X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=9ac8acf3645ce9e8db160af7f574a1992b5f5ba6;hb=52fd681e0f239e20df19fd7560d4b999104ba222;hp=f322daa78a49e2a44204ce9d06f3db4814fec2c7;hpb=dc1d2d1779b2ccd4d67b2afa094f269db77732e2;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index f322daa..9ac8acf 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -150,6 +150,11 @@ public class Preferences extends GPreferences
         pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );
         pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
 
+        modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));
+
+        autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+        padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));
+
   /****************************************************
    * Set up Connections
    */
@@ -276,8 +281,13 @@ public class Preferences extends GPreferences
         Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );
         Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );
         Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );
+        jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 
-
+        Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+                                                Boolean.toString(autoCalculateConsCheck.isSelected()));
+        Cache.applicationProperties.setProperty("PAD_GAPS",
+                                                Boolean.toString(padGaps.isSelected()));
         Cache.saveProperties();
         try
         {