\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
- Desktop.addInternalFrame(frame, "Preferences", 480, 390);\r
- frame.setMinimumSize(new Dimension(480,390));\r
+ Desktop.addInternalFrame(frame, "Preferences", 480, 395);\r
+ frame.setMinimumSize(new Dimension(480,395));\r
\r
seqLimit.setSelected( Cache.getDefault("SHOW_JVSUFFIX", true));\r
fullScreen.setSelected( Cache.getDefault("SHOW_FULLSCREEN", false));\r
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