From 81ff22cb93d98ebb1f32d06bf719091fa1db0e07 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 12 Jun 2009 15:56:21 +0000
Subject: [PATCH] reinstate links on features

---
 src/jalview/io/vamsas/Sequencefeature.java |   25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/src/jalview/io/vamsas/Sequencefeature.java b/src/jalview/io/vamsas/Sequencefeature.java
index 1348227..55db09d 100644
--- a/src/jalview/io/vamsas/Sequencefeature.java
+++ b/src/jalview/io/vamsas/Sequencefeature.java
@@ -158,7 +158,10 @@ public class Sequencefeature extends Rangetype
       dsSeq.deleteFeature(feature);
       replaceJvObjMapping(feature, newsf);
       dsSeq.addSequenceFeature(newsf);
-      feature.otherDetails.clear();
+      if (feature.otherDetails!=null) {
+        // TODO later: leave this to finalise method ? 
+        feature.otherDetails.clear();
+      }
     }
   }
 
@@ -197,15 +200,14 @@ public class Sequencefeature extends Rangetype
       {
         String link = (String) feature.links.elementAt(i);
         UrlLink ulink = new UrlLink(link);
-        /*
-         * int sep = link.indexOf('|'); if (sep > -1) { Link vLink = new Link();
-         * if (sep > 0) { vLink.setContent(link.substring(0, sep - 1)); } else {
-         * vLink.setContent(""); } vLink.setHref(link.substring(sep + 1)); //
-         * TODO: validate href. dsa.addLink(vLink); }
-         */
-        Link vLink = new Link();
-        vLink.setContent(ulink.getLabel());
-        vLink.setHref(ulink.getUrl_prefix());
+        if (ulink.isValid())
+        {
+          // We only add static links to the document.
+          Link vLink = new Link();
+          vLink.setContent(ulink.getLabel());
+          vLink.setHref(ulink.getTarget());
+          dsa.addLink(vLink);
+        }
       }
     }
     dsa.setGroup(feature.getFeatureGroup());
@@ -275,7 +277,8 @@ public class Sequencefeature extends Rangetype
     {
       Link[] links = dseta.getLink();
       for (int i = 0; i < links.length; i++)
-      {
+      { 
+        // TODO: use URLLink parsing/validation here.
         sf.addLink(links[i].getContent() + "|" + links[i].getHref());
       }
     }
-- 
1.7.10.2