X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=1b822136ecfb135628cdf83ebcbc83cf9e33ae22;hb=0de37d1a047209510bab82225109ae2a47931f79;hp=74c82eb929d200bb7c43b83a8857c103b2c40085;hpb=5969ead0fd401f4435a3435ede9e4e87cf9c1d0b;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 74c82eb..1b82213 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;
@@ -92,19 +92,16 @@ 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);
-  }
-
-  public void LoadFile(AlignViewport viewport, File selectedFile,
-          DataSourceType protocol, FileFormatI format)
-  {
-    this.viewport = viewport;
-    this.selectedFile = selectedFile;
-    LoadFile(selectedFile.getPath(), 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,
@@ -168,6 +165,24 @@ 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
@@ -194,6 +209,7 @@ public class FileLoader implements Runnable
   protected AlignFrame _LoadFileWaitTillLoaded()
   {
     this.run();
+
     return alignFrame;
   }
 
@@ -256,6 +272,7 @@ public class FileLoader implements Runnable
             ? "Copied From Clipboard"
             : file;
     Runtime rt = Runtime.getRuntime();
+
     try
     {
       if (Desktop.instance != null)
@@ -270,7 +287,8 @@ public class FileLoader implements Runnable
           format = new IdentifyFile().identify(source, false);
           // identify stream and rewind rather than close
         }
-        else if (selectedFile != null) {
+        else if (selectedFile != null)
+        {
           format = new IdentifyFile().identify(selectedFile, protocol);
         }
         else
@@ -318,7 +336,9 @@ 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
       {
@@ -346,22 +366,29 @@ public class FileLoader implements Runnable
                       file.lastIndexOf("."));
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);
-              UrlDownloadClient.download(file, tempStructureFileStr);
-              al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
-                      format);
+
+              // 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
             {
-              if (selectedFile == null) {
-                al = fa.readFile(file, protocol, format);
-                
-              } else {
-                al = fa.readFile(selectedFile, protocol, format);
-                             }
+              if (selectedFile == null)
+              {
+                al = fa.readFile(null, file, protocol, format);
+
+              }
+              else
+              {
+                al = fa.readFile(selectedFile, null, protocol, format);
+              }
               source = fa.getAlignFile(); // keep reference for later if
-              
-                                          // necessary.
+
+              // necessary.
             }
           }
         } catch (java.io.IOException ex)
@@ -395,12 +422,9 @@ 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
           {
@@ -441,13 +465,15 @@ public class FileLoader implements Runnable
             if (!(protocol == DataSourceType.PASTE))
             {
               alignFrame.setFileName(file, format);
+              alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
+              alignFrame.getViewport().setSavedUpToDate(true);
             }
             if (proxyColourScheme != null)
             {
               alignFrame.getViewport()
                       .applyFeaturesStyle(proxyColourScheme);
             }
-            alignFrame.statusBar.setText(MessageManager.formatMessage(
+            alignFrame.setStatus(MessageManager.formatMessage(
                     "label.successfully_loaded_file", new String[]
                     { title }));
 
@@ -460,12 +486,18 @@ 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
             {
-              alignFrame.setMaximum(jalview.bin.Cache
-                      .getDefault("SHOW_FULLSCREEN", false));
+              alignFrame.setMaximum(
+                      Cache.getDefault("SHOW_FULLSCREEN", false));
             } catch (java.beans.PropertyVetoException ex)
             {
             }