From b767520161c3366c44d63e242a0652c99ee9f4be Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 8 Dec 2004 13:35:43 +0000
Subject: [PATCH] add biojava comments
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2118 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/ArtemisMain.java | 23 +++++++++++--------
1 file changed, 14 insertions(+), 9 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/ArtemisMain.java b/uk/ac/sanger/artemis/components/ArtemisMain.java
index 11a9bc4dc..b277c8f10 100644
--- a/uk/ac/sanger/artemis/components/ArtemisMain.java
+++ b/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 1.3 2004-12-03 17:47:04 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ArtemisMain.java,v 1.4 2004-12-08 13:35:43 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -44,7 +44,7 @@ import java.io.*;
* The main window for the Artemis sequence editor.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: ArtemisMain.java,v 1.3 2004-12-03 17:47:04 tjc Exp $
+ * @version $Id: ArtemisMain.java,v 1.4 2004-12-08 13:35:43 tjc Exp $
**/
public class ArtemisMain extends Splash
@@ -279,14 +279,22 @@ public class ArtemisMain extends Splash
}
/**
+ *
* Handle the -biojava option
+ *
+ * Command line syntax:
+ * art -biojava org.biojava.bio.seq.io.EmblLikeFormat foo.embl
+ *
+ * BioJava formats:
+ * EmblLikeFormat, FastaFormat, GAMEFormat, GenbankFormat, PhredFormat
+ *
**/
private void handleBioJava(final String [] args)
{
if(args.length == 3)
{
final String class_name = args[1];
- final String location = args[2];
+ final String location = args[2];
final Document location_document =
DocumentFactory.makeDocument(location);
@@ -303,18 +311,15 @@ public class ArtemisMain extends Splash
if(biojava_object instanceof SequenceFormat)
{
- final SequenceFormat sequence_format =
- (SequenceFormat) biojava_object;
+ final SequenceFormat sequence_format = (SequenceFormat)biojava_object;
emblEntry =
new uk.ac.sanger.artemis.io.BioJavaEntry(entry_information,
- location_document,
- sequence_format);
+ location_document,
+ sequence_format);
final Entry new_entry = new Entry(emblEntry);
-
final EntryEdit new_entry_edit = makeEntryEdit(new_entry);
-
new_entry_edit.setVisible(true);
}
else
--
GitLab