From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 3 Feb 2006 17:39:41 +0000 (+0000)
Subject: Reads annotation files
X-Git-Tag: Root_VamJalview_2_07b+~183
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=8f8dbc28e40a7e23e984882191ef2f9772bb1dbb;p=jalview.git

Reads annotation files
---

diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java
index 331e7f5..a26b9d0 100755
--- a/src/jalview/bin/JalviewLite.java
+++ b/src/jalview/bin/JalviewLite.java
@@ -81,15 +81,6 @@ public class JalviewLite extends Applet
 
         this.setBackground(new Color(r, g, b));
 
-
-        param = getParameter("features");
-        if(param!=null)
-        {
-          if(param.indexOf("://")==-1)
-               param = getCodeBase() + param;
-        }
-        final String featuresFile = param;
-
         file = getParameter("file");
         if(file.indexOf("://")==-1)
                file = getCodeBase() + file;
@@ -101,7 +92,6 @@ public class JalviewLite extends Applet
           embedded = true;
           LoadingThread loader = new LoadingThread(file,
                             "URL",
-                            featuresFile,
                             applet);
           loader.start();
         }
@@ -115,7 +105,6 @@ public class JalviewLite extends Applet
                     {
                         LoadingThread loader = new LoadingThread(file,
                             "URL",
-                            featuresFile,
                             applet);
                         loader.start();
                       }
@@ -243,18 +232,15 @@ public class JalviewLite extends Applet
         String file;
         String protocol;
         String format;
-        String featuresFile;
         JalviewLite applet;
 
         public LoadingThread(String file,
                              String protocol,
-                             String features,
                              JalviewLite applet)
         {
             this.file = file;
             this.protocol = protocol;
             format = jalview.io.IdentifyFile.Identify(file, "URL");
-            featuresFile = features;
             this.applet = applet;
         }
 
@@ -272,12 +258,13 @@ public class JalviewLite extends Applet
 
               currentAlignFrame.statusBar.setText("Successfully loaded file " + file);
 
-              if (featuresFile != null)
-                  currentAlignFrame.parseFeaturesFile(featuresFile);
 
                 String treeFile = applet.getParameter("treeFile");
                 if (treeFile != null)
                 {
+                  if (treeFile.indexOf("://") == -1)
+                  treeFile = getCodeBase() + treeFile;
+
                   try
                   {
                     jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.
@@ -300,6 +287,28 @@ public class JalviewLite extends Applet
                   }
               }
 
+              String param = getParameter("features");
+              if (param != null)
+              {
+                if (param.indexOf("://") == -1)
+                  param = getCodeBase() + param;
+
+                currentAlignFrame.parseFeaturesFile(param);
+              }
+
+             param = getParameter("annotations");
+             if (param != null)
+             {
+               if (param.indexOf("://") == -1)
+                 param = getCodeBase() + param;
+
+               new AnnotationReader().readAnnotationFile(
+                   currentAlignFrame.viewport.getAlignment(),
+                   param);
+
+               currentAlignFrame.alignPanel.fontChanged();
+             }
+
 
                 String pdbfile = applet.getParameter("PDBFILE");
                 if(pdbfile!=null)