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 be1455b..9ac8acf 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -18,8 +18,6 @@
  */\r
 package jalview.gui;\r
 \r
-import jalview.bin.*;\r
-\r
 import jalview.io.*;\r
 \r
 import jalview.jbgui.*;\r
@@ -78,14 +76,14 @@ 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
-        fullID.setSelected(      Cache.getDefault("SHOW_FULL_ID", true));\r
+        seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));\r
         fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));\r
-        annotations.setSelected( Cache.getDefault("SHOW_FULL_ID", true));\r
-        conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
+        annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 \r
+        conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
         quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
         identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
 \r
@@ -123,6 +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
@@ -132,6 +132,29 @@ public class Preferences extends GPreferences
         startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
          "http://www.jalview.org/examples/exampleFile.jar"));\r
 \r
+        sortby.addItem("No sort");\r
+        sortby.addItem("Id");\r
+        sortby.addItem("Pairwise Identity");\r
+        sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
+\r
+        epsRendering.addItem("Prompt each time");\r
+        epsRendering.addItem("Lineart");\r
+        epsRendering.addItem("Text");\r
+        epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
+\r
+        blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );\r
+        clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );\r
+        fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );\r
+        msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );\r
+        pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );\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
@@ -173,7 +196,7 @@ public class Preferences extends GPreferences
     public void ok_actionPerformed(ActionEvent e)\r
     {\r
 \r
-      Cache.applicationProperties.setProperty("SHOW_FULL_ID", Boolean.toString(fullID.isSelected()));\r
+      Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
       Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
 \r
       Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
@@ -188,9 +211,18 @@ 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
+      Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
+\r
+      if(epsRendering.getSelectedItem().equals("Prompt each time"))\r
+        Cache.applicationProperties.remove("EPS_RENDERING");\r
+      else\r
+        Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());\r
+\r
       if(defaultBrowser.getText().trim().length()<1)\r
         Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
       else\r
@@ -242,7 +274,20 @@ public class Preferences extends GPreferences
         }\r
 \r
 \r
-\r
+        Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
+        Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
+        Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
+        Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\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
+        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