Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index b6701a3..31a4deb 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;
@@ -41,13 +48,8 @@ import jalview.structure.StructureSelectionManager;
 import jalview.util.MessageManager;
 import jalview.ws.utils.UrlDownloadClient;
 
-import java.io.File;
-import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
-import java.util.StringTokenizer;
-
-import javax.swing.SwingUtilities;
 
 public class FileLoader implements Runnable
 {
@@ -74,6 +76,8 @@ public class FileLoader implements Runnable
 
   boolean raiseGUI = true;
 
+  private File selectedFile;
+
   /**
    * default constructor always raised errors in GUI dialog boxes
    */
@@ -93,11 +97,15 @@ 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,
@@ -161,6 +169,24 @@ 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
@@ -179,28 +205,14 @@ 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)
-      {
-        System.out.println(
-                "Exception caught while waiting for FileLoader thread");
-        ex.printStackTrace();
-      }
-    }
+    this.run();
 
     return alignFrame;
   }
@@ -208,28 +220,15 @@ public class FileLoader implements Runnable
   public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport,
           String file, DataSourceType sourceType, FileFormatI format)
   {
+    Vector<String> recent = new Vector<>();
+    if (protocol == DataSourceType.PASTE)
     this.viewport = viewport;
     this.file = file;
     this.protocol = sourceType;
     this.format = format;
-    _LoadAlignmentFileWaitTillLoaded();
+    _LoadFileWaitTillLoaded();
   }
 
-  protected void _LoadAlignmentFileWaitTillLoaded()
-  {
-    Thread loader = new Thread(this);
-    loader.start();
-
-    while (loader.isAlive())
-    {
-      try
-      {
-        Thread.sleep(500);
-      } catch (Exception ex)
-      {
-      }
-    }
-  }
 
   /**
    * Updates (or creates) the tab-separated list of recently opened files held
@@ -268,10 +267,7 @@ public class FileLoader implements Runnable
       while (st.hasMoreTokens())
       {
         String trimmed = st.nextToken().trim();
-        if (!recent.contains(trimmed))
-        {
-          recent.add(trimmed);
-        }
+       recent.add(trimmed);
       }
     }
 
@@ -317,6 +313,9 @@ 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);
@@ -362,7 +361,8 @@ 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
       {
@@ -390,15 +390,26 @@ 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.
             }
           }
@@ -495,6 +506,7 @@ public class FileLoader implements Runnable
             if (!(protocol == DataSourceType.PASTE))
             {
               alignFrame.setFileName(file, format);
+              alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
             }
             if (proxyColourScheme != null)
             {