JAL-3446 no need for SHIFT_DOWN or ALT_DOWN masks

[jalview.git] / src / jalview / io / FileLoader.java

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 95f85e6..7eda110 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -20,6 +20,14 @@
  */
 package jalview.io;
 
+import java.awt.Dimension;
+import java.io.File;
+import java.io.IOException;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.SwingUtilities;
+
 import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
@@ -42,18 +50,6 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.utils.UrlDownloadClient;
 
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.SwingUtilities;
-
 public class FileLoader implements Runnable
 {
   String file;
@@ -214,6 +210,7 @@ public class FileLoader implements Runnable
   protected AlignFrame _LoadFileWaitTillLoaded()
   {
     this.run();
+
     return alignFrame;
   }
 
@@ -278,9 +275,9 @@ 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 +299,12 @@ 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 +315,7 @@ 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
@@ -411,7 +408,7 @@ public class FileLoader implements Runnable
                 // register PDB entries with desktop's structure selection
                 // manager
                 StructureSelectionManager
-                        .getStructureSelectionManager(Desktop.instance)
+                        .getStructureSelectionManager(Desktop.getInstance())
                         .registerPDBEntry(pdbe);
               }
             }
@@ -485,8 +482,12 @@ public class FileLoader implements Runnable
               // status in Jalview 3
               // TODO: define 'virtual desktop' for benefit of headless scripts
               // that perform queries to find the 'current working alignment'
-              Desktop.addInternalFrame(alignFrame, title,
+              
+              Dimension dim = Platform.getDimIfEmbedded(alignFrame,
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+              alignFrame.setSize(dim);
+              Desktop.addInternalFrame(alignFrame, title, dim.width,
+                      dim.height);
             }
 
             try
@@ -500,23 +501,23 @@ 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 +545,7 @@ 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 +567,7 @@ 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 +589,7 @@ 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 +611,9 @@ public class FileLoader implements Runnable
       }
     }
     // remove the visual delay indicator
-    if (Desktop.instance != null)
+    if (Desktop.getInstance() != null)
     {
-      Desktop.instance.stopLoading();
+      Desktop.getInstance().stopLoading();
     }
 
   }
@@ -640,23 +641,4 @@ public class FileLoader implements Runnable
     return tempStructFile.toString();
   }
 
-  /**
-   * 
-   * @param file a File, or a String which is a name of a file
-   * @return
-   * @throws FileNotFoundException 
-   */
-  public static BufferedReader getBufferedReader(Object file) throws FileNotFoundException {
-    if (file instanceof String)
-    {
-      return new BufferedReader(new FileReader((String) file));
-    }
-    byte[] bytes = Platform.getFileBytes((File) file);
-    if (bytes != null)
-    {
-      return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes)));
-    }
-    return  new BufferedReader(new FileReader((File) file));
-  }
-
 }