From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 25 Nov 2015 14:24:04 +0000 (+0000)
Subject: JAL-1479 bugfix after decoupling SIFTS preference settings
X-Git-Tag: Release_2_10_0~335
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=239d28bd8c08790bbc513a09b2b869fff862f63f

JAL-1479 bugfix after decoupling SIFTS preference settings
---

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 4ea90e8..67d359a 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -22,6 +22,7 @@ package jalview.bin;
 
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+import jalview.ws.sifts.SiftsSettings;
 
 import java.awt.Color;
 import java.io.BufferedReader;
@@ -394,6 +395,10 @@ public class Cache
       codeInstallation = " (" + codeInstallation + ")";
     }
     new BuildDetails(codeVersion, null, codeInstallation);
+
+    SiftsSettings
+            .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+
     System.out
             .println("Jalview Version: " + codeVersion + codeInstallation);
 
@@ -407,6 +412,7 @@ public class Cache
 
       class VersionChecker extends Thread
       {
+        @Override
         public void run()
         {
           String orgtimeout = System
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 33068a8..c7e1332 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -317,14 +317,15 @@ public class Preferences extends GPreferences
     if (Cache.getDefault("MAP_WITH_SIFTS", false))
     {
       siftsMapping.setSelected(true);
-      SiftsSettings.setMapWithSifts(true);
     }
     else
     {
       nwMapping.setSelected(true);
-      SiftsSettings.setMapWithSifts(false);
     }
 
+    SiftsSettings
+            .setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+
     /*
      * Set Connections tab defaults
      */
diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java
index c205e9e..4951d2f 100644
--- a/src/jalview/ws/sifts/SiftsClient.java
+++ b/src/jalview/ws/sifts/SiftsClient.java
@@ -324,10 +324,10 @@ public class SiftsClient implements SiftsClientI
       DBRefEntry[] dbRefs = seq.getDBRefs();
       if (dbRefs == null || dbRefs.length < 1)
       {
-        // final SequenceI[] seqs = new SequenceI[] { seq };
-        // new jalview.ws.DBRefFetcher(seqs, null, null, null, false)
-        // .fetchDBRefs(true);
-        // dbRefs = seq.getDBRefs();
+        final SequenceI[] seqs = new SequenceI[] { seq };
+        new jalview.ws.DBRefFetcher(seqs, null, null, null, false)
+                .fetchDBRefs(true);
+        dbRefs = seq.getDBRefs();
       }
 
       if (dbRefs == null || dbRefs.length < 1)