X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=9ac8acf3645ce9e8db160af7f574a1992b5f5ba6;hb=52fd681e0f239e20df19fd7560d4b999104ba222;hp=8cbe03fb3c12f170a54310e6af928fd9014b2af0;hpb=92f2bdf5a7a89ceefe2bff76ca75414cf0fb633c;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 8cbe03f..9ac8acf 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -150,7 +150,10 @@ 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
@@ -278,10 +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
         {