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Commit b7675201 authored by tjc's avatar tjc
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add biojava comments

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2118 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent 7c08cec5
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...@@ -20,7 +20,7 @@ ...@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software * along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. * 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; package uk.ac.sanger.artemis.components;
...@@ -44,7 +44,7 @@ import java.io.*; ...@@ -44,7 +44,7 @@ import java.io.*;
* The main window for the Artemis sequence editor. * The main window for the Artemis sequence editor.
* *
* @author Kim Rutherford <kmr@sanger.ac.uk> * @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 public class ArtemisMain extends Splash
...@@ -279,7 +279,15 @@ public class ArtemisMain extends Splash ...@@ -279,7 +279,15 @@ public class ArtemisMain extends Splash
} }
/** /**
*
* Handle the -biojava option * 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) private void handleBioJava(final String [] args)
{ {
...@@ -303,8 +311,7 @@ public class ArtemisMain extends Splash ...@@ -303,8 +311,7 @@ public class ArtemisMain extends Splash
if(biojava_object instanceof SequenceFormat) if(biojava_object instanceof SequenceFormat)
{ {
final SequenceFormat sequence_format = final SequenceFormat sequence_format = (SequenceFormat)biojava_object;
(SequenceFormat) biojava_object;
emblEntry = emblEntry =
new uk.ac.sanger.artemis.io.BioJavaEntry(entry_information, new uk.ac.sanger.artemis.io.BioJavaEntry(entry_information,
...@@ -312,9 +319,7 @@ public class ArtemisMain extends Splash ...@@ -312,9 +319,7 @@ public class ArtemisMain extends Splash
sequence_format); sequence_format);
final Entry new_entry = new Entry(emblEntry); final Entry new_entry = new Entry(emblEntry);
final EntryEdit new_entry_edit = makeEntryEdit(new_entry); final EntryEdit new_entry_edit = makeEntryEdit(new_entry);
new_entry_edit.setVisible(true); new_entry_edit.setVisible(true);
} }
else else
......
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