Merge branch 'develop' into features/JAL-1956_featureStyles

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 24b6e78..3a16bb8 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -20,6 +20,7 @@
  */
 package jalview.gui;
 
+import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
@@ -71,7 +72,7 @@ import jalview.schemabinding.version2.Viewport;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.GraduatedColor;
+import jalview.schemes.FeatureColour;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
@@ -1196,31 +1197,31 @@ public class Jalview2XML
                 .toArray(new String[0]);
 
         Vector<String> settingsAdded = new Vector<String>();
-        Object gstyle = null;
-        GraduatedColor gcol = null;
         if (renderOrder != null)
         {
           for (String featureType : renderOrder)
           {
-            gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+            FeatureColourI fcol = ap.getSeqPanel().seqCanvas
+                    .getFeatureRenderer()
                     .getFeatureStyle(featureType);
             Setting setting = new Setting();
             setting.setType(featureType);
-            if (gstyle instanceof GraduatedColor)
+            if (!fcol.isSimpleColour())
             {
-              gcol = (GraduatedColor) gstyle;
-              setting.setColour(gcol.getMaxColor().getRGB());
-              setting.setMincolour(gcol.getMinColor().getRGB());
-              setting.setMin(gcol.getMin());
-              setting.setMax(gcol.getMax());
-              setting.setColourByLabel(gcol.isColourByLabel());
-              setting.setAutoScale(gcol.isAutoScale());
-              setting.setThreshold(gcol.getThresh());
-              setting.setThreshstate(gcol.getThreshType());
+              setting.setColour(fcol.getMaxColour().getRGB());
+              setting.setMincolour(fcol.getMinColour().getRGB());
+              setting.setMin(fcol.getMin());
+              setting.setMax(fcol.getMax());
+              setting.setColourByLabel(fcol.isColourByLabel());
+              setting.setAutoScale(fcol.isAutoScaled());
+              setting.setThreshold(fcol.getThreshold());
+              // -1 = No threshold, 0 = Below, 1 = Above
+              setting.setThreshstate(fcol.isAboveThreshold() ? 1
+                      : (fcol.isBelowThreshold() ? 0 : -1));
             }
             else
             {
-              setting.setColour(((Color) gstyle).getRGB());
+              setting.setColour(fcol.getColour().getRGB());
             }
 
             setting.setDisplay(av.getFeaturesDisplayed().isVisible(
@@ -1257,7 +1258,6 @@ public class Jalview2XML
           groupsAdded.addElement(grp);
         }
         jms.setFeatureSettings(fs);
-
       }
 
       if (av.hasHiddenColumns())
@@ -4328,25 +4328,33 @@ public class Jalview2XML
       af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
       String[] renderOrder = new String[jms.getFeatureSettings()
               .getSettingCount()];
-      Hashtable featureGroups = new Hashtable();
-      Hashtable featureColours = new Hashtable();
-      Hashtable featureOrder = new Hashtable();
+      Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
+      Map<String, Float> featureOrder = new Hashtable<String, Float>();
 
       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
       {
         Setting setting = jms.getFeatureSettings().getSetting(fs);
         if (setting.hasMincolour())
         {
-          GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
-                  new java.awt.Color(setting.getMincolour()),
-                  new java.awt.Color(setting.getColour()),
-                  setting.getMin(), setting.getMax()) : new GraduatedColor(
-                  new java.awt.Color(setting.getMincolour()),
-                  new java.awt.Color(setting.getColour()), 0, 1);
+          FeatureColourI gc = setting.hasMin() ? new FeatureColour(
+                  new Color(setting.getMincolour()), new Color(
+                          setting.getColour()), setting.getMin(),
+                  setting.getMax()) : new FeatureColour(new Color(
+                  setting.getMincolour()), new Color(setting.getColour()),
+                  0, 1);
           if (setting.hasThreshold())
           {
-            gc.setThresh(setting.getThreshold());
-            gc.setThreshType(setting.getThreshstate());
+            gc.setThreshold(setting.getThreshold());
+            int threshstate = setting.getThreshstate();
+            // -1 = None, 0 = Below, 1 = Above threshold
+            if (threshstate == 0)
+            {
+              gc.setBelowThreshold(true);
+            }
+            else if (threshstate == 1)
+            {
+              gc.setAboveThreshold(true);
+            }
           }
           gc.setAutoScaled(true); // default
           if (setting.hasAutoScale())
@@ -4362,8 +4370,8 @@ public class Jalview2XML
         }
         else
         {
-          featureColours.put(setting.getType(),
-                  new java.awt.Color(setting.getColour()));
+          featureColours.put(setting.getType(), new FeatureColour(
+                  new Color(setting.getColour())));
         }
         renderOrder[fs] = setting.getType();
         if (setting.hasOrder())
@@ -4380,7 +4388,7 @@ public class Jalview2XML
           fdi.setVisible(setting.getType());
         }
       }
-      Hashtable fgtable = new Hashtable();
+      Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
       for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
       {
         Group grp = jms.getFeatureSettings().getGroup(gs);