X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=1edf8320848eecf9aabd1f192ae0ca8fcbd75c2b;hb=67b3acb8df1438ef37a756c04e14f5a3b8406808;hp=ac3c5d38022e9c02692897f3e681f305cf9c41f0;hpb=6ddec2b963d01f867f19976cd5c6aa7d6b2dc88a;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index ac3c5d3..1edf832 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,211 +1,550 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-
-package jalview.io;
-
-import jalview.gui.AlignFrame;
-import jalview.gui.Jalview2XML;
-import javax.swing.JOptionPane;
-
-import jalview.gui.*;
-import jalview.datamodel.*;
-import java.util.Vector;
-import java.util.StringTokenizer;
-
-public class FileLoader
-{
-  String file;
-  String protocol;
-  String format;
-  AlignViewport viewport;
-
-  public void LoadFile(AlignViewport viewport, String file, String protocol, String format)
-  {
-    this.viewport = viewport;
-    LoadFile(file, protocol, format);
-  }
-
-  public void LoadFile(String file, String protocol, String format)
-  {
-    this.file = file;
-    this.protocol = protocol;
-    this.format = format;
-
-    LoadingThread loader = new LoadingThread();
-    loader.start();
-  }
-
-  public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
-                                                  String format)
-  {
-    this.file = file;
-    this.protocol = protocol;
-    this.format = format;
-
-    LoadingThread loader = new LoadingThread();
-    loader.start();
-    while (loader.isAlive())
-    {
-      try
-      {
-        Thread.sleep(500);
-      }
-      catch (Exception ex)
-      {}
-    }
-
-    return loader.af;
-  }
-
-
-
-  public void updateRecentlyOpened()
-  {
-    Vector recent = new Vector();
-
-    String type = protocol.equals(FormatAdapter.FILE)
-        ? "RECENT_FILE" : "RECENT_URL";
-
-    String historyItems = jalview.bin.Cache.getProperty(type);
-
-    StringTokenizer st;
-
-    if (historyItems != null)
-    {
-      st = new StringTokenizer(historyItems, "\t");
-
-      while (st.hasMoreTokens())
-      {
-        recent.addElement(st.nextElement().toString().trim());
-      }
-    }
-
-    if (recent.contains(file))
-    {
-      recent.remove(file);
-    }
-
-    StringBuffer newHistory = new StringBuffer(file);
-    for (int i = 0; i < recent.size() && i < 10; i++)
-    {
-      newHistory.append("\t");
-      newHistory.append(recent.elementAt(i));
-    }
-
-    jalview.bin.Cache.setProperty(type, newHistory.toString());
-
-    if(type.equals(FormatAdapter.FILE))
-      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
-  }
-
-
-  class LoadingThread
-      extends Thread
-  {
-
-    AlignFrame af;
-
-
-
-    public void run()
-    {
-      if (Desktop.instance != null)
-        Desktop.instance.startLoading(file);
-
-      SequenceI[] sequences = null;
-
-      if (format.equalsIgnoreCase("Jalview"))
-      {
-        af = new Jalview2XML().LoadJalviewAlign(file);
-      }
-      else
-      {
-        String error = AppletFormatAdapter.SUPPORTED_FORMATS;
-
-        if (FormatAdapter.isValidFormat(format))
-        {
-          try
-          {
-            sequences = new FormatAdapter().readFile(file, protocol, format);
-          }
-          catch (java.io.IOException ex)
-          {
-            error = ex.getMessage();
-          }
-        }
-
-        if ( (sequences != null) && (sequences.length > 0))
-        {
-          if(viewport!=null)
-          {
-            for(int i=0; i<sequences.length; i++)
-              viewport.getAlignment().addSequence(sequences[i]);
-
-              viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
-          }
-          else
-          {
-            af = new AlignFrame(new Alignment(sequences));
-            af.currentFileFormat = format;
-            af.statusBar.setText("Successfully loaded file " + file);
-
-            Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
-                                     AlignFrame.NEW_WINDOW_HEIGHT);
-
-            try
-            {
-              af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
-            }
-            catch (java.beans.PropertyVetoException ex)
-            {
-            }
-          }
-        }
-        else
-        {
-          if (Desktop.instance != null)
-            Desktop.instance.stopLoading();
-
-          final String errorMessage = "Couldn't load file "+file+"\n"+error;
-
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
-          {
-            public void run()
-            {
-              JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                                    errorMessage,
-                                                    "Error loading file",
-                                                    JOptionPane.WARNING_MESSAGE);
-            }
-          });
-        }
-      }
-
-      if (af != null)
-      {
-        updateRecentlyOpened();
-      }
-
-      if (Desktop.instance != null)
-        Desktop.instance.stopLoading();
-
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeaturesDisplayedI;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
+import jalview.gui.Jalview2XML;
+import jalview.schemes.ColourSchemeI;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+public class FileLoader implements Runnable
+{
+  String file;
+
+  String protocol;
+
+  String format;
+
+  FileParse source = null; // alternative specification of where data comes
+
+  // from
+
+  AlignViewport viewport;
+
+  AlignFrame alignFrame;
+
+  long loadtime;
+
+  long memused;
+
+  boolean raiseGUI = true;
+
+  /**
+   * default constructor always raised errors in GUI dialog boxes
+   */
+  public FileLoader()
+  {
+    this(true);
+  }
+
+  /**
+   * construct a Fileloader that may raise errors non-interactively
+   * 
+   * @param raiseGUI
+   *          true if errors are to be raised as GUI dialog boxes
+   */
+  public FileLoader(boolean raiseGUI)
+  {
+    this.raiseGUI = raiseGUI;
+  }
+
+  public void LoadFile(AlignViewport viewport, String file,
+          String protocol, String format)
+  {
+    this.viewport = viewport;
+    LoadFile(file, protocol, format);
+  }
+
+  public void LoadFile(String file, String protocol, String format)
+  {
+    this.file = file;
+    this.protocol = protocol;
+    this.format = format;
+
+    final Thread loader = new Thread(this);
+
+    SwingUtilities.invokeLater(new Runnable()
+    {
+      public void run()
+      {
+        loader.start();
+      }
+    });
+  }
+
+  /**
+   * Load a (file, protocol) source of unknown type
+   * 
+   * @param file
+   * @param protocol
+   */
+  public void LoadFile(String file, String protocol)
+  {
+    LoadFile(file, protocol, null);
+  }
+
+  /**
+   * Load alignment from (file, protocol) and wait till loaded
+   * 
+   * @param file
+   * @param protocol
+   * @return alignFrame constructed from file contents
+   */
+  public AlignFrame LoadFileWaitTillLoaded(String file, String protocol)
+  {
+    return LoadFileWaitTillLoaded(file, protocol, null);
+  }
+
+  /**
+   * Load alignment from (file, protocol) of type format and wait till loaded
+   * 
+   * @param file
+   * @param protocol
+   * @param format
+   * @return alignFrame constructed from file contents
+   */
+  public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
+          String format)
+  {
+    this.file = file;
+    this.protocol = protocol;
+    this.format = 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(FileParse source, String format)
+  {
+    this.source = source;
+
+    file = source.getInFile();
+    protocol = source.type;
+    this.format = format;
+    return _LoadFileWaitTillLoaded();
+  }
+
+  /**
+   * start thread and wait until finished, 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)
+      {
+      }
+    }
+
+    return alignFrame;
+  }
+
+  public void updateRecentlyOpened()
+  {
+    Vector recent = new Vector();
+    if (protocol.equals(FormatAdapter.PASTE))
+    {
+      // do nothing if the file was pasted in as text... there is no filename to
+      // refer to it as.
+      return;
+    }
+    String type = protocol.equals(FormatAdapter.FILE) ? "RECENT_FILE"
+            : "RECENT_URL";
+
+    String historyItems = Cache.getProperty(type);
+
+    StringTokenizer st;
+
+    if (historyItems != null)
+    {
+      st = new StringTokenizer(historyItems, "\t");
+
+      while (st.hasMoreTokens())
+      {
+        recent.addElement(st.nextElement().toString().trim());
+      }
+    }
+
+    if (recent.contains(file))
+    {
+      recent.remove(file);
+    }
+
+    StringBuffer newHistory = new StringBuffer(file);
+    for (int i = 0; i < recent.size() && i < 10; i++)
+    {
+      newHistory.append("\t");
+      newHistory.append(recent.elementAt(i));
+    }
+
+    Cache.setProperty(type, newHistory.toString());
+
+    if (protocol.equals(FormatAdapter.FILE))
+    {
+      Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+    }
+  }
+
+  public void run()
+  {
+    String title = protocol.equals(AppletFormatAdapter.PASTE) ? "Copied From Clipboard"
+            : file;
+    Runtime rt = Runtime.getRuntime();
+    try
+    {
+      if (Desktop.instance != null)
+      {
+        Desktop.instance.startLoading(file);
+      }
+      if (format == null)
+      {
+        // just in case the caller didn't identify the file for us
+        if (source != null)
+        {
+          format = new IdentifyFile().Identify(source, false); // identify
+          // stream and
+          // rewind rather
+          // than close
+        }
+        else
+        {
+          format = new IdentifyFile().Identify(file, protocol);
+        }
+
+      }
+
+      if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
+      {
+        Desktop.instance.stopLoading();
+        System.err.println("The input file \"" + file
+                + "\" has no data content!");
+        if (!Jalview.isHeadlessMode())
+        {
+          JOptionPane.showMessageDialog(null, "The input file \""
+                  + file + "\" has no data content!", "Empty data file",
+                  JOptionPane.ERROR_MESSAGE);
+        }
+        return;
+      }
+      // TODO: cache any stream datasources as a temporary file (eg. PDBs
+      // retrieved via URL)
+      if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+      {
+        System.gc();
+        memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
+        // memory
+        // before
+        // load
+      }
+      loadtime = -System.currentTimeMillis();
+      AlignmentI al = null;
+
+      if (format.equalsIgnoreCase("Jalview"))
+      {
+        if (source != null)
+        {
+          // Tell the user (developer?) that this is going to cause a problem
+          System.err
+                  .println("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);
+      }
+      else
+      {
+        String error = AppletFormatAdapter.SUPPORTED_FORMATS;
+        if (FormatAdapter.isValidFormat(format))
+        {
+          try
+          {
+            if (source != null)
+            {
+              // read from the provided source
+              al = new FormatAdapter().readFromFile(source, format);
+            }
+            else
+            {
+
+              // open a new source and read from it
+              FormatAdapter fa = new FormatAdapter();
+              al = fa.readFile(file, protocol, format);
+              source = fa.getAlignFile(); // keep reference for later if
+                                          // necessary.
+            }
+          } catch (java.io.IOException ex)
+          {
+            error = ex.getMessage();
+          }
+        }
+        else
+        {
+          if (format != null && format.length() > 7)
+          {
+            // ad hoc message in format.
+            error = format + "\n" + error;
+          }
+        }
+
+        if ((al != null) && (al.getHeight() > 0))
+        {
+          // construct and register dataset sequences
+          for (SequenceI sq : al.getSequences())
+          {
+            while (sq.getDatasetSequence() != null)
+            {
+              sq = sq.getDatasetSequence();
+            }
+            if (sq.getPDBId() != null)
+            {
+              for (PDBEntry pdbe : sq.getPDBId())
+              {
+                // register PDB entries with desktop's structure selection
+                // manager
+                StructureSelectionManager.getStructureSelectionManager(
+                        Desktop.instance).registerPDBEntry(pdbe);
+              }
+            }
+          }
+
+          if (viewport != null)
+          {
+            // append to existing alignment
+            viewport.addAlignment(al, title);
+          }
+          else
+          {
+            // otherwise construct the alignFrame
+
+            if (source instanceof ComplexAlignFile)
+            {
+              ColumnSelection colSel = ((ComplexAlignFile) source)
+                      .getColumnSelection();
+              SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+                      .getHiddenSequences();
+              boolean showSeqFeatures = ((ComplexAlignFile) source)
+                      .isShowSeqFeatures();
+              ColourSchemeI cs = ((ComplexAlignFile) source)
+                      .getColourScheme();
+              FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+                      .getDisplayedFeatures();
+              alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
+                      AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+              alignFrame.getViewport().setShowSequenceFeatures(
+                      showSeqFeatures);
+              alignFrame.getViewport().setFeaturesDisplayed(fd);
+              alignFrame.changeColour(cs);
+            }
+            else
+            {
+              alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+                      AlignFrame.DEFAULT_HEIGHT);
+            }
+            // add metadata and update ui
+            if (!protocol.equals(AppletFormatAdapter.PASTE))
+            {
+              alignFrame.setFileName(file, format);
+            }
+
+            alignFrame.statusBar.setText(MessageManager.formatMessage(
+                    "label.successfully_loaded_file", new String[]
+                    { title }));
+
+            if (raiseGUI)
+            {
+              // add the window to the GUI
+              // note - this actually should happen regardless of raiseGUI
+              // 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,
+                      AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+            }
+
+            try
+            {
+              alignFrame.setMaximum(Cache.getDefault(
+                      "SHOW_FULLSCREEN", false));
+            } catch (java.beans.PropertyVetoException ex)
+            {
+            }
+          }
+        }
+        else
+        {
+          if (Desktop.instance != null)
+          {
+            Desktop.instance.stopLoading();
+          }
+
+          final String errorMessage = "Couldn't load file " + title + "\n"
+                  + error;
+          // TODO: refactor FileLoader to be independent of Desktop / Applet GUI
+          // bits ?
+          if (raiseGUI && Desktop.desktop != null)
+          {
+            javax.swing.SwingUtilities.invokeLater(new Runnable()
+            {
+              public void run()
+              {
+                JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                        errorMessage, MessageManager
+                                .getString("label.error_loading_file"),
+                        JOptionPane.WARNING_MESSAGE);
+              }
+            });
+          }
+          else
+          {
+            System.err.println(errorMessage);
+          }
+        }
+      }
+
+      updateRecentlyOpened();
+
+    } catch (Exception er)
+    {
+      System.err.println("Exception whilst opening file '" + file);
+      er.printStackTrace();
+      if (raiseGUI)
+      {
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(
+                    Desktop.desktop, MessageManager.formatMessage(
+                            "label.problems_opening_file", new String[]
+                            { file }), MessageManager
+                            .getString("label.file_open_error"),
+                    javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
+      }
+      alignFrame = null;
+    } catch (OutOfMemoryError er)
+    {
+
+      er.printStackTrace();
+      alignFrame = null;
+      if (raiseGUI)
+      {
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
+        {
+          public void run()
+          {
+            javax.swing.JOptionPane.showInternalMessageDialog(
+                    Desktop.desktop, MessageManager.formatMessage(
+                            "warn.out_of_memory_loading_file", new String[]
+                            { file }), MessageManager
+                            .getString("label.out_of_memory"),
+                    javax.swing.JOptionPane.WARNING_MESSAGE);
+          }
+        });
+      }
+      System.err.println("Out of memory loading file " + file + "!!");
+
+    }
+    loadtime += System.currentTimeMillis();
+    // TODO: Estimate percentage of memory used by a newly loaded alignment -
+    // warn if more memory will be needed to work with it
+    // System.gc();
+    memused = memused
+            - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference
+    // in free
+    // memory
+    // after
+    // load
+    if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+    {
+      if (alignFrame != null)
+      {
+        AlignmentI al = alignFrame.getViewport().getAlignment();
+
+        System.out.println("Loaded '" + title + "' in "
+                + (loadtime / 1000.0) + "s, took an additional "
+                + (1.0 * memused / (1024.0 * 1024.0)) + " MB ("
+                + al.getHeight() + " seqs by " + al.getWidth() + " cols)");
+      }
+      else
+      {
+        // report that we didn't load anything probably due to an out of memory
+        // error
+        System.out.println("Failed to load '" + title + "' in "
+                + (loadtime / 1000.0) + "s, took an additional "
+                + (1.0 * memused / (1024.0 * 1024.0))
+                + " MB (alignment is null)");
+      }
+    }
+    // remove the visual delay indicator
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.stopLoading();
+    }
+
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see java.lang.Object#finalize()
+   */
+  protected void finalize() throws Throwable
+  {
+    source = null;
+    alignFrame = null;
+    viewport = null;
+    super.finalize();
+  }
+
+}