X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Fxdb%2Fembl%2FEmblFile.java;h=52542aa3d1bafc42c1b56401138d55fcbaa610c6;hb=c834ec02c02dec46f84960605bd7490aa8ac5a3a;hp=bc8cbbef230ace38615113e6bbebcdcecf6bc483;hpb=0879ca19b6df4983f82521a479b848526b2d14d4;p=jalview.git

diff --git a/src/jalview/datamodel/xdb/embl/EmblFile.java b/src/jalview/datamodel/xdb/embl/EmblFile.java
index bc8cbbe..52542aa 100644
--- a/src/jalview/datamodel/xdb/embl/EmblFile.java
+++ b/src/jalview/datamodel/xdb/embl/EmblFile.java
@@ -1,90 +1,90 @@
-package jalview.datamodel.xdb.embl;
-
-
-import java.io.File;
-import java.io.FileReader;
-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;
-    }
-    /**
-     * @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 {
-            return EmblFile.getEmblFile(new FileReader(file));
-        }
-        catch (Exception e) {
-            System.err.println("Exception whilst reading EMBLfile from "+file);
-            e.printStackTrace(System.err);
-        }
-        return null;
-    }
-    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);
-
-          // 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);
-
-          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\\embleRecord.xml"));
-        if (myfile!=null && myfile.entries!=null && myfile.entries.size()>0)
-            System.out.println(myfile.entries.size()+" Records read.");
-        }
-}
+package jalview.datamodel.xdb.embl;
+
+
+import java.io.File;
+import java.io.FileReader;
+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;
+    }
+    /**
+     * @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 {
+            return EmblFile.getEmblFile(new FileReader(file));
+        }
+        catch (Exception e) {
+            System.err.println("Exception whilst reading EMBLfile from "+file);
+            e.printStackTrace(System.err);
+        }
+        return null;
+    }
+    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);
+
+          // 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);
+
+          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.");
+        }
+}