Correct title for sequence parameter applets

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

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