X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=1f2cbb1708024243be75be38434d2a4cf228e8d0;hb=76b6b31c53b099a3034e0622ec78d4c2b455a309;hp=f1f8bb7fd9f5846a3ec5d549e64eed13f4de889f;hpb=73b285377601705bd5f500fee0ae6b5a06b1f2c4;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index f1f8bb7..1f2cbb1 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -623,6 +623,8 @@ public class Jalview2XML
 
           String [] renderOrder =
               af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+
+          Vector settingsAdded = new Vector();
           for(int ro=0; ro<renderOrder.length; ro++)
           {
             Setting setting = new Setting();
@@ -636,8 +638,30 @@ public class Jalview2XML
                 );
 
             fs.addSetting(setting);
+            settingsAdded.addElement(renderOrder[ro]);
+          }
+
+          //Make sure we save none displayed feature settings
+          Enumeration en =
+              af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
+          while(en.hasMoreElements())
+          {
+            String key = en.nextElement().toString();
+            if(settingsAdded.contains(key))
+              continue;
 
+            Setting setting = new Setting();
+            setting.setType(key);
+            setting.setColour(
+                af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
+                );
+
+            setting.setDisplay(false);
+
+            fs.addSetting(setting);
+            settingsAdded.addElement(key);
           }
+
           jms.setFeatureSettings(fs);
 
         }
@@ -796,6 +820,9 @@ public class Jalview2XML
         }
         catch(java.net.UnknownHostException ex)
         {
+          if (Desktop.instance != null)
+            Desktop.instance.stopLoading();
+
           ex.printStackTrace();
           System.err.println("Couldn't locate Jalview XML file : " +
               ex + "\n");
@@ -807,6 +834,9 @@ public class Jalview2XML
         }
         catch (Exception ex)
         {
+          if (Desktop.instance != null)
+            Desktop.instance.stopLoading();
+
           //Is Version 1 Jar file?
           af =  new Jalview2XML_V1().LoadJalviewAlign(file);