From c821d24532dd69f788dfa78227b5c7dbb79338fb Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Thu, 26 Jul 2012 16:44:38 +0100
Subject: [PATCH] mark obsolete and partial features
---
.../artemis/components/FeatureList.java | 40 +++++++++++++++++--
1 file changed, 37 insertions(+), 3 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/FeatureList.java b/uk/ac/sanger/artemis/components/FeatureList.java
index 9eca416c6..9c938f41e 100644
--- a/uk/ac/sanger/artemis/components/FeatureList.java
+++ b/uk/ac/sanger/artemis/components/FeatureList.java
@@ -763,7 +763,11 @@ public class FeatureList extends EntryGroupPanel
{
try
{
- note = feature.getValueOfQualifier("comment");
+ if(feature.getValueOfQualifier("isObsolete") != null &&
+ feature.getValueOfQualifier("isObsolete").equals("true"))
+ note = "obsolete";
+ else
+ note = feature.getValueOfQualifier("comment");
}
catch(InvalidRelationException e){}
}
@@ -786,9 +790,9 @@ public class FeatureList extends EntryGroupPanel
description_string_buffer.append(getQualifierString(feature));
}
- final String low_pos;
- final String high_pos;
+ String low_pos;
+ String high_pos;
if(low_marker == null || high_marker == null)
{
low_pos = "unknown";
@@ -807,6 +811,36 @@ public class FeatureList extends EntryGroupPanel
high_pos = String.valueOf(low_marker.getRawPosition());
}
}
+
+
+ if(isDatabaseGroup)
+ {
+ try
+ {
+ if(feature.getQualifierByName("isFminPartial") != null)
+ low_pos = "<"+low_pos;
+ if(feature.getQualifierByName("isFmaxPartial") != null)
+ high_pos = ">"+high_pos;
+ }
+ catch (InvalidRelationException e){}
+ }
+ else
+ {
+ if(feature.getLocation().isPartial(true)) // 5prime
+ {
+ if(feature.isForwardFeature())
+ low_pos = "<"+low_pos;
+ else
+ high_pos = ">"+high_pos;
+ }
+ if(feature.getLocation().isPartial(false)) // 3prime
+ {
+ if(feature.isForwardFeature())
+ high_pos = ">"+high_pos;
+ else
+ low_pos = "<"+low_pos;
+ }
+ }
StringBuffer new_list_line = new StringBuffer();
--
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