X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=a64582dc1a9eaca84d8125bbaae2c19629cf1052;hb=refs%2Fheads%2FJAL-3253_applet_omnibus-BH;hp=1d5be1b832a5452184c66e0d8f838aba1f609f11;hpb=ab0e5f2223a993371761baf240d815abdfcbb950;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 1d5be1b..a64582d 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -37,11 +37,11 @@ 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.util.Platform;
 import jalview.ws.utils.UrlDownloadClient;
 
+import java.awt.Dimension;
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.File;
@@ -49,23 +49,35 @@ import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
-import java.util.StringTokenizer;
-import java.util.Vector;
+import java.util.ArrayList;
+import java.util.List;
 
 import javax.swing.SwingUtilities;
 
 public class FileLoader implements Runnable
 {
+  private static final String DEFAULT_FILE_FORMAT_PROPERTY = "DEFAULT_FILE_FORMAT";
+
+  private static final String RECENT_URL_PROPERTY = "RECENT_URL";
+
+  private static final String RECENT_FILE_PROPERTY = "RECENT_FILE";
+
+  private static final String TAB = "\t";
+
+  /*
+   * maximum number of items in file/url history lists;
+   * pseudo-constant (not final) so amendable by Groovy if wanted
+   */
+  private static int MAX_HISTORY = 11;
+
   String file;
 
   DataSourceType protocol;
 
   FileFormatI format;
 
-  AlignmentFileReaderI source = null; // alternative specification of where data
-                                      // comes
-
-  // from
+  AlignmentFileReaderI source; // alternative specification of where data
+                               // comes from
 
   AlignViewport viewport;
 
@@ -98,20 +110,90 @@ public class FileLoader implements Runnable
     this.raiseGUI = raiseGUI;
   }
 
-  public void LoadFile(AlignViewport viewport, Object file,
+  /**
+   * It is critical that all these fields are set, as this instance is reused.
+   * 
+   * @param source
+   * @param file
+   * @param inFile
+   * @param dataSourceType
+   * @param format
+   */
+  private void setFileFields(AlignmentFileReaderI source, File file,
+          String inFile, DataSourceType dataSourceType, FileFormatI format)
+  {
+    this.source = source;
+    this.file = inFile;
+    this.selectedFile = file;
+    this.protocol = dataSourceType;
+    this.format = format;
+  }
+
+
+  /**
+   * Uppercase LoadFile is deprecated because it does not pass byte[] data to
+   * JavaScript
+   * 
+   * @param viewport
+   * @param file
+   * @param protocol
+   * @param format
+   */
+  @Deprecated
+  public void LoadFile(AlignViewport viewport, String file,
           DataSourceType protocol, FileFormatI format)
   {
-    this.viewport = viewport;
-    if (file instanceof File) {
-      this.selectedFile = (File) file;
-      file = selectedFile.getPath();
+    if (viewport != null)
+    {
+      this.viewport = viewport;
     }
-    LoadFile(file.toString(), protocol, format);
+    loadFile(file, protocol, format);
   }
 
+  public void LoadFile(AlignViewport viewport, File file,
+          DataSourceType protocol, FileFormatI format)
+  {
+    loadFile(viewport, file, protocol, format);
+  }
+
+  /**
+   * Uppercase LoadFile is deprecated because it does not pass byte[] data to
+   * JavaScript
+   * 
+   * @param file
+   * @param protocol
+   * @param format
+   */
+  @Deprecated
   public void LoadFile(String file, DataSourceType protocol,
           FileFormatI format)
   {
+    loadFile(file, protocol, format);
+  }
+
+  /**
+   * necessary to use Object here in order to pass the file data
+   * 
+   * @param viewport
+   * @param file
+   *          File preferably to String
+   * @param protocol
+   * @param format
+   */
+  public void loadFile(AlignViewport viewport, File file,
+          DataSourceType protocol, FileFormatI format)
+  {
+    if (viewport != null)
+    {
+      this.viewport = viewport;
+    }
+    this.selectedFile = file;
+    loadFile(selectedFile.getPath(), protocol, format);
+  }
+
+  private void loadFile(String file, DataSourceType protocol,
+          FileFormatI format)
+  {
     this.file = file;
     this.protocol = protocol;
     this.format = format;
@@ -129,23 +211,13 @@ public class FileLoader implements Runnable
   }
 
   /**
-   * Load a (file, protocol) source of unknown type
-   * 
-   * @param file
-   * @param protocol
-   */
-  public void LoadFile(String file, DataSourceType protocol)
-  {
-    LoadFile(file, protocol, null);
-  }
-
-  /**
    * Load alignment from (file, protocol) and wait till loaded
    * 
    * @param file
    * @param sourceType
    * @return alignFrame constructed from file contents
    */
+  @Deprecated
   public AlignFrame LoadFileWaitTillLoaded(String file,
           DataSourceType sourceType)
   {
@@ -160,93 +232,84 @@ public class FileLoader implements Runnable
    * @param format
    * @return alignFrame constructed from file contents
    */
+  @Deprecated
   public AlignFrame LoadFileWaitTillLoaded(String file,
           DataSourceType sourceType, FileFormatI format)
   {
-    this.file = file;
-    this.protocol = sourceType;
-    this.format = format;
-    return _LoadFileWaitTillLoaded();
+    setFileFields(null, null, file, sourceType, format);
+    return _loadFileWaitTillLoaded();
   }
 
   /**
    * Load alignment from (file, protocol) of type format and wait till loaded
    * 
-   * @param file
+   * @param fileObject
    * @param sourceType
    * @param format
    * @return alignFrame constructed from file contents
+   * @throws NullPointerException
+   *           if {@code file} is null
    */
-  public AlignFrame LoadFileWaitTillLoaded(File file,
+  public AlignFrame loadFileWaitTillLoaded(File fileObject,
           DataSourceType sourceType, FileFormatI format)
   {
-    this.selectedFile = file;
-    this.file = file.getPath();
-    this.protocol = sourceType;
-    this.format = format;
-    return _LoadFileWaitTillLoaded();
+    setFileFields(null, fileObject, fileObject.getPath(), sourceType, format);
+    return _loadFileWaitTillLoaded();
   }
 
   /**
-   * Load alignment from FileParse source of type format and wait till loaded
-   * 
-   * @param source
-   * @param format
-   * @return alignFrame constructed from file contents
-   */
-  public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source,
-          FileFormatI format)
-  {
-    this.source = source;
-
-    file = source.getInFile();
-    protocol = source.getDataSourceType();
-    this.format = format;
-    return _LoadFileWaitTillLoaded();
-  }
-
-  /**
-   * runs the 'run' method (in this thread), then return the alignFrame that's
-   * (hopefully) been read
+   * Runs the 'run' method (in this thread), then returns the alignFrame that
+   * (hopefully) has been constructed
    * 
    * @return
    */
-  protected AlignFrame _LoadFileWaitTillLoaded()
+  private AlignFrame _loadFileWaitTillLoaded()
   {
     this.run();
-
     return alignFrame;
   }
 
+  /**
+   * Updates the Jalview properties file to add the last file or URL read to the
+   * tab-separated list in property RECENT_FILE or RECENT_URL respectively. The
+   * property is created if it does not already exist. The new entry is added as
+   * the first item (without duplication). If the list exceeds some maximum
+   * length (currently 10 entries), the oldest (last) entry is dropped.
+   * <p>
+   * Files read from the temporary file directory are not added to the property.
+   * <p>
+   * Property DEFAULT_FILE_FORMAT (e.g. "Fasta" etc) is also set if currently
+   * reading from file.
+   */
   public void updateRecentlyOpened()
   {
-    Vector<String> recent = new Vector<>();
+    List<String> recent = new ArrayList<>();
     if (protocol == DataSourceType.PASTE)
     {
       // do nothing if the file was pasted in as text... there is no filename to
       // refer to it as.
       return;
     }
-    if (file != null
-            && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
+    // BH logic change here just includes ignoring file==null
+    if (file == null
+            || file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
     {
       // ignore files loaded from the system's temporary directory
       return;
     }
-    String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
-            : "RECENT_URL";
+    String type = protocol == DataSourceType.FILE ? RECENT_FILE_PROPERTY
+            : RECENT_URL_PROPERTY;
 
     String historyItems = Cache.getProperty(type);
 
-    StringTokenizer st;
-
+    // BH simpler coding
     if (historyItems != null)
     {
-      st = new StringTokenizer(historyItems, "\t");
+      String[] tokens = historyItems.split("\\t");
 
-      while (st.hasMoreTokens())
+      for (String token : tokens)
       {
-        recent.addElement(st.nextToken().trim());
+        recent.add(token.trim());
       }
     }
 
@@ -255,18 +318,18 @@ public class FileLoader implements Runnable
       recent.remove(file);
     }
 
-    StringBuffer newHistory = new StringBuffer(file);
-    for (int i = 0; i < recent.size() && i < 10; i++)
+    StringBuilder newHistory = new StringBuilder(file);
+    for (int i = 0; i < recent.size() && i < MAX_HISTORY - 1; i++)
     {
-      newHistory.append("\t");
-      newHistory.append(recent.elementAt(i));
+      newHistory.append(TAB);
+      newHistory.append(recent.get(i));
     }
 
     Cache.setProperty(type, newHistory.toString());
 
     if (protocol == DataSourceType.FILE)
     {
-      Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
+      Cache.setProperty(DEFAULT_FILE_FORMAT_PROPERTY, format.getName());
     }
   }
 
@@ -279,9 +342,9 @@ public class FileLoader implements Runnable
     Runtime rt = Runtime.getRuntime();
     try
     {
-      if (Desktop.instance != null)
+      if (Desktop.getInstance() != null)
       {
-        Desktop.instance.startLoading(file);
+        Desktop.getInstance().startLoading(file);
       }
       if (format == null)
       {
@@ -303,12 +366,12 @@ public class FileLoader implements Runnable
 
       if (format == null)
       {
-        Desktop.instance.stopLoading();
+        Desktop.getInstance().stopLoading();
         System.err.println("The input file \"" + file
                 + "\" has null or unidentifiable data content!");
         if (!Jalview.isHeadlessMode())
         {
-          JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+          JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                   MessageManager.getString("label.couldnt_read_data")
                           + " in " + file + "\n"
                           + AppletFormatAdapter.getSupportedFormats(),
@@ -319,7 +382,7 @@ public class FileLoader implements Runnable
       }
       // TODO: cache any stream datasources as a temporary file (eg. PDBs
       // retrieved via URL)
-      if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+      if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
       {
         System.gc();
         memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
@@ -340,7 +403,10 @@ public class FileLoader implements Runnable
           // We read the data anyway - it might make sense.
         }
         // BH 2018 switch to File object here instead of filename
+        Platform.timeCheck(null, Platform.TIME_MARK);
         alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
+        Platform.timeCheck("JVP loaded", Platform.TIME_MARK);
+
       }
       else
       {
@@ -362,15 +428,15 @@ public class FileLoader implements Runnable
             if (downloadStructureFile)
             {
               String structExt = format.getExtensions().split(",")[0];
-              String urlLeafName = file.substring(
-                      file.lastIndexOf(
-                              System.getProperty("file.separator")),
+              int pt = file.lastIndexOf(file.indexOf('/') >= 0 ? "/"
+                      : System.getProperty("file.separator"));
+              String urlLeafName = file.substring(pt,
                       file.lastIndexOf("."));
               String tempStructureFileStr = createNamedJvTempFile(
                       urlLeafName, structExt);
               
-              // BH - switching to File object here so as to hold
-              // ._bytes array directly
+              // BH - switching to File object here so as to hold on to the
+              // bytes array directly
               File tempFile = new File(tempStructureFileStr);
               UrlDownloadClient.download(file, tempFile);
               
@@ -411,8 +477,7 @@ public class FileLoader implements Runnable
               {
                 // register PDB entries with desktop's structure selection
                 // manager
-                StructureSelectionManager
-                        .getStructureSelectionManager(Desktop.instance)
+                Desktop.getStructureSelectionManager()
                         .registerPDBEntry(pdbe);
               }
             }
@@ -486,8 +551,13 @@ public class FileLoader implements Runnable
               // status in Jalview 3
               // TODO: define 'virtual desktop' for benefit of headless scripts
               // that perform queries to find the 'current working alignment'
-              Desktop.addInternalFrame(alignFrame, title,
+              
+              
+              Dimension dim = Platform.getDimIfEmbedded(alignFrame,
                       AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+              alignFrame.setSize(dim);
+              Desktop.addInternalFrame(alignFrame, title, dim.width,
+                      dim.height);
             }
 
             try
@@ -501,23 +571,23 @@ public class FileLoader implements Runnable
         }
         else
         {
-          if (Desktop.instance != null)
+          if (Desktop.getInstance() != null)
           {
-            Desktop.instance.stopLoading();
+            Desktop.getInstance().stopLoading();
           }
 
           final String errorMessage = MessageManager.getString(
                   "label.couldnt_load_file") + " " + title + "\n" + error;
           // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
           // bits ?
-          if (raiseGUI && Desktop.desktop != null)
+          if (raiseGUI && Desktop.getDesktopPane() != null)
           {
             javax.swing.SwingUtilities.invokeLater(new Runnable()
             {
               @Override
               public void run()
               {
-                JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+                JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                         errorMessage,
                         MessageManager
                                 .getString("label.error_loading_file"),
@@ -545,7 +615,7 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                     MessageManager.formatMessage(
                             "label.problems_opening_file", new String[]
                             { file }),
@@ -567,7 +637,7 @@ public class FileLoader implements Runnable
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+            JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
                     MessageManager.formatMessage(
                             "warn.out_of_memory_loading_file", new String[]
                             { file }),
@@ -589,7 +659,7 @@ public class FileLoader implements Runnable
     // memory
     // after
     // load
-    if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+    if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
     {
       if (alignFrame != null)
       {
@@ -611,9 +681,9 @@ public class FileLoader implements Runnable
       }
     }
     // remove the visual delay indicator
-    if (Desktop.instance != null)
+    if (Desktop.getInstance() != null)
     {
-      Desktop.instance.stopLoading();
+      Desktop.getInstance().stopLoading();
     }
 
   }