From fff4b2f9988b0077d25f034622eea77da49696f7 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 20 Jun 2006 11:25:22 +0000
Subject: [PATCH] include extra qualifiers and keys
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4437 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/io/GFFEntryInformation.java | 27 ++++++++++++++++---
1 file changed, 23 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/GFFEntryInformation.java b/uk/ac/sanger/artemis/io/GFFEntryInformation.java
index c1eab74a7..cfece2343 100644
--- a/uk/ac/sanger/artemis/io/GFFEntryInformation.java
+++ b/uk/ac/sanger/artemis/io/GFFEntryInformation.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/io/GFFEntryInformation.java,v 1.3 2005-10-11 14:20:31 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFEntryInformation.java,v 1.4 2006-06-20 11:25:22 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -37,7 +37,7 @@ import uk.ac.sanger.artemis.Options;
* An EntryInformation object for GFFDocumentEntry objects.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: GFFEntryInformation.java,v 1.3 2005-10-11 14:20:31 tjc Exp $
+ * @version $Id: GFFEntryInformation.java,v 1.4 2006-06-20 11:25:22 tjc Exp $
**/
public class GFFEntryInformation extends SimpleEntryInformation
@@ -72,14 +72,13 @@ public class GFFEntryInformation extends SimpleEntryInformation
**/
private void makeEntryInformation()
throws IOException, QualifierInfoException
- {
+ {
final InputStream feature_keys_stream =
Options.class.getResourceAsStream("/etc/feature_keys_gff");
final InputStream qualifier_types_stream =
Options.class.getResourceAsStream("/etc/qualifier_types_gff");
-
QualifierInfoVector qualifier_info_vector =
readQualifierInfo(qualifier_types_stream, feature_keys_stream);
@@ -90,6 +89,26 @@ public class GFFEntryInformation extends SimpleEntryInformation
addQualifierInfo(qualifier_info);
}
+
+ //
+ // include extra keys and qualifiers
+ final QualifierInfoVector extra_qualifiers =
+ Options.getOptions().getExtraQualifiers();
+ final StringVector extra_keys =
+ Options.getOptions().getOptionValues("extra_keys");
+
+ for(int i = 0 ; i < extra_keys.size() ; ++i)
+ {
+ final Key new_key = new Key((String)extra_keys.elementAt(i));
+ addKey(new_key);
+ }
+
+ for(int i = 0 ; i < extra_qualifiers.size() ; ++i)
+ {
+ final QualifierInfo new_qualifier_info = extra_qualifiers.elementAt(i);
+ System.out.println(new_qualifier_info.getName());
+ addQualifierInfo(new_qualifier_info);
+ }
// entry_information.setEMBLFormat(true);
}
--
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