From e59cf027d804dbf68293cd67ad99da3f598a7c58 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 23 Jun 2010 15:23:24 +0000
Subject: [PATCH] mark as gap
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@14108 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/AddMenu.java | 18 ++++++++++++++----
1 file changed, 14 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/AddMenu.java b/uk/ac/sanger/artemis/components/AddMenu.java
index 7c89aa7dc..e4503c7ff 100644
--- a/uk/ac/sanger/artemis/components/AddMenu.java
+++ b/uk/ac/sanger/artemis/components/AddMenu.java
@@ -59,6 +59,7 @@ import java.awt.event.WindowEvent;
import java.util.Comparator;
import java.util.Vector;
import java.util.Enumeration;
+import java.util.regex.Pattern;
import javax.swing.Box;
import javax.swing.JCheckBox;
@@ -1692,6 +1693,8 @@ public class AddMenu extends SelectionMenu
else
unsure = new Key ("unsure");
+ Pattern p = Pattern.compile("^(n|N)+$"); // pattern match for all n's
+
for (int i = 1 ; i <= bases.getLength () ; ++i) {
try {
if (! Bases.isLegalBase (bases.getBaseAt (i))) {
@@ -1717,10 +1720,17 @@ public class AddMenu extends SelectionMenu
final QualifierVector qualifiers = new QualifierVector ();
- qualifiers.setQualifier (new Qualifier ("note", unsure_bases));
-
- final Feature feature =
- new_entry.createFeature (unsure, location, qualifiers);
+ if(p.matcher(unsure_bases).matches())
+ {
+ final Feature feature =
+ new_entry.createFeature (new Key("gap"), location, qualifiers);
+ }
+ else
+ {
+ qualifiers.setQualifier (new Qualifier ("note", unsure_bases));
+ final Feature feature =
+ new_entry.createFeature (unsure, location, qualifiers);
+ }
}
} catch (ReadOnlyException e) {
throw new Error ("internal error - unexpected exception: " + e);
--
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