JAL-3210 Merge branch 'develop' into trialMerge

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

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3afbaad..1d5be1b 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -39,10 +39,16 @@ 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;
 
@@ -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
@@ -176,35 +206,21 @@ 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)
-      {
-        System.out.println(
-                "Exception caught while waiting for FileLoader thread");
-        ex.printStackTrace();
-      }
-    }
+    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
@@ -220,7 +236,7 @@ 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;
 
@@ -230,7 +246,7 @@ public class FileLoader implements Runnable
 
       while (st.hasMoreTokens())
       {
-        recent.addElement(st.nextElement().toString().trim());
+        recent.addElement(st.nextToken().trim());
       }
     }
 
@@ -275,6 +291,9 @@ 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);
@@ -320,7 +339,8 @@ 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
       {
@@ -348,15 +368,26 @@ 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.
             }
           }
@@ -437,6 +468,7 @@ public class FileLoader implements Runnable
             if (!(protocol == DataSourceType.PASTE))
             {
               alignFrame.setFileName(file, format);
+              alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
             }
             if (proxyColourScheme != null)
             {
@@ -609,4 +641,23 @@ 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));
+  }
+
 }