load and save graduated feature colours in XML

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index d8a674f..7bf291d 100755 (executable)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -33,6 +33,7 @@ import javax.swing.event.*;
 import javax.swing.table.*;
 
 import jalview.analysis.AlignmentSorter;
+import jalview.bin.Cache;
 import jalview.commands.OrderCommand;
 import jalview.datamodel.*;
 import jalview.io.*;
@@ -606,15 +607,62 @@ public class FeatureSettings extends JPanel
         InputStreamReader in = new InputStreamReader(new FileInputStream(
                 file), "UTF-8");
 
-        jalview.binding.JalviewUserColours jucs = new jalview.binding.JalviewUserColours();
-        jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);
-
+        jalview.schemabinding.version2.JalviewUserColours jucs = new jalview.schemabinding.version2.JalviewUserColours();
+        jucs = (jalview.schemabinding.version2.JalviewUserColours) jucs.unmarshal(in);
+        
         for (int i = jucs.getColourCount() - 1; i >= 0; i--)
         {
           String name;
-          // TODO: update Colour XML
-          fr.setColour(name = jucs.getColour(i).getName(), new Color(
+          jalview.schemabinding.version2.Colour newcol = jucs.getColour(i);
+          if (newcol.hasMax())
+          {
+            Color mincol=null,maxcol=null;
+            float thrsh=Float.NaN;
+            try {
+              mincol = new Color(
+                      Integer.parseInt(newcol.getMinRGB(), 16));
+              maxcol = new Color(
+                      Integer.parseInt(newcol.getRGB(), 16));
+              
+            } catch (Exception e)
+            {
+              Cache.log.warn("Couldn't parse out graduated feature color.",e);
+            }
+            GraduatedColor gcol = 
+              new GraduatedColor(mincol,maxcol, 
+                  newcol.getMin(),newcol.getMax());
+            if (newcol.hasAutoScale())
+            {
+              gcol.setAutoScaled(newcol.getAutoScale());
+            }
+            if (newcol.hasColourByLabel())
+            {
+              gcol.setColourByLabel(newcol.getColourByLabel());
+            }
+            if (newcol.hasThreshold())
+            {
+              gcol.setThresh(newcol.getThreshold());
+              gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD); // default
+            }
+            if (newcol.getThreshType().length()>0)
+            {
+              String ttyp = newcol.getThreshType();
+              if (ttyp.equalsIgnoreCase("NONE")) {
+                gcol.setThreshType(AnnotationColourGradient.NO_THRESHOLD);
+              }
+              if (ttyp.equalsIgnoreCase("ABOVE"))
+              {
+                gcol.setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+              }
+              if (ttyp.equalsIgnoreCase("BELOW")){
+                gcol.setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+              } 
+            }
+            fr.setColour(name = newcol.getName(), gcol);
+          } else {
+            fr.setColour(name = jucs.getColour(i).getName(), new Color(
                   Integer.parseInt(jucs.getColour(i).getRGB(), 16)));
+          }
           fr.setOrder(name, (i == 0) ? 0 : i / jucs.getColourCount());
         }
         if (table != null)
@@ -648,7 +696,7 @@ public class FeatureSettings extends JPanel
     if (value == JalviewFileChooser.APPROVE_OPTION)
     {
       String choice = chooser.getSelectedFile().getPath();
-      jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();
+      jalview.schemabinding.version2.JalviewUserColours ucs = new jalview.schemabinding.version2.JalviewUserColours();
       ucs.setSchemeName("Sequence Features");
       try
       {
@@ -667,12 +715,38 @@ public class FeatureSettings extends JPanel
         }
         jalview.util.QuickSort.sort(sortOrder, sortTypes);
         sortOrder = null;
+        Object fcol;
+        GraduatedColor gcol;
         for (i = 0; i < sortTypes.length; i++)
         {
-          jalview.binding.Colour col = new jalview.binding.Colour();
+          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]);
+          if (fcol instanceof GraduatedColor)
+          {
+            gcol = (GraduatedColor) fcol;
+            col.setMin(gcol.getMin());
+            col.setMax(gcol.getMax());
+            col.setMinRGB(jalview.util.Format.getHexString(gcol
+                    .getMinColor()));
+            col.setAutoScale(gcol.isAutoScale());
+            col.setThreshold(gcol.getThresh());
+            col.setColourByLabel(gcol.isColourByLabel());
+            switch (gcol.getThreshType())
+            {
+            case AnnotationColourGradient.NO_THRESHOLD:
+              col.setThreshType("NONE");
+              break;
+            case AnnotationColourGradient.ABOVE_THRESHOLD:
+              col.setThreshType("ABOVE");
+              break;
+            case AnnotationColourGradient.BELOW_THRESHOLD:
+              col.setThreshType("BELOW");
+              break;
+            }
+          }
           ucs.addColour(col);
         }
         ucs.marshal(out);