Remove start end for now??

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

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 199a843..373e916 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -28,7 +28,6 @@ import java.applet.*;
 \r
 import java.awt.*;\r
 import java.awt.event.*;\r
-import jalview.appletgui.TreePanel;\r
 \r
 \r
 /**\r
@@ -290,6 +289,7 @@ public class JalviewLite extends Applet
                                                  file,\r
                                                  embedded);\r
 \r
+\r
               initialAlignFrame = currentAlignFrame;\r
 \r
               currentAlignFrame.statusBar.setText("Successfully loaded file " + file);\r
@@ -329,7 +329,13 @@ 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
@@ -338,11 +344,38 @@ 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
                currentAlignFrame.alignPanel.fontChanged();\r
+               currentAlignFrame.alignPanel.setScrollValues(0,0);\r
+\r
+             }\r
+\r
+             param = getParameter("jnetfile");\r
+             if (param != null)\r
+             {\r
+               try\r
+               {\r
+                 if (inArchive(param))\r
+                   protocol = AppletFormatAdapter.CLASSLOADER;\r
+                 else\r
+                 {\r
+                   protocol = AppletFormatAdapter.URL;\r
+                   param = addProtocol(param);\r
+                 }\r
+\r
+                 jalview.io.JPredFile predictions = new jalview.io.JPredFile(\r
+                     param, protocol);\r
+                 new JnetAnnotationMaker().add_annotation(predictions,\r
+                     currentAlignFrame.viewport.getAlignment(),\r
+                     0,false); // do not add sequence profile from concise output\r
+                 currentAlignFrame.alignPanel.fontChanged();\r
+                 currentAlignFrame.alignPanel.setScrollValues(0, 0);\r
+               } catch (Exception ex) {\r
+                 ex.printStackTrace();\r
+               }\r
              }\r
 \r
 \r