X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=ac5591157314e08432c891e782791a8911bd994d;hb=51b0b157926ed477cb558ca5971126bf9fccbd31;hp=dcfdd22ce13be4e1a9b6ec3458b77c452df40eb0;hpb=3516fc4a1037ffc86d51f900850ed7a04a0174cb;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index dcfdd22..ac55911 100755
--- 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;
@@ -33,27 +41,15 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.Desktop;
-import jalview.gui.Jalview2XML;
 import jalview.gui.JvOptionPane;
 import jalview.json.binding.biojson.v1.ColourSchemeMapper;
+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;
-import java.io.ByteArrayInputStream;
-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;
-
-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;
   }
 
@@ -338,7 +335,8 @@ public class FileLoader implements Runnable
                   "IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
           // We read the data anyway - it might make sense.
         }
-        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
+        // BH 2018 switch to File object here instead of filename
+        alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
       }
       else
       {
@@ -484,8 +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
@@ -639,21 +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 
-   */
-  @SuppressWarnings("unused")
-  public static BufferedReader getBuffereReader(Object file) throws FileNotFoundException {
-    if (file instanceof String)
-      return new BufferedReader(new FileReader((String) file));
-    
-    byte[] bytes = /** @j2sNative file._bytes || */ null;
-    if (bytes != null)
-      return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes)));
-    return  new BufferedReader(new FileReader((File) file));
-  }
-
 }