Correct title for sequence parameter applets

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

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 55d60a2..081efa6 100755 (executable)
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -88,6 +88,20 @@ public class JalviewLite extends Applet
 \r
         file = getParameter("file");\r
 \r
+        if(file==null)\r
+        {\r
+          //Maybe the sequences are added as parameters\r
+          StringBuffer data = new StringBuffer("PASTE");\r
+          int i=1;\r
+          while( (file=getParameter("sequence"+i))!=null)\r
+          {\r
+            data.append(file.toString()+"\n");\r
+            i++;\r
+          }\r
+          if(data.length()>5)\r
+            file = data.toString();\r
+        }\r
+\r
         final JalviewLite applet = this;\r
         if(getParameter("embedded")!=null\r
            && getParameter("embedded").equalsIgnoreCase("true"))\r
@@ -261,7 +275,12 @@ public class JalviewLite extends Applet
                              JalviewLite _applet)\r
         {\r
             file = _file;\r
-            if(inArchive(file))\r
+            if(file.startsWith("PASTE"))\r
+            {\r
+              file = file.substring(5);\r
+              protocol = AppletFormatAdapter.PASTE;\r
+            }\r
+            else if(inArchive(file))\r
               protocol = AppletFormatAdapter.CLASSLOADER;\r
             else\r
             {\r
@@ -289,13 +308,17 @@ public class JalviewLite extends Applet
                                                  file,\r
                                                  embedded);\r
 \r
+              if(protocol==jalview.io.AppletFormatAdapter.PASTE)\r
+                currentAlignFrame.setTitle("Sequences from "+getDocumentBase());\r
 \r
               initialAlignFrame = currentAlignFrame;\r
 \r
               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
@@ -329,12 +352,13 @@ 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.viewport.showSequenceFeatures(true);\r
                 currentAlignFrame.featureSettings_actionPerformed();\r
               }\r
 \r
@@ -344,7 +368,7 @@ 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