X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=38594dfbf1fa9fc0948c7ca612afc3c269da783c;hb=6babd7c2387996384a49042ed4290095c13d5ed9;hp=f244d14a12500d827f88fe1dc11aefdf5c25382c;hpb=59d9dfb7b746fcc396af9b572b40636028df9fed;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index f244d14..38594df 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -39,6 +39,7 @@ import jalview.project.Jalview2XML;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.ws.utils.UrlDownloadClient;
 
 import java.io.BufferedReader;
@@ -47,7 +48,6 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
-import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.util.StringTokenizer;
 import java.util.Vector;
@@ -278,9 +278,9 @@ public class FileLoader implements Runnable
     Runtime rt = Runtime.getRuntime();
     try
     {
-      if (Desktop.instance != null)
+      if (Desktop.getInstance() != null)
       {
-        Desktop.instance.startLoading(file);
+        Desktop.getInstance().startLoading(file);
       }
       if (format == null)
       {
@@ -302,12 +302,12 @@ public class FileLoader implements Runnable
 
       if (format == null)
       {
-        Desktop.instance.stopLoading();
+        Desktop.getInstance().stopLoading();
         System.err.println("The input file \"" + file
                 + "\" has null or unidentifiable data content!");
         if (!Jalview.isHeadlessMode())
         {
-          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+          JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                   MessageManager.getString("label.couldnt_read_data")
                           + " in " + file + "\n"
                           + AppletFormatAdapter.getSupportedFormats(),
@@ -318,7 +318,7 @@ public class FileLoader implements Runnable
       }
       // TODO: cache any stream datasources as a temporary file (eg. PDBs
       // retrieved via URL)
-      if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+      if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
       {
         System.gc();
         memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
@@ -361,9 +361,9 @@ public class FileLoader implements Runnable
             if (downloadStructureFile)
             {
               String structExt = format.getExtensions().split(",")[0];
-              String urlLeafName = file.substring(
-                      file.lastIndexOf(
-                              System.getProperty("file.separator")),
+              int pt = file.lastIndexOf(file.indexOf('/') >= 0 ? "/"
+                      : System.getProperty("file.separator"));
+              String urlLeafName = file.substring(pt,
                       file.lastIndexOf("."));
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);
@@ -411,7 +411,7 @@ public class FileLoader implements Runnable
                 // register PDB entries with desktop's structure selection
                 // manager
                 StructureSelectionManager
-                        .getStructureSelectionManager(Desktop.instance)
+                        .getStructureSelectionManager(Desktop.getInstance())
                         .registerPDBEntry(pdbe);
               }
             }
@@ -500,23 +500,23 @@ public class FileLoader implements Runnable
         }
         else
         {
-          if (Desktop.instance != null)
+          if (Desktop.getInstance() != null)
           {
-            Desktop.instance.stopLoading();
+            Desktop.getInstance().stopLoading();
           }
 
           final String errorMessage = MessageManager.getString(
                   "label.couldnt_load_file") + " " + title + "\n" + error;
           // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
           // bits ?
-          if (raiseGUI && Desktop.desktop != null)
+          if (raiseGUI && Desktop.getDesktopPane() != null)
           {
             javax.swing.SwingUtilities.invokeLater(new Runnable()
             {
               @Override
               public void run()
               {
-                JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                         errorMessage,
                         MessageManager
                                 .getString("label.error_loading_file"),
@@ -544,7 +544,7 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                     MessageManager.formatMessage(
                             "label.problems_opening_file", new String[]
                             { file }),
@@ -566,7 +566,7 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                     MessageManager.formatMessage(
                             "warn.out_of_memory_loading_file", new String[]
                             { file }),
@@ -588,7 +588,7 @@ public class FileLoader implements Runnable
     // memory
     // after
     // load
-    if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+    if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
     {
       if (alignFrame != null)
       {
@@ -610,9 +610,9 @@ public class FileLoader implements Runnable
       }
     }
     // remove the visual delay indicator
-    if (Desktop.instance != null)
+    if (Desktop.getInstance() != null)
     {
-      Desktop.instance.stopLoading();
+      Desktop.getInstance().stopLoading();
     }
 
   }
@@ -646,14 +646,16 @@ public class FileLoader implements Runnable
    * @return
    * @throws FileNotFoundException 
    */
-  @SuppressWarnings("unused")
-  public static BufferedReader getBuffereReader(Object file) throws FileNotFoundException {
+  public static BufferedReader getBufferedReader(Object file) throws FileNotFoundException {
     if (file instanceof String)
+    {
       return new BufferedReader(new FileReader((String) file));
-    
-    byte[] bytes = /** @j2sNative file._bytes || */ null;
+    }
+    byte[] bytes = Platform.getFileBytes((File) file);
     if (bytes != null)
+    {
       return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes)));
+    }
     return  new BufferedReader(new FileReader((File) file));
   }