JAL-2018 export graduated feature colours correctly

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

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 40635c0..f250583 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -28,7 +28,9 @@ import jalview.gui.Help.HelpId;
 import jalview.io.JalviewFileChooser;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.GraduatedColor;
+import jalview.util.Format;
 import jalview.util.MessageManager;
+import jalview.util.QuickSort;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
 
@@ -830,7 +832,7 @@ public class FeatureSettings extends JPanel implements
   void save()
   {
     JalviewFileChooser chooser = new JalviewFileChooser(
-            jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+            Cache.getProperty("LAST_DIRECTORY"),
             new String[] { "fc" },
             new String[] { "Sequence Feature Colours" },
             "Sequence Feature Colours");
@@ -851,34 +853,35 @@ public class FeatureSettings extends JPanel implements
         PrintWriter out = new PrintWriter(new OutputStreamWriter(
                 new FileOutputStream(choice), "UTF-8"));
 
-        Set fr_colours = fr.getAllFeatureColours();
-        Iterator e = fr_colours.iterator();
+        Set<String> fr_colours = fr.getAllFeatureColours();
+        Iterator<String> e = fr_colours.iterator();
         float[] sortOrder = new float[fr_colours.size()];
         String[] sortTypes = new String[fr_colours.size()];
         int i = 0;
         while (e.hasNext())
         {
-          sortTypes[i] = e.next().toString();
+          sortTypes[i] = e.next();
           sortOrder[i] = fr.getOrder(sortTypes[i]);
           i++;
         }
-        jalview.util.QuickSort.sort(sortOrder, sortTypes);
+        QuickSort.sort(sortOrder, sortTypes);
         sortOrder = null;
         Object fcol;
         GraduatedColor gcol;
-        for (i = 0; i < sortTypes.length; i++)
+        for (String featureType : sortTypes)
         {
           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
-          col.setName(sortTypes[i]);
-          col.setRGB(jalview.util.Format.getHexString(fr.getColour(col
-                  .getName())));
-          fcol = fr.getFeatureStyle(sortTypes[i]);
+          col.setName(featureType);
+          fcol = fr.getFeatureStyle(featureType);
+          Color colour = fcol instanceof Color ? (Color) fcol
+                  : ((GraduatedColor) fcol).getMaxColor();
+          col.setRGB(Format.getHexString(colour));
           if (fcol instanceof GraduatedColor)
           {
             gcol = (GraduatedColor) fcol;
             col.setMin(gcol.getMin());
             col.setMax(gcol.getMax());
-            col.setMinRGB(jalview.util.Format.getHexString(gcol
+            col.setMinRGB(Format.getHexString(gcol
                     .getMinColor()));
             col.setAutoScale(gcol.isAutoScale());
             col.setThreshold(gcol.getThresh());