JAL-1713 JAL-3119 JAL-3785 refactored get/set Overview bounds and title

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 1d5be1b..480a26e 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -20,6 +20,13 @@
  */
 package jalview.io;
 
+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;
@@ -39,21 +46,8 @@ 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.InputStreamReader;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.SwingUtilities;
-
 public class FileLoader implements Runnable
 {
   String file;
@@ -488,6 +482,12 @@ public class FileLoader implements Runnable
               // that perform queries to find the 'current working alignment'
               Desktop.addInternalFrame(alignFrame, title,
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+              /*
+               * for an Overview automatically opened with alignment,
+               * set its title now alignFrame title has been set
+               */
+              alignFrame.alignPanel.setOverviewTitle(alignFrame);
             }
 
             try
@@ -641,23 +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));
-  }
-
 }