X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblFile.java;h=4091222cb42055b2c27bba454de8136ae4aeebfb;hb=59d682209891099d46b960509907c79e3fb276fe;hp=52542aa3d1bafc42c1b56401138d55fcbaa610c6;hpb=586c640e0c55327a34d72c3cab6eb8052abc3029;p=jalview.git

diff --git a/src/jalview/datamodel/xdb/embl/EmblFile.java b/src/jalview/datamodel/xdb/embl/EmblFile.java
index 52542aa..4091222 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFile.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFile.java
@@ -1,6 +1,22 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.datamodel.xdb.embl;
 
-
 import java.io.File;
 import java.io.FileReader;
 import java.io.Reader;
@@ -9,82 +25,119 @@ 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;
-    }
-    /**
-     * @param errors the errors to set
-     */
-    public void setErrors(Vector 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)
+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;
+  }
+
+  /**
+   * @param errors
+   *          the errors to set
+   */
+  public void setErrors(Vector 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;
+    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);
-        }
-        return null;
+      return EmblFile.getEmblFile(new FileReader(file));
+    } catch (Exception e)
+    {
+      System.err.println("Exception whilst reading EMBLfile from " + file);
+      e.printStackTrace(System.err);
     }
-    public static EmblFile getEmblFile(Reader file) {
-        EmblFile record = new EmblFile();
-        try
-        {
-          // 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);
+    return null;
+  }
 
-          // 2. Unmarshal the data
-          Unmarshaller unmar = new Unmarshaller(record);
-          try {
-              // uncomment to DEBUG EMBLFile reading unmar.setDebug(jalview.bin.Cache.log.isDebugEnabled());
-          } catch (Exception e) {};
-          unmar.setIgnoreExtraElements(true);
-          unmar.setMapping(map);
+  public static EmblFile getEmblFile(Reader file)
+  {
+    EmblFile record = new EmblFile();
+    try
+    {
+      // 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);
 
-          record = (EmblFile) unmar.unmarshal(file);
-        }
-        catch (Exception e)
-        {
-          e.printStackTrace(System.err);
-          record=null;
-        }
+      // 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);
+    } catch (Exception e)
+    {
+      e.printStackTrace(System.err);
+      record = null;
+    }
 
-        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.");
-        }
+    return record;
+  }
+
+  public static void main(String args[])
+  {
+    File mf = null;
+    if (args.length == 1)
+    {
+      mf = new File(args[0]);
+    }
+    if (!mf.exists())
+    {
+      mf = new File(
+              "C:\\Documents and Settings\\JimP\\workspace-3.2\\Jalview Release\\schemas\\embleRecordV1.1.xml");
+    }
+    EmblFile myfile = EmblFile.getEmblFile(mf);
+    if (myfile != null && myfile.entries != null
+            && myfile.entries.size() > 0)
+      System.out.println(myfile.entries.size() + " Records read. (" + mf
+              + ")");
+  }
 }