pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
\r
+ modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));\r
+\r
+ autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
+ padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));\r
+\r
/****************************************************\r
* Set up Connections\r
*/\r
Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );\r
+ jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
\r
-\r
+ Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
+ Boolean.toString(autoCalculateConsCheck.isSelected()));\r
+ Cache.applicationProperties.setProperty("PAD_GAPS",\r
+ Boolean.toString(padGaps.isSelected()));\r
Cache.saveProperties();\r
try\r
{\r