\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
);\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
}\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
}\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