clean up

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index ef7ca27..1b274a8 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -61,6 +61,15 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  */
 public class Preferences extends GPreferences
 {
+  public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
+
+  public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+
+  public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
+
+  public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
+
+  public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
 
   public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
 
@@ -165,11 +174,11 @@ public class Preferences extends GPreferences
     dasTab.add(dasSource, BorderLayout.CENTER);
     wsPrefs = new WsPreferences();
     wsTab.add(wsPrefs, BorderLayout.CENTER);
-    int width = 500, height = 420;
+    int width = 500, height = 450;
     if (new jalview.util.Platform().isAMac())
     {
       width = 570;
-      height = 460;
+      height = 480;
     }
 
     Desktop.addInternalFrame(frame,
@@ -225,6 +234,8 @@ public class Preferences extends GPreferences
             + ""));
 
     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+    scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
+            false));
 
     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 
@@ -267,10 +278,14 @@ public class Preferences extends GPreferences
      */
     for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
     {
-      colour.addItem(ColourSchemeProperty.getColourName(i));
+      protColour.addItem(ColourSchemeProperty.getColourName(i));
+      nucColour.addItem(ColourSchemeProperty.getColourName(i));
     }
-    String string = Cache.getDefault("DEFAULT_COLOUR", "None");
-    colour.setSelectedItem(string);
+    String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
+    String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
+    protColour.setSelectedItem(newProp != null ? newProp : oldProp);
+    newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
+    nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
             Color.orange));
     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
@@ -350,6 +365,8 @@ 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));
+    embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
+            true));
 
     /*
      * Set Editing tab defaults
@@ -420,6 +437,8 @@ public class Preferences extends GPreferences
             Boolean.toString(showConsensLogo.isSelected()));
     Cache.applicationProperties.setProperty("ANTI_ALIAS",
             Boolean.toString(smoothFont.isSelected()));
+    Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
+            Boolean.toString(scaleProteinToCdna.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
             Boolean.toString(showNpTooltip.isSelected()));
     Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
@@ -452,7 +471,9 @@ public class Preferences extends GPreferences
     /*
      * Save Colours settings
      */
-    Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
+    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
+            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
             .getSelectedItem().toString());
     Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
             minColour.getBackground());
@@ -570,6 +591,8 @@ public class Preferences extends GPreferences
             Boolean.toString(pirjv.isSelected()));
     Cache.applicationProperties.setProperty("PIR_MODELLER",
             Boolean.toString(modellerOutput.isSelected()));
+    Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
+            Boolean.toString(embbedBioJSON.isSelected()));
     jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
 
     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",