refactored to decouple dependencies due to FileParse's derived classes

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 57fb00a..0316655 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -36,7 +36,6 @@ import java.util.*;
 import javax.swing.*;
 
 import jalview.gui.*;
-import jalview.io.FileParse;
 import jalview.util.Platform;
 
 /**
@@ -249,7 +248,7 @@ public class Jalview
       {
         try
         {
-          String viprotocol = FileParse.checkProtocol(vamsasImport);
+          String viprotocol = jalview.io.AppletFormatAdapter.checkProtocol(vamsasImport);
           if (viprotocol == jalview.io.FormatAdapter.FILE)
           {
             inSession = desktop.vamsasImport(new File(vamsasImport));
@@ -334,7 +333,7 @@ public class Jalview
         }
       }
 
-      protocol = FileParse.checkProtocol(file);
+      protocol = jalview.io.AppletFormatAdapter.checkProtocol(file);
 
       format = new jalview.io.IdentifyFile().Identify(file, protocol);
 
@@ -370,13 +369,13 @@ public class Jalview
       data = aparser.getValue("groups", true);
       if (data != null)
       {
-        af.parseFeaturesFile(data, FileParse.checkProtocol(data));
+        af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
         System.out.println("Added " + data);
       }
       data = aparser.getValue("features", true);
       if (data != null)
       {
-        af.parseFeaturesFile(data, FileParse.checkProtocol(data));
+        af.parseFeaturesFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
         System.out.println("Added " + data);
       }
 
@@ -401,7 +400,7 @@ public class Jalview
         jalview.io.NewickFile fin = null;
         try
         {
-          fin = new jalview.io.NewickFile(data, FileParse.checkProtocol(data));
+          fin = new jalview.io.NewickFile(data, jalview.io.AppletFormatAdapter.checkProtocol(data));
           if (fin != null)
           {
             af.getViewport().setCurrentTree(

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index b1952a9..5eb4d2b 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -463,6 +463,17 @@ public class AppletFormatAdapter
     return null;
   }
 
+  public static String checkProtocol(String file)
+  {
+    String protocol = FILE;
+  
+    if (file.indexOf("http:") > -1 || file.indexOf("file:") > -1)
+    {
+      protocol = URL;
+    }
+    return protocol;
+  }
+
   public static void main(String[] args)
   {
     int i = 0;

diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index e972679..9f87c3a 100755 (executable)
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -391,15 +391,4 @@ public class FileParse
     }
     return null;
   }
-
-  public 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;
-  }
 }