From cb6336f9291738ee189b77beab166486be360c27 Mon Sep 17 00:00:00 2001
From: hansonr <hansonr@stolaf.edu>
Date: Sat, 23 Jun 2018 18:01:20 +0100
Subject: [PATCH] RELATIVE_URL

---
 src/jalview/bin/JalviewJS.java |   11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/src/jalview/bin/JalviewJS.java b/src/jalview/bin/JalviewJS.java
index 3fff67d..84a17a4 100644
--- a/src/jalview/bin/JalviewJS.java
+++ b/src/jalview/bin/JalviewJS.java
@@ -3,7 +3,6 @@ package jalview.bin;
 import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.AlignmentI;
 import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
 import jalview.gui.SplitFrame;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormatException;
@@ -201,7 +200,6 @@ public class JalviewJS
     /*
      * convert to SplitFrame if a valid file2 is supplied
      */
-    int height = AlignFrame.DEFAULT_HEIGHT;
     AlignFrame alignFrame2 = createAlignFrame(PARAM_FILE2);
     if (alignFrame2 != null)
     {
@@ -209,7 +207,6 @@ public class JalviewJS
       if (splitFrame != null)
       {
         internalFrame = splitFrame;
-        height *= 2;
       }
     }
 
@@ -222,10 +219,10 @@ public class JalviewJS
 
     // fudge so that dialogs can be opened with this frame as parent
     // todo JAL-3031 also override Desktop.addInternalFrame etc
-    Desktop.parent = frame.getContentPane();
+    // Desktop.parent = frame.getContentPane();
 
     frame.pack();
-    frame.setSize(AlignFrame.DEFAULT_WIDTH, height);
+    frame.setSize(AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
     frame.setVisible(true);
   }
 
@@ -290,7 +287,7 @@ public class JalviewJS
       // todo extract helper for protocol resolution from JalviewLite
       DataSourceType sourceType = featureFile.startsWith("http")
               ? DataSourceType.URL
-              : DataSourceType.LOCALURL;
+              : DataSourceType.RELATIVE_URL;
       alignFrame.parseFeaturesFile(featureFile, sourceType);
     }
   }
@@ -311,7 +308,7 @@ public class JalviewJS
     if (file != null)
     {
       DataSourceType protocol = file.startsWith("http") ? DataSourceType.URL
-              : DataSourceType.LOCALURL;
+              : DataSourceType.RELATIVE_URL;
       // DataSourceType protocol = AppletFormatAdapter.checkProtocol(file);
       FileFormatI format = new IdentifyFile().identify(file, protocol);
       FileLoader fileLoader = new FileLoader(false);
-- 
1.7.10.2