import jalview.io.JalviewFileView;
import jalview.jbgui.GPreferences;
import jalview.jbgui.GSequenceLink;
-import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
import jalview.urls.UrlLinkTableModel;
import jalview.urls.api.UrlProviderFactoryI;
import jalview.urls.api.UrlProviderI;
public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+ public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+
private static final int MIN_FONT_SIZE = 1;
private static final int MAX_FONT_SIZE = 30;
openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
showUnconserved
.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+ showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, false));
showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
false));
showGroupConservation.setSelected(Cache.getDefault(
/*
* Set Colours tab defaults
*/
- for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
+ protColour.addItem(ResidueColourScheme.NONE);
+ nucColour.addItem(ResidueColourScheme.NONE);
+ for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
{
- protColour.addItem(ColourSchemeProperty.getColourName(i));
- nucColour.addItem(ColourSchemeProperty.getColourName(i));
+ String name = cs.getSchemeName();
+ protColour.addItem(name);
+ nucColour.addItem(name);
}
- String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
+ String oldProp = Cache.getDefault(DEFAULT_COLOUR,
+ ResidueColourScheme.NONE);
String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
protColour.setSelectedItem(newProp != null ? newProp : oldProp);
newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
Boolean.toString(idItalics.isSelected()));
Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
Boolean.toString(showUnconserved.isSelected()));
+ Cache.applicationProperties.setProperty(SHOW_OCCUPANCY,
+ Boolean.toString(showOccupancy.isSelected()));
Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
Boolean.toString(showGroupConsensus.isSelected()));
Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
conservation.setEnabled(annotations.isSelected());
quality.setEnabled(annotations.isSelected());
identity.setEnabled(annotations.isSelected());
+ showOccupancy.setEnabled(annotations.isSelected());
showGroupConsensus.setEnabled(annotations.isSelected());
showGroupConservation.setEnabled(annotations.isSelected());
showConsensHistogram.setEnabled(annotations.isSelected()