tidy

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8043 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/EntryFileDialog.java

@@ -20,7 +20,7 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  *
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/EntryFileDialog.java,v 1.8 2008-06-23 13:31:26 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/EntryFileDialog.java,v 1.9 2008-06-23 13:53:46 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.components;
@@ -42,7 +42,7 @@ import javax.swing.*;
  *  This class is a JFileChooser that can read EMBL Entry objects.
  *
  *  @author Kim Rutherford
- *  @version $Id: EntryFileDialog.java,v 1.8 2008-06-23 13:31:26 tjc Exp $
+ *  @version $Id: EntryFileDialog.java,v 1.9 2008-06-23 13:53:46 tjc Exp $
  **/
 
 public class EntryFileDialog extends StickyFileChooser 
@@ -442,7 +442,7 @@ public class EntryFileDialog extends StickyFileChooser
         try 
         {
           if(entry.getEMBLEntry() instanceof DatabaseDocumentEntry)
-            ReadAndWriteEntry.writeEntry(entry, file, 
+            ReadAndWriteEntry.writeDatabaseEntryToFile(entry, file, 
                 flattenGeneModel.isSelected(), false, destination_type);
           else if(include_diana_extensions) 
             entry.save(file, destination_type, false);
@@ -460,7 +460,7 @@ public class EntryFileDialog extends StickyFileChooser
             try 
             {
               if(entry.getEMBLEntry() instanceof DatabaseDocumentEntry)
-                ReadAndWriteEntry.writeEntry(entry, file, 
+                ReadAndWriteEntry.writeDatabaseEntryToFile(entry, file, 
                     flattenGeneModel.isSelected(), true, destination_type);
               else if(include_diana_extensions) 
                 entry.save(file, destination_type, true);

uk/ac/sanger/artemis/components/ReadAndWriteEntry.java

@@ -102,14 +102,21 @@ class ReadAndWriteEntry
    * Write entry to a file
    * @param entry
    * @param file
-   * @param flatten if true the gene model is flattened
+   * @param flatten Flatten the gene model and combine the qualifiers if true.
+   *    If false it will write all features and qualifiers out.
+   * @param force invalid qualifiers and any features with invalid keys will 
+   *    be quietly thrown away when saving.
+   * @param destination_type Should be one of EMBL_FORMAT, GENBANK_FORMAT,
+   *    GFF_FORMAT or ANY_FORMAT.  If ANY_FORMAT then the Entry will
+   *    be saved in the same format it was created, otherwise it will be saved
+   *    in the given format.
    * @throws IOException
    * @throws EntryInformationException
    */
-  public static void writeEntry(final Entry entry, final File file,
-                                final boolean flatten, 
-                                final boolean force,
-                                final int destination_type) 
+  public static void writeDatabaseEntryToFile(final Entry entry, final File file,
+                                              final boolean flatten, 
+                                              final boolean force,
+                                              final int destination_type) 
          throws IOException, EntryInformationException
   {
     GeneUtils.lazyLoadAll(entry, null);
@@ -195,11 +202,11 @@ class ReadAndWriteEntry
     try
     {
       Entry entry = ReadAndWriteEntry.readEntryFromDatabase("Pf3D7_03");
-      ReadAndWriteEntry.writeEntry(
+      ReadAndWriteEntry.writeDatabaseEntryToFile(
           entry, new File("Pf3D7_03.flatten"), true, false, 
           DocumentEntryFactory.EMBL_FORMAT);
       
-      ReadAndWriteEntry.writeEntry(
+      ReadAndWriteEntry.writeDatabaseEntryToFile(
           entry, new File("Pf3D7_03.not-flatten"), false, false,
           DocumentEntryFactory.EMBL_FORMAT);
     }