Replaced image

[jalview.git] / src / jalview / bin / JalviewLite.java

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index cd0b835..53d55f3 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -295,7 +295,9 @@ public class JalviewLite extends Applet
               currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
 \r
 \r
-                String treeFile = applet.getParameter("treeFile");\r
+                String treeFile = applet.getParameter("tree");\r
+                if(treeFile==null)\r
+                  applet.getParameter("treeFile");\r
                 if (treeFile != null)\r
                 {\r
                   try\r
@@ -329,7 +331,13 @@ public class JalviewLite extends Applet
                 if( !inArchive(param) )\r
                   param = addProtocol( param );\r
 \r
-                currentAlignFrame.parseFeaturesFile(param);\r
+                currentAlignFrame.parseFeaturesFile(param, protocol);\r
+              }\r
+\r
+              param = getParameter("showFeatureSettings");\r
+              if(param !=null && param.equalsIgnoreCase("true"))\r
+              {\r
+                currentAlignFrame.featureSettings_actionPerformed();\r
               }\r
 \r
              param = getParameter("annotations");\r
@@ -338,7 +346,7 @@ public class JalviewLite extends Applet
                if( !inArchive(param) )\r
                   param = addProtocol( param );\r
 \r
-               new AnnotationReader().readAnnotationFile(\r
+               new AnnotationFile().readAnnotationFile(\r
                    currentAlignFrame.viewport.getAlignment(),\r
                    param);\r
 \r