add range option for opening db entry

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@6962 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/ArtemisMain.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/ArtemisMain.java,v 1.27 2008-01-18 15:50:11 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ArtemisMain.java,v 1.28 2008-01-21 16:15:39 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.components;
@@ -52,7 +52,7 @@ import javax.swing.JOptionPane;
  *  The main window for the Artemis sequence editor.
  *
  *  @author Kim Rutherford <kmr@sanger.ac.uk>
- *  @version $Id: ArtemisMain.java,v 1.27 2008-01-18 15:50:11 tjc Exp $
+ *  @version $Id: ArtemisMain.java,v 1.28 2008-01-21 16:15:39 tjc Exp $
  **/
 
 public class ArtemisMain extends Splash 
@@ -362,6 +362,7 @@ public class ArtemisMain extends Splash
       }
       else if(System.getProperty("chado") != null && new_entry_name.indexOf(':')>-1)
       {
+        // open from database e.g. Pfalciparum:Pf3D7_09:95000..150000
         Splash.logger4j.info("OPEN ENTRY "+new_entry_name);
         getStatusLabel().setText("Connecting ...");
         DatabaseEntrySource entry_source = new DatabaseEntrySource();

uk/ac/sanger/artemis/components/database/DatabaseEntrySource.java

@@ -44,6 +44,7 @@ import uk.ac.sanger.artemis.util.OutOfRangeException;
 import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
 import uk.ac.sanger.artemis.io.InvalidKeyException;
 import uk.ac.sanger.artemis.io.EntryInformationException;
+import uk.ac.sanger.artemis.io.Range;
 
 /**
  * 
@@ -108,7 +109,14 @@ public class DatabaseEntrySource implements EntrySource, Serializable
       InputStreamProgressListener progress_listener)
       throws OutOfRangeException, NoSequenceException, IOException
   {
-    return makeFromID(null, id, schema, false, progress_listener);
+    return makeFromID(null, id, schema, false, progress_listener, null);
+  }
+  
+  public Entry getEntry(String id, String schema,
+      InputStreamProgressListener progress_listener, Range range)
+      throws OutOfRangeException, NoSequenceException, IOException
+  {
+    return makeFromID(null, id, schema, false, progress_listener, range);
   }
 
   /**
@@ -251,9 +259,10 @@ public class DatabaseEntrySource implements EntrySource, Serializable
    *              Thrown if one of the features in the Entry is out of range of
    *              the Bases object.
    */
-  protected Entry makeFromID(final Bases bases, final String id,
+  private Entry makeFromID(final Bases bases, final String id,
                              final String schema, final boolean read_only,
-                             InputStreamProgressListener progress_listener)
+                             InputStreamProgressListener progress_listener, 
+                             final Range range)
              throws OutOfRangeException, IOException
   {
     try
@@ -266,7 +275,10 @@ public class DatabaseEntrySource implements EntrySource, Serializable
       else
       {
         DatabaseDocument doc = new DatabaseDocument(location, pfield, id,
-                                                    schema, splitGFFEntry, progress_listener);
+                                                    schema, splitGFFEntry, 
+                                                    progress_listener);
+        if(range != null)
+          doc.setRange(range);
         db_entry = new DatabaseDocumentEntry(doc, null);
       }
 

uk/ac/sanger/artemis/components/database/DatabaseJPanel.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/database/DatabaseJPanel.java,v 1.13 2008-01-18 15:54:47 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java,v 1.14 2008-01-21 16:15:39 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.components.database;
@@ -34,6 +34,7 @@ import uk.ac.sanger.artemis.util.InputStreamProgressListener;
 import uk.ac.sanger.artemis.util.OutOfRangeException;
 import uk.ac.sanger.artemis.util.DatabaseDocument;
 import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
+import uk.ac.sanger.artemis.io.Range;
 
 import javax.swing.JComponent;
 import javax.swing.JTree;
@@ -167,7 +168,8 @@ public class DatabaseJPanel extends JPanel
    * @param entry_source
    * @param splash_main
    * @param stream_progress_listener
-   * @param entryName                 e.g. Pfalciparum:Pf3D7_09
+   * @param entryName                 e.g. Pfalciparum:Pf3D7_09 or 
+   *                                  Pfalciparum:Pf3D7_09:20050..40000
    * @return
    */
   public static EntryEdit show(final DatabaseEntrySource entry_source,
@@ -184,11 +186,30 @@ public class DatabaseJPanel extends JPanel
       userName = userName.substring(5);
     
     DatabaseDocument doc = entry_source.getDatabaseDocument();
+    
+    Range range = null;
+    if(entry.length>2)
+    {
+      if(entry[2].indexOf("..") > -1)
+      {
+        String ranges[] = entry[2].split("\\.\\.");
+        if(ranges.length == 2)
+        {
+          try
+          {
+            range = new Range(Integer.parseInt(ranges[0]), 
+                              Integer.parseInt(ranges[1]));
+          }
+          catch(Exception e){ e.printStackTrace(); }
+        }
+      }
+    }
+    
     Feature f = doc.getFeatureByUniquename(entry[1]);
     
     return openEntry(Integer.toString(f.getFeatureId()), entry_source, 
         splash_main.getCanvas(), splash_main.getStatusLabel(), stream_progress_listener,
-        false, splash_main,  entry[1], userName);
+        false, splash_main,  entry[1], userName, range);
   }
 
   /**
@@ -226,7 +247,7 @@ public class DatabaseJPanel extends JPanel
         try
         {
           openEntry(srcfeatureId, entry_source, srcComponent, status_line, stream_progress_listener,
-              splitGFFEntry, splash_main, dbDocumentName, userName);
+              splitGFFEntry, splash_main, dbDocumentName, userName, null);
         }
         catch(RuntimeException re)
         {
@@ -242,7 +263,7 @@ public class DatabaseJPanel extends JPanel
             userName = userName.substring(5);
             
           openEntry(srcfeatureId, entry_source, srcComponent, status_line, stream_progress_listener,
-              splitGFFEntry, splash_main, dbDocumentName, userName);
+              splitGFFEntry, splash_main, dbDocumentName, userName, null);
         }
         srcComponent.setCursor(cdone);
         return null;
@@ -253,7 +274,20 @@ public class DatabaseJPanel extends JPanel
 
   }
 
-  
+  /**
+   * 
+   * @param srcfeatureId
+   * @param entry_source
+   * @param srcComponent
+   * @param status_line
+   * @param stream_progress_listener
+   * @param splitGFFEntry
+   * @param splash_main
+   * @param dbDocumentName
+   * @param userName
+   * @param range           range for to retrieve features in
+   * @return
+   */
   private static EntryEdit openEntry(
       final String srcfeatureId,
       final DatabaseEntrySource entry_source, 
@@ -263,15 +297,18 @@ public class DatabaseJPanel extends JPanel
       final boolean splitGFFEntry,
       final Splash splash_main, 
       final String dbDocumentName,
-      final String userName) 
+      final String userName,
+      final Range range) 
   {
     Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
     try
     {
+      if(range != null)
+        logger4j.info("LOAD FEATURES IN THE RANGE : "+range.toString());
       entry_source.setSplitGFF(splitGFFEntry);
 
       final Entry entry = entry_source.getEntry(srcfeatureId, userName,
-          stream_progress_listener);
+          stream_progress_listener, range);
 
       DatabaseDocumentEntry db_entry = (DatabaseDocumentEntry) entry
           .getEMBLEntry();