X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=9ac8acf3645ce9e8db160af7f574a1992b5f5ba6;hb=b437b816507d2acc59e34f70a9cf8c7f81921681;hp=2243a3d10738674be7d8b1c0b1741080cba3d6f2;hpb=9c5d69ef1e102b1eac18ec13c362522f40c9000d;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 2243a3d..9ac8acf 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -76,8 +76,8 @@ public class Preferences extends GPreferences
 
         frame = new JInternalFrame();
         frame.setContentPane(this);
-        Desktop.addInternalFrame(frame, "Preferences", 480, 390);
-        frame.setMinimumSize(new Dimension(480,390));
+        Desktop.addInternalFrame(frame, "Preferences", 480, 395);
+        frame.setMinimumSize(new Dimension(480,395));
 
         seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));
         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));
@@ -121,6 +121,8 @@ public class Preferences extends GPreferences
         fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
         fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );
 
+        smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+
         gapSymbolCB.addItem("-");
         gapSymbolCB.addItem(".");
 
@@ -148,6 +150,11 @@ 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
    */
@@ -204,6 +211,8 @@ public class Preferences extends GPreferences
       Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());
       Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());
 
+      Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));
+
       Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());
       Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));
 
@@ -272,8 +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
         {