X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=38033ff1a19542d495789270535d32b217483027;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=3a77b7301e5f7754f7b08e7068dced0bc40c5238;hpb=b92eeace1b8b5237b3719a4d5b42e8a60af015e9;p=jalview.git
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3a77b73..38033ff 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,30 +1,41 @@
/*
- * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.io;
-import java.util.*;
+import jalview.datamodel.AlignmentI;
+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.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
-import javax.swing.*;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
-import jalview.datamodel.*;
-import jalview.gui.*;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
{
@@ -47,15 +58,20 @@ public class FileLoader implements Runnable
long memused;
boolean raiseGUI = true;
+
/**
- * default constructor always raised errors in GUI dialog boxes
+ * default constructor always raised errors in GUI dialog boxes
*/
- public FileLoader() {
+ 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
+ * 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)
{
@@ -136,6 +152,7 @@ public class FileLoader implements Runnable
public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
{
this.source = source;
+
file = source.getInFile();
protocol = source.type;
this.format = format;
@@ -169,7 +186,12 @@ public class FileLoader implements Runnable
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";
@@ -233,13 +255,18 @@ public class FileLoader implements Runnable
format = new IdentifyFile().Identify(file, protocol);
}
}
+ // 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
+ memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
+ // memory
+ // before
+ // load
}
loadtime = -System.currentTimeMillis();
- Alignment al = null;
+ AlignmentI al = null;
if (format.equalsIgnoreCase("Jalview"))
{
@@ -250,7 +277,7 @@ public class FileLoader implements Runnable
.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);
+ alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
}
else
{
@@ -288,29 +315,59 @@ public class FileLoader implements Runnable
if ((al != null) && (al.getHeight() > 0))
{
+ for (SequenceI sq : al.getSequences())
+ {
+ while (sq.getDatasetSequence() != null)
+ {
+ sq = sq.getDatasetSequence();
+ }
+ if (sq.getPDBId() != null)
+ {
+ for (PDBEntry pdbe : (List) sq.getPDBId())
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerPDBEntry(pdbe);
+ }
+ }
+ }
if (viewport != null)
{
+ // TODO: create undo object for this JAL-1101
for (int i = 0; i < al.getHeight(); i++)
{
viewport.getAlignment().addSequence(al.getSequenceAt(i));
}
viewport.firePropertyChange("alignment", null, viewport
.getAlignment().getSequences());
-
}
else
{
alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
- alignFrame.statusBar.setText("Successfully loaded file "
- + title);
+ alignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new String[]
+ { title }));
if (!protocol.equals(AppletFormatAdapter.PASTE))
+ {
alignFrame.setFileName(file, format);
+ }
+ if (source instanceof HtmlFile)
+ {
+ ((HtmlFile) source).LoadAlignmentFeatures(alignFrame);
- Desktop.addInternalFrame(alignFrame, title,
- AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ }
+ 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
{
@@ -337,7 +394,8 @@ public class FileLoader implements Runnable
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- errorMessage, "Error loading file",
+ errorMessage, MessageManager
+ .getString("label.error_loading_file"),
JOptionPane.WARNING_MESSAGE);
}
});
@@ -351,10 +409,9 @@ public class FileLoader implements Runnable
updateRecentlyOpened();
- }
- catch (Exception er)
+ } catch (Exception er)
{
- System.err.println("Exception whilst opening file '"+file);
+ System.err.println("Exception whilst opening file '" + file);
er.printStackTrace();
if (raiseGUI)
{
@@ -362,20 +419,17 @@ public class FileLoader implements Runnable
{
public void run()
{
- javax.swing.JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- "Encountered problems opening "
- + file
- + "!!"
- , "File open error",
- javax.swing.JOptionPane.WARNING_MESSAGE);
+ 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)
+ } catch (OutOfMemoryError er)
{
er.printStackTrace();
@@ -389,31 +443,28 @@ public class FileLoader implements 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",
+ MessageManager.formatMessage("warn.out_of_memory_loading_file", new String[]{file}),
+ MessageManager.getString("label.out_of_memory"),
javax.swing.JOptionPane.WARNING_MESSAGE);
}
});
}
- else
- {
- System.err.println("Out of memory loading file " + file + "!!");
- }
- }
- loadtime += System.currentTimeMillis();
+ System.err.println("Out of memory loading file " + file + "!!");
- if (Desktop.instance != null)
- {
- Desktop.instance.stopLoading();
}
+ 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 (alignFrame != null)
+ memused = memused
+ - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference
+ // in free
+ // memory
+ // after
+ // load
+ if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
{
- if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ if (alignFrame != null)
{
AlignmentI al = alignFrame.getViewport().getAlignment();
@@ -422,6 +473,20 @@ public class FileLoader implements Runnable
+ (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();
}
}