From fe824fb5a19fa46d1c12b9248d268c5b839f48a6 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Fri, 21 Mar 2014 15:25:06 +0000
Subject: [PATCH] remove rank from alternative products
---
.../artemis/io/PublicDBDocumentEntry.java | 24 +++++++++++--------
1 file changed, 14 insertions(+), 10 deletions(-)
diff --git a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
index 11284b4b9..1c1756fc6 100644
--- a/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/PublicDBDocumentEntry.java
@@ -473,27 +473,31 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
{
final StringVector values = productQualifier.getValues();
final StringVector tmpNewValues = new StringVector();
- for(int j=0; j<values.size(); j++)
+ for(String val: values)
{
- String val = (String)values.get(j);
-
int ind = 0;
-
if((ind=val.indexOf(";db_xref="))>-1 && this instanceof EmblDocumentEntry)
val = val.substring(0,ind);
-
+
if((ind=val.indexOf(";evidence="))>-1 && this instanceof EmblDocumentEntry)
val = val.substring(0,ind);
-
+
if((ind=val.indexOf(";with="))>-1 && this instanceof EmblDocumentEntry)
val = val.substring(0,ind);
-
+
+ if((ind=val.indexOf("rank="))>-1 && this instanceof EmblDocumentEntry)
+ {
+ int ind2 = val.indexOf(";", ind);
+ if(ind == 0 && ind2 > -1)
+ val = val.substring(ind2+1);
+ }
+
if(val.startsWith("term="))
val = val.substring(5, val.length());
-
+
if(val.endsWith(";"))
val = val.substring(0, val.length()-1);
-
+
tmpNewValues.add(val);
}
return tmpNewValues;
@@ -741,7 +745,7 @@ public class PublicDBDocumentEntry extends SimpleDocumentEntry
Enumeration qualifiersenum = qualifierMapProperties.propertyNames();
n = 0;
- Vector qualifiersToRemove = new Vector();
+ Vector<String> qualifiersToRemove = new Vector<String>();
while(qualifiersenum.hasMoreElements())
{
String current_map_name = (String) qualifiersenum.nextElement();
--
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