From ee8afbd0f2831e8480a69f19757cad43e14493c6 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Sun, 14 Nov 2010 14:58:59 +0000
Subject: [PATCH] refactored protocol check to jalview.io.FileParse

---
 src/jalview/bin/Jalview.java |   22 ++++++----------------
 1 file changed, 6 insertions(+), 16 deletions(-)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 39daac6..57fb00a 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -36,6 +36,7 @@ import java.util.*;
 import javax.swing.*;
 
 import jalview.gui.*;
+import jalview.io.FileParse;
 import jalview.util.Platform;
 
 /**
@@ -248,7 +249,7 @@ public class Jalview
       {
         try
         {
-          String viprotocol = Jalview.checkProtocol(vamsasImport);
+          String viprotocol = FileParse.checkProtocol(vamsasImport);
           if (viprotocol == jalview.io.FormatAdapter.FILE)
           {
             inSession = desktop.vamsasImport(new File(vamsasImport));
@@ -333,7 +334,7 @@ public class Jalview
         }
       }
 
-      protocol = checkProtocol(file);
+      protocol = FileParse.checkProtocol(file);
 
       format = new jalview.io.IdentifyFile().Identify(file, protocol);
 
@@ -369,13 +370,13 @@ public class Jalview
       data = aparser.getValue("groups", true);
       if (data != null)
       {
-        af.parseFeaturesFile(data, checkProtocol(data));
+        af.parseFeaturesFile(data, FileParse.checkProtocol(data));
         System.out.println("Added " + data);
       }
       data = aparser.getValue("features", true);
       if (data != null)
       {
-        af.parseFeaturesFile(data, checkProtocol(data));
+        af.parseFeaturesFile(data, FileParse.checkProtocol(data));
         System.out.println("Added " + data);
       }
 
@@ -400,7 +401,7 @@ public class Jalview
         jalview.io.NewickFile fin = null;
         try
         {
-          fin = new jalview.io.NewickFile(data, checkProtocol(data));
+          fin = new jalview.io.NewickFile(data, FileParse.checkProtocol(data));
           if (fin != null)
           {
             af.getViewport().setCurrentTree(
@@ -791,17 +792,6 @@ public class Jalview
     }
     return ff;
   }
-
-  private static String checkProtocol(String file)
-  {
-    String protocol = jalview.io.FormatAdapter.FILE;
-
-    if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
-    {
-      protocol = jalview.io.FormatAdapter.URL;
-    }
-    return protocol;
-  }
 }
 
 /**
-- 
1.7.10.2