-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
-package jalview.io;\r
-\r
-import jalview.gui.AlignFrame;\r
-import jalview.gui.Jalview2XML;\r
-import javax.swing.JOptionPane;\r
-\r
-import jalview.gui.*;\r
-import jalview.datamodel.*;\r
-import java.util.Vector;\r
-import java.util.StringTokenizer;\r
-\r
-public class FileLoader\r
-{\r
- String file;\r
- String protocol;\r
- String format;\r
- AlignViewport viewport;\r
-\r
- public void LoadFile(AlignViewport viewport, String file, String protocol, String format)\r
- {\r
- this.viewport = viewport;\r
- LoadFile(file, protocol, format);\r
- }\r
-\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- this.file = file;\r
- this.protocol = protocol;\r
- this.format = format;\r
-\r
- LoadingThread loader = new LoadingThread();\r
- loader.start();\r
- }\r
-\r
- public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,\r
- String format)\r
- {\r
- this.file = file;\r
- this.protocol = protocol;\r
- this.format = format;\r
-\r
- LoadingThread loader = new LoadingThread();\r
- loader.start();\r
- while (loader.isAlive())\r
- {\r
- try\r
- {\r
- Thread.sleep(500);\r
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
-\r
- return loader.af;\r
- }\r
-\r
-\r
-\r
- public void updateRecentlyOpened()\r
- {\r
- Vector recent = new Vector();\r
-\r
- String type = protocol.equals(FormatAdapter.FILE)\r
- ? "RECENT_FILE" : "RECENT_URL";\r
-\r
- String historyItems = jalview.bin.Cache.getProperty(type);\r
-\r
- StringTokenizer st;\r
-\r
- if (historyItems != null)\r
- {\r
- st = new StringTokenizer(historyItems, "\t");\r
-\r
- while (st.hasMoreTokens())\r
- {\r
- recent.addElement(st.nextElement().toString().trim());\r
- }\r
- }\r
-\r
- if (recent.contains(file))\r
- {\r
- recent.remove(file);\r
- }\r
-\r
- StringBuffer newHistory = new StringBuffer(file);\r
- for (int i = 0; i < recent.size() && i < 10; i++)\r
- {\r
- newHistory.append("\t");\r
- newHistory.append(recent.elementAt(i));\r
- }\r
-\r
- jalview.bin.Cache.setProperty(type, newHistory.toString());\r
-\r
- if(type.equals(FormatAdapter.FILE))\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);\r
- }\r
-\r
-\r
- class LoadingThread\r
- extends Thread\r
- {\r
-\r
- AlignFrame af;\r
-\r
-\r
- public void run()\r
- {\r
- SequenceI[] sequences = null;\r
-\r
- if (format.equalsIgnoreCase("Jalview"))\r
- {\r
- af = new Jalview2XML().LoadJalviewAlign(file);\r
- }\r
- else\r
- {\r
- String errorMessage = AppletFormatAdapter.SUPPORTED_FORMATS;\r
-\r
- if (FormatAdapter.formats.contains(format))\r
- {\r
- try\r
- {\r
- sequences = new FormatAdapter().readFile(file, protocol, format);\r
- }\r
- catch (java.io.IOException ex)\r
- {\r
- errorMessage = ex.getMessage();\r
- }\r
- }\r
-\r
- if ( (sequences != null) && (sequences.length > 0))\r
- {\r
- if(viewport!=null)\r
- {\r
- for(int i=0; i<sequences.length; i++)\r
- viewport.getAlignment().addSequence(sequences[i]);\r
-\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
- else\r
- {\r
- af = new AlignFrame(new Alignment(sequences));\r
- af.currentFileFormat = format;\r
- af.statusBar.setText("Successfully loaded file " + file);\r
-\r
- Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
-\r
- if(jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))\r
- {\r
- af.wrapMenuItem.setSelected(true);\r
- af.wrapMenuItem_actionPerformed(null);\r
- }\r
- try\r
- {\r
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
- }\r
- catch (java.beans.PropertyVetoException ex)\r
- {\r
- }\r
- }\r
-\r
- }\r
- else\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Couldn't load file " + file +\r
- "\n"\r
- + errorMessage,\r
- "Error loading file",\r
- JOptionPane.WARNING_MESSAGE);\r
- }\r
- }\r
-\r
- if (af != null)\r
- {\r
- updateRecentlyOpened();\r
- }\r
- }\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.io;
+
+import java.util.*;
+
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.gui.*;
+
+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 = 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 (protocol.equals(FormatAdapter.FILE))
+ {
+ jalview.bin.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);
+ }
+ }
+ // 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();
+ Alignment 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.afile; // 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))
+ {
+ if (viewport != null)
+ {
+ 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);
+
+ if (!protocol.equals(AppletFormatAdapter.PASTE))
+ alignFrame.setFileName(file, format);
+
+ Desktop.addInternalFrame(alignFrame, title,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+ try
+ {
+ alignFrame.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 " + title + "\n"
+ + error;
+ if (raiseGUI)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ errorMessage, "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, "Encountered problems opening " + file
+ + "!!", "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,
+ "Out of memory loading file "
+ + file
+ + "!!"
+ + "\nSee help files for increasing Java Virtual Machine memory.",
+ "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();
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff