Merge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL...

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 00b2a38..cccdd2e 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -29,7 +29,9 @@ import jalview.io.JalviewFileChooser;
 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;
@@ -105,6 +107,8 @@ public class Preferences extends GPreferences
 
   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;
@@ -208,6 +212,7 @@ public class Preferences extends GPreferences
     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(
@@ -284,12 +289,16 @@ public class Preferences extends GPreferences
     /*
      * 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);
@@ -346,7 +355,7 @@ public class Preferences extends GPreferences
     List<RowSorter.SortKey> sortKeys = new ArrayList<>();
 
     UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
-    sortKeys.add(new RowSorter.SortKey(m.getDefaultColumn(),
+    sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
             SortOrder.DESCENDING));
     sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
             SortOrder.DESCENDING));
@@ -429,7 +438,7 @@ public class Preferences extends GPreferences
 
     // set up radio buttons
     int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
-            .getDefaultColumn();
+            .getPrimaryColumn();
     String onClickName = linkUrlTable.getColumnName(onClickCol);
     linkUrlTable.getColumn(onClickName).setCellRenderer(
                new RadioButtonRenderer());
@@ -459,8 +468,6 @@ public class Preferences extends GPreferences
 
     useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
     useProxy_actionPerformed(); // make sure useProxy is correctly initialised
-    proxyServerTB.setEnabled(useProxy.isSelected());
-    proxyPortTB.setEnabled(useProxy.isSelected());
     proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
     proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
 
@@ -568,6 +575,8 @@ public class Preferences extends GPreferences
             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",
@@ -676,7 +685,7 @@ public class Preferences extends GPreferences
     }
 
     Cache.applicationProperties.setProperty("DEFAULT_URL",
-            sequenceUrlLinks.getDefaultUrlId());
+            sequenceUrlLinks.getPrimaryUrlId());
 
     Cache.applicationProperties.setProperty("USE_PROXY",
             Boolean.toString(useProxy.isSelected()));
@@ -809,7 +818,7 @@ public class Preferences extends GPreferences
       if (format != null)
       {
         Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
-                format.toString());
+                format.getName());
       }
       startupFileTextfield.setText(chooser.getSelectedFile()
               .getAbsolutePath());
@@ -847,6 +856,7 @@ public class Preferences extends GPreferences
     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()
@@ -902,8 +912,13 @@ public class Preferences extends GPreferences
       return;
     }
 
-    link.setName(linkUrlTable.getValueAt(index, 0).toString());
-    link.setURL(linkUrlTable.getValueAt(index, 1).toString());
+    int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+            .getNameColumn();
+    int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+            .getUrlColumn();
+    String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
+    link.setName(oldName);
+    link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
 
     boolean valid = false;
     while (!valid)
@@ -914,11 +929,12 @@ public class Preferences extends GPreferences
       {
         if (link.checkValid())
         {
-          if (((UrlLinkTableModel) linkUrlTable.getModel())
-                  .isUniqueName(link.getName()))
+          if ((oldName.equals(link.getName()))
+                  || (((UrlLinkTableModel) linkUrlTable.getModel())
+                          .isUniqueName(link.getName())))
           {
-            linkUrlTable.setValueAt(link.getName(), index, 0);
-            linkUrlTable.setValueAt(link.getURL(), index, 1);
+            linkUrlTable.setValueAt(link.getName(), index, nameCol);
+            linkUrlTable.setValueAt(link.getURL(), index, urlCol);
             valid = true;
           }
           else