X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=dcfdd22ce13be4e1a9b6ec3458b77c452df40eb0;hb=3516fc4a1037ffc86d51f900850ed7a04a0174cb;hp=9dd740b3a470d2363b49acb823a5183d4c5cf8fc;hpb=c5fc6f81bb87ee53a081ed9d0ec452c051da2e70;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 9dd740b..dcfdd22 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -41,8 +41,14 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 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;
 
@@ -71,6 +77,8 @@ public class FileLoader implements Runnable
 
   boolean raiseGUI = true;
 
+  private File selectedFile;
+
   /**
    * default constructor always raised errors in GUI dialog boxes
    */
@@ -90,11 +98,15 @@ public class FileLoader implements Runnable
     this.raiseGUI = raiseGUI;
   }
 
-  public void LoadFile(AlignViewport viewport, String file,
+  public void LoadFile(AlignViewport viewport, Object file,
           DataSourceType protocol, FileFormatI format)
   {
     this.viewport = viewport;
-    LoadFile(file, protocol, format);
+    if (file instanceof File) {
+      this.selectedFile = (File) file;
+      file = selectedFile.getPath();
+    }
+    LoadFile(file.toString(), protocol, format);
   }
 
   public void LoadFile(String file, DataSourceType protocol,
@@ -158,6 +170,24 @@ public class FileLoader implements Runnable
   }
 
   /**
+   * Load alignment from (file, protocol) of type format and wait till loaded
+   * 
+   * @param file
+   * @param sourceType
+   * @param format
+   * @return alignFrame constructed from file contents
+   */
+  public AlignFrame LoadFileWaitTillLoaded(File file,
+          DataSourceType sourceType, FileFormatI format)
+  {
+    this.selectedFile = file;
+    this.file = file.getPath();
+    this.protocol = sourceType;
+    this.format = format;
+    return _LoadFileWaitTillLoaded();
+  }
+
+  /**
    * Load alignment from FileParse source of type format and wait till loaded
    * 
    * @param source
@@ -260,6 +290,9 @@ public class FileLoader implements Runnable
           format = new IdentifyFile().identify(source, false);
           // identify stream and rewind rather than close
         }
+        else if (selectedFile != null) {
+          format = new IdentifyFile().identify(selectedFile, protocol);
+        }
         else
         {
           format = new IdentifyFile().identify(file, protocol);
@@ -333,15 +366,26 @@ public class FileLoader implements Runnable
                       file.lastIndexOf("."));
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);
-              UrlDownloadClient.download(file, tempStructureFileStr);
-              al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
+              
+              // BH - switching to File object here so as to hold
+              // ._bytes array directly
+              File tempFile = new File(tempStructureFileStr);
+              UrlDownloadClient.download(file, tempFile);
+              
+              al = fa.readFile(tempFile, DataSourceType.FILE,
                       format);
               source = fa.getAlignFile();
             }
             else
             {
-              al = fa.readFile(file, protocol, format);
+              if (selectedFile == null) {
+                al = fa.readFile(file, protocol, format);
+                
+              } else {
+                al = fa.readFile(selectedFile, protocol, format);
+                             }
               source = fa.getAlignFile(); // keep reference for later if
+              
                                           // necessary.
             }
           }
@@ -422,13 +466,14 @@ public class FileLoader implements Runnable
             if (!(protocol == DataSourceType.PASTE))
             {
               alignFrame.setFileName(file, format);
+              alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
             }
             if (proxyColourScheme != null)
             {
               alignFrame.getViewport()
                       .applyFeaturesStyle(proxyColourScheme);
             }
-            alignFrame.statusBar.setText(MessageManager.formatMessage(
+            alignFrame.setStatus(MessageManager.formatMessage(
                     "label.successfully_loaded_file", new String[]
                     { title }));
 
@@ -594,4 +639,21 @@ 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));
+  }
+
 }