2.08, not 2.07

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 2243a3d..9ac8acf 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -76,8 +76,8 @@ public class Preferences extends GPreferences
 \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
@@ -121,6 +121,8 @@ public class Preferences extends GPreferences
         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
@@ -148,6 +150,11 @@ public class Preferences extends GPreferences
         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
@@ -204,6 +211,8 @@ public class Preferences extends GPreferences
       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
@@ -272,8 +281,13 @@ public class Preferences extends GPreferences
         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