X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=1edf8320848eecf9aabd1f192ae0ca8fcbd75c2b;hb=67b3acb8df1438ef37a756c04e14f5a3b8406808;hp=6310cc456573b37a7ddc8aa70c6f9ea932daf965;hpb=a4fca83856b96df2fe8701bb5cc14c8d1d0a6b09;p=jalview.git

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 6310cc4..1edf832 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,42 +1,90 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * 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.
- *
- * 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
-
 package jalview.io;
 
-import java.util.*;
-
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.gui.*;
-
-public class FileLoader
-    implements Runnable
+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;
 
-  public void LoadFile(AlignViewport viewport, String file, String protocol,
-                       String format)
+  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);
@@ -59,13 +107,71 @@ public class FileLoader
     });
   }
 
+  /**
+   * 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)
+          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();
 
@@ -74,9 +180,9 @@ public class FileLoader
       try
       {
         Thread.sleep(500);
+      } catch (Exception ex)
+      {
       }
-      catch (Exception ex)
-      {}
     }
 
     return alignFrame;
@@ -85,11 +191,16 @@ public class FileLoader
   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 type = protocol.equals(FormatAdapter.FILE)
-        ? "RECENT_FILE" : "RECENT_URL";
-
-    String historyItems = jalview.bin.Cache.getProperty(type);
+    String historyItems = Cache.getProperty(type);
 
     StringTokenizer st;
 
@@ -115,87 +226,195 @@ public class FileLoader
       newHistory.append(recent.elementAt(i));
     }
 
-    jalview.bin.Cache.setProperty(type, newHistory.toString());
+    Cache.setProperty(type, newHistory.toString());
 
     if (protocol.equals(FormatAdapter.FILE))
     {
-      jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+      Cache.setProperty("DEFAULT_FILE_FORMAT", format);
     }
   }
 
   public void run()
   {
-    String title = protocol.equals(AppletFormatAdapter.PASTE)
-        ? "Copied From Clipboard" : file;
-
+    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);
+        }
+
+      }
 
-      Alignment al = null;
+      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"))
       {
-        alignFrame = new Jalview2XML().LoadJalviewAlign(file);
+        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
           {
-            al = new FormatAdapter().readFile(file, protocol, format);
-          }
-          catch (java.io.IOException ex)
+            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)
+        }
+        else
+        {
+          if (format != null && format.length() > 7)
           {
             // ad hoc message in format.
-            error = format +"\n"+error;
+            error = format + "\n" + error;
           }
         }
 
-        if ( (al != null) && (al.getHeight() > 0))
+        if ((al != null) && (al.getHeight() > 0))
         {
-          if (viewport != null)
+          // construct and register dataset sequences
+          for (SequenceI sq : al.getSequences())
           {
-            for (int i = 0; i < al.getHeight(); i++)
+            while (sq.getDatasetSequence() != null)
+            {
+              sq = sq.getDatasetSequence();
+            }
+            if (sq.getPDBId() != null)
             {
-              viewport.getAlignment().addSequence(al.getSequenceAt(i));
+              for (PDBEntry pdbe : sq.getPDBId())
+              {
+                // register PDB entries with desktop's structure selection
+                // manager
+                StructureSelectionManager.getStructureSelectionManager(
+                        Desktop.instance).registerPDBEntry(pdbe);
+              }
             }
-            viewport.firePropertyChange("alignment", null,
-                                        viewport.getAlignment().getSequences());
+          }
 
+          if (viewport != null)
+          {
+            // append to existing alignment
+            viewport.addAlignment(al, title);
           }
           else
           {
-            alignFrame = new AlignFrame(al,
-                                        AlignFrame.DEFAULT_WIDTH,
-                                        AlignFrame.DEFAULT_HEIGHT);
-
-            alignFrame.statusBar.setText("Successfully loaded file " + title);
+            // 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);
+            }
 
-            Desktop.addInternalFrame(alignFrame, title,
-                                     AlignFrame.DEFAULT_WIDTH,
-                                     AlignFrame.DEFAULT_HEIGHT);
+            alignFrame.statusBar.setText(MessageManager.formatMessage(
+                    "label.successfully_loaded_file", new String[]
+                    { title }));
 
-            try
+            if (raiseGUI)
             {
-              alignFrame.setMaximum(jalview.bin.Cache.getDefault(
-                  "SHOW_FULLSCREEN", false));
+              // 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);
             }
-            catch (java.beans.PropertyVetoException ex)
+
+            try
+            {
+              alignFrame.setMaximum(Cache.getDefault(
+                      "SHOW_FULLSCREEN", false));
+            } catch (java.beans.PropertyVetoException ex)
             {
             }
           }
@@ -207,46 +426,107 @@ public class FileLoader
             Desktop.instance.stopLoading();
           }
 
-          final String errorMessage = "Couldn't load file " + title + "\n" +
-              error;
-
-          javax.swing.SwingUtilities.invokeLater(new Runnable()
+          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)
           {
-            public void run()
+            javax.swing.SwingUtilities.invokeLater(new Runnable()
             {
-              JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                  errorMessage,
-                  "Error loading file",
-                  JOptionPane.WARNING_MESSAGE);
-            }
-          });
+              public void run()
+              {
+                JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                        errorMessage, MessageManager
+                                .getString("label.error_loading_file"),
+                        JOptionPane.WARNING_MESSAGE);
+              }
+            });
+          }
+          else
+          {
+            System.err.println(errorMessage);
+          }
         }
       }
 
       updateRecentlyOpened();
 
-    }
-    catch (OutOfMemoryError er)
+    } 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)
+    {
 
-      javax.swing.SwingUtilities.invokeLater(new Runnable()
+      er.printStackTrace();
+      alignFrame = null;
+      if (raiseGUI)
       {
-        public void run()
+        javax.swing.SwingUtilities.invokeLater(new Runnable()
         {
-          javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,
-              "Out of memory loading file " + file + "!!"
-              +
-              "\nSee help files for increasing Java Virtual Machine memory."
-              , "Out of memory",
-              javax.swing.JOptionPane.WARNING_MESSAGE);
-        }
-      });
+          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.gc();
+        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();
@@ -254,4 +534,17 @@ public class FileLoader
 
   }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see java.lang.Object#finalize()
+   */
+  protected void finalize() throws Throwable
+  {
+    source = null;
+    alignFrame = null;
+    viewport = null;
+    super.finalize();
+  }
+
 }