\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
fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));\r
fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );\r
\r
+ smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));\r
+\r
gapSymbolCB.addItem("-");\r
gapSymbolCB.addItem(".");\r
\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("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
\r
+ Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));\r
+\r
Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean.toString(startupCheckbox.isSelected()));\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