        }
-        catch (Exception e) {
-            System.err.println("Exception whilst reading EMBLfile from "+file);
-            e.printStackTrace(System.err);
+      // 1. Load the mapping information from the file
+      Mapping map = new Mapping(record.getClass().getClassLoader());
+
+      java.net.URL url = record.getClass().getResource("/embl_mapping.xml");
+      map.loadMapping(url);
+
+      // 2. Unmarshal the data
+      Unmarshaller unmar = new Unmarshaller(record);
+      try
+      {
+        // uncomment to DEBUG EMBLFile reading
+        if (jalview.bin.Cache
+                .getDefault(jalview.bin.Cache.CASTORLOGLEVEL, "debug")
+                .equalsIgnoreCase("DEBUG"))
+        {
+          unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
         }
-        return null;
+      } catch (Exception e)
+      {
+      }
+      unmar.setIgnoreExtraElements(true);
+      unmar.setIgnoreExtraAttributes(true);
+      unmar.setMapping(map);
+      unmar.setLogWriter(new PrintWriter(System.out));
+      record = (EmblFile) unmar.unmarshal(file);
+
+      canonicaliseDbRefs(record);
+    } catch (Exception e)
+    {
+      e.printStackTrace(System.err);
+      record = null;
+    }
+
+    return record;
+  }
+
+  /**
+   * Change blank version to "0" in any DBRefEntry, to ensure consistent
+   * comparison with other DBRefEntry in Jalview
+   * 
+   * @param record
+   * @see Uniprot#getDbVersion
+   */
+  static void canonicaliseDbRefs(EmblFile record)
+  {
+    if (record.getEntries() == null)
+    {
+      return;
     }
-    public static EmblFile getEmblFile(Reader file) {
-        EmblFile record = new EmblFile();
-        try
+    for (EmblEntry entry : record.getEntries())
+    {
+      if (entry.getDbRefs() != null)
+      {
+        for (DBRefEntry dbref : entry.getDbRefs())
         {
-          // 1. Load the mapping information from the file
-          Mapping map = new Mapping(record.getClass().getClassLoader());
-          java.net.URL url = record.getClass().getResource("/embl_mapping.xml");
-          map.loadMapping(url);
-
-          // 2. Unmarshal the data
-          Unmarshaller unmar = new Unmarshaller(record);
-          try {
-              // uncomment to DEBUG EMBLFile reading 
-            if (((String)jalview.bin.Cache.getDefault(jalview.bin.Cache.CASTORLOGLEVEL, "debug")).equalsIgnoreCase("DEBUG")
-                    ) unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
-          } catch (Exception e) {};
-          unmar.setIgnoreExtraElements(true);
-          unmar.setMapping(map);
-
-          record = (EmblFile) unmar.unmarshal(file);
+          if ("".equals(dbref.getVersion()))
+          {
+            dbref.setVersion("0");
+          }
         }
-        catch (Exception e)
+      }
+
+      if (entry.getFeatures() != null)
+      {
+        for (EmblFeature feature : entry.getFeatures())
         {
-          e.printStackTrace(System.err);
-          record=null;
+          if (feature.getDbRefs() != null)
+          {
+            for (DBRefEntry dbref : feature.getDbRefs())
+            {
+              if ("".equals(dbref.getVersion()))
+              {
+                dbref.setVersion("0");
+              }
+            }
+          }
         }
+      }
+    }
+  }
 
+  public String getText()
+  {
+    return text;
+  }
 
-        return record;
-      }
-    public static void main(String args[]) {
-        EmblFile myfile = EmblFile.getEmblFile(new File("C:\\Documents and Settings\\JimP\\workspace-3.2\\Jalview Release\\schemas\\embleRecordV1.1.xml"));
-        if (myfile!=null && myfile.entries!=null && myfile.entries.size()>0)
-            System.out.println(myfile.entries.size()+" Records read.");
-        }
+  public void setText(String text)
+  {
+    this.text = text;
+  }
 }