X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;fp=src%2Fjalview%2Fgui%2FJalview2XML.java;h=08b39038dbc17c19a78bb2d2d81de6573ce29b67;hb=58f946af1280918a6f2893534e66104bc20a52c7;hp=bbe338944252658a2e31bf40f855c07f6eaa8d52;hpb=a358ceab461b61acbfd9f38dc595bea2e24e398f;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index bbe3389..08b3903 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -452,8 +452,33 @@ public class Jalview2XML
         view.setShowText(av.getShowText());
         view.setWrapAlignment(av.getWrapAlignment());
 
+        if(af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)
+        {
+          jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
+
+          Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
+          while (e.hasMoreElements())
+          {
+            String type = e.nextElement().toString();
+            Setting setting = new Setting();
+            setting.setType(type);
+            setting.setColour(
+                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB()
+                );
+            setting.setDisplay(
+                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.contains(type)
+                );
+
+            fs.addSetting(setting);
+
+          }
+          jms.setFeatureSettings(fs);
+
+        }
+
         jms.addViewport(view);
 
+
         object.setJalviewModelSequence(jms);
         object.getVamsasModel().addSequenceSet(vamsasSet);
 
@@ -711,6 +736,7 @@ public class Jalview2XML
 
         AlignFrame af = new AlignFrame(al);
 
+
         //  af.changeColour() );
         /////////////////////////
         //LOAD GROUPS
@@ -850,6 +876,22 @@ public class Jalview2XML
            af.sequenceFeatures.setSelected(true);
         }
 
+        if(jms.getFeatureSettings()!=null)
+        {
+          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed = new Vector();
+         // af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)
+         // jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
+         for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
+         {
+           Setting setting = jms.getFeatureSettings().getSetting(fs);
+
+           af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
+               new java.awt.Color(setting.getColour()));
+           if(setting.getDisplay())
+             af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.addElement(setting.getType());
+         }
+        }
+
         Desktop.addInternalFrame(af, view.getTitle(),
              view.getWidth(), view.getHeight());