X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=3d2ddedfee15fb8180f4a3c86671fa088c831fe0;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=90f9e439fb9cc2a4f1740923c9fff9a6053c5839;hpb=fd5f6d3eed59b5f6d9a7cc09e4ddeb7e78eb2f17;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 90f9e43..3d2dded 100755
--- 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;
@@ -33,21 +40,14 @@ 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.ws.utils.UrlDownloadClient;
 
-import java.io.File;
-import java.io.IOException;
-import java.util.StringTokenizer;
-import java.util.Vector;
-
-import javax.swing.SwingUtilities;
-
 public class FileLoader implements Runnable
 {
   String file;
@@ -71,6 +71,8 @@ public class FileLoader implements Runnable
 
   boolean raiseGUI = true;
 
+  private File selectedFile;
+
   /**
    * default constructor always raised errors in GUI dialog boxes
    */
@@ -90,11 +92,15 @@ 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 +164,24 @@ 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
@@ -176,32 +200,21 @@ public class FileLoader implements Runnable
   }
 
   /**
-   * start thread and wait until finished, then return the alignFrame that's
-   * (hopefully) been read.
+   * runs the 'run' method (in this thread), then return the alignFrame that's
+   * (hopefully) been read
    * 
    * @return
    */
   protected AlignFrame _LoadFileWaitTillLoaded()
   {
-    Thread loader = new Thread(this);
-    loader.start();
-
-    while (loader.isAlive())
-    {
-      try
-      {
-        Thread.sleep(500);
-      } catch (Exception ex)
-      {
-      }
-    }
+    this.run();
 
     return alignFrame;
   }
 
   public void updateRecentlyOpened()
   {
-    Vector recent = new Vector();
+    Vector<String> recent = new Vector<>();
     if (protocol == DataSourceType.PASTE)
     {
       // do nothing if the file was pasted in as text... there is no filename to
@@ -217,7 +230,7 @@ public class FileLoader implements Runnable
     String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
             : "RECENT_URL";
 
-    String historyItems = jalview.bin.Cache.getProperty(type);
+    String historyItems = Cache.getProperty(type);
 
     StringTokenizer st;
 
@@ -227,7 +240,7 @@ public class FileLoader implements Runnable
 
       while (st.hasMoreTokens())
       {
-        recent.addElement(st.nextElement().toString().trim());
+        recent.addElement(st.nextToken().trim());
       }
     }
 
@@ -272,6 +285,9 @@ 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);
@@ -317,7 +333,8 @@ 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
       {
@@ -345,15 +362,26 @@ 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.
             }
           }
@@ -388,12 +416,9 @@ public class FileLoader implements Runnable
                   .getFeatureColourScheme();
           if (viewport != null)
           {
-            if (proxyColourScheme != null)
-            {
-              viewport.applyFeaturesStyle(proxyColourScheme);
-            }
             // append to existing alignment
             viewport.addAlignment(al, title);
+            viewport.applyFeaturesStyle(proxyColourScheme);
           }
           else
           {
@@ -434,6 +459,7 @@ public class FileLoader implements Runnable
             if (!(protocol == DataSourceType.PASTE))
             {
               alignFrame.setFileName(file, format);
+              alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
             }
             if (proxyColourScheme != null)
             {
@@ -457,7 +483,7 @@ public class FileLoader implements Runnable
 
             try
             {
-              alignFrame.setMaximum(jalview.bin.Cache
+              alignFrame.setMaximum(Cache
                       .getDefault("SHOW_FULLSCREEN", false));
             } catch (java.beans.PropertyVetoException ex)
             {