JAL-2018 export graduated feature colours correctly

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

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 2799a7e..24b6e78 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -90,6 +90,7 @@ import jalview.ws.params.ArgumentI;
 import jalview.ws.params.AutoCalcSetting;
 import jalview.ws.params.WsParamSetI;
 
+import java.awt.Color;
 import java.awt.Rectangle;
 import java.io.BufferedReader;
 import java.io.DataInputStream;
@@ -1194,17 +1195,17 @@ public class Jalview2XML
                 .getFeatureRenderer().getRenderOrder()
                 .toArray(new String[0]);
 
-        Vector settingsAdded = new Vector();
+        Vector<String> settingsAdded = new Vector<String>();
         Object gstyle = null;
         GraduatedColor gcol = null;
         if (renderOrder != null)
         {
-          for (int ro = 0; ro < renderOrder.length; ro++)
+          for (String featureType : renderOrder)
           {
             gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                    .getFeatureStyle(renderOrder[ro]);
+                    .getFeatureStyle(featureType);
             Setting setting = new Setting();
-            setting.setType(renderOrder[ro]);
+            setting.setType(featureType);
             if (gstyle instanceof GraduatedColor)
             {
               gcol = (GraduatedColor) gstyle;
@@ -1219,57 +1220,30 @@ public class Jalview2XML
             }
             else
             {
-              setting.setColour(ap.getSeqPanel().seqCanvas
-                      .getFeatureRenderer().getColour(renderOrder[ro])
-                      .getRGB());
+              setting.setColour(((Color) gstyle).getRGB());
             }
 
             setting.setDisplay(av.getFeaturesDisplayed().isVisible(
-                    renderOrder[ro]));
+                    featureType));
             float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                    .getOrder(renderOrder[ro]);
+                    .getOrder(featureType);
             if (rorder > -1)
             {
               setting.setOrder(rorder);
             }
             fs.addSetting(setting);
-            settingsAdded.addElement(renderOrder[ro]);
+            settingsAdded.addElement(featureType);
           }
         }
 
-        // Make sure we save none displayed feature settings
-        Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                .getFeatureColours().keySet().iterator();
-        while (en.hasNext())
-        {
-          String key = en.next().toString();
-          if (settingsAdded.contains(key))
-          {
-            continue;
-          }
-
-          Setting setting = new Setting();
-          setting.setType(key);
-          setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                  .getColour(key).getRGB());
-
-          setting.setDisplay(false);
-          float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
-                  .getOrder(key);
-          if (rorder > -1)
-          {
-            setting.setOrder(rorder);
-          }
-          fs.addSetting(setting);
-          settingsAdded.addElement(key);
-        }
         // is groups actually supposed to be a map here ?
-        en = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+        Iterator<String> en = ap.getSeqPanel().seqCanvas
+                .getFeatureRenderer()
                 .getFeatureGroups().iterator();
-        Vector groupsAdded = new Vector();
+        Vector<String> groupsAdded = new Vector<String>();
         while (en.hasNext())
         {
-          String grp = en.next().toString();
+          String grp = en.next();
           if (groupsAdded.contains(grp))
           {
             continue;