-/*\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
-import jalview.datamodel.Alignment;\r
-import jalview.gui.Desktop;\r
-import jalview.datamodel.SequenceI;\r
-\r
-public class FileLoader\r
-{\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- LoadingThread loader = new LoadingThread(file, protocol, format);\r
- loader.start();\r
- }\r
-\r
- public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,\r
- String format)\r
- {\r
- LoadingThread loader = new LoadingThread(file, protocol, format);\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
- class LoadingThread\r
- extends Thread\r
-{\r
- String file;\r
- String protocol;\r
- String format;\r
- AlignFrame af;\r
-\r
- public LoadingThread(String file, String protocol, String format)\r
- {\r
- this.file = file;\r
- this.protocol = protocol;\r
- this.format = format;\r
- }\r
-\r
- public void run()\r
- {\r
- SequenceI[] sequences = null;\r
-\r
- if (format.equalsIgnoreCase("Jalview"))\r
- {\r
- af = Jalview2XML.LoadJalviewAlign(file);\r
- }\r
- else\r
- {\r
- if (FormatAdapter.formats.contains(format))\r
- {\r
- sequences = FormatAdapter.readFile(file, protocol, format);\r
- }\r
-\r
- if ( (sequences != null) && (sequences.length > 0))\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
-\r
- try\r
- {\r
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
- else\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Couldn't open file.\n" +\r
- "Formats currently supported are\n" +\r
- "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!\r
- , "Error loading file",\r
- JOptionPane.WARNING_MESSAGE);\r
- }\r
- }\r
- }\r
-}\r
-\r
-}\r
+/*
+ * 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.FeatureSettingsModelI;
+import jalview.api.FeaturesDisplayedI;
+import jalview.api.FeaturesSourceI;
+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.gui.JvOptionPane;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
+import jalview.schemes.ColourSchemeI;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.SwingUtilities;
+
+public class FileLoader implements Runnable
+{
+ String file;
+
+ DataSourceType protocol;
+
+ FileFormatI format;
+
+ AlignmentFileReaderI 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,
+ DataSourceType protocol, FileFormatI format)
+ {
+ this.viewport = viewport;
+ LoadFile(file, protocol, format);
+ }
+
+ public void LoadFile(String file, DataSourceType protocol,
+ FileFormatI format)
+ {
+ this.file = file;
+ this.protocol = protocol;
+ this.format = format;
+
+ final Thread loader = new Thread(this);
+
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ loader.start();
+ }
+ });
+ }
+
+ /**
+ * 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
+ */
+ public AlignFrame LoadFileWaitTillLoaded(String file,
+ DataSourceType sourceType)
+ {
+ return LoadFileWaitTillLoaded(file, sourceType, null);
+ }
+
+ /**
+ * Load alignment from (file, protocol) of type format and wait till loaded
+ *
+ * @param file
+ * @param sourceType
+ * @param format
+ * @return alignFrame constructed from file contents
+ */
+ public AlignFrame LoadFileWaitTillLoaded(String file,
+ DataSourceType sourceType, FileFormatI format)
+ {
+ this.file = file;
+ this.protocol = sourceType;
+ 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(AlignmentFileReaderI source,
+ FileFormatI format)
+ {
+ this.source = source;
+
+ file = source.getInFile();
+ protocol = source.getDataSourceType();
+ 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 == DataSourceType.PASTE)
+ {
+ // do nothing if the file was pasted in as text... there is no filename to
+ // refer to it as.
+ return;
+ }
+ String type = protocol == DataSourceType.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));
+ }
+
+ Cache.setProperty(type, newHistory.toString());
+
+ if (protocol == DataSourceType.FILE)
+ {
+ Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName());
+ }
+ }
+
+ @Override
+ public void run()
+ {
+ String title = protocol == DataSourceType.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)
+ {
+ Desktop.instance.stopLoading();
+ System.err.println("The input file \"" + file
+ + "\" has null or unidentifiable data content!");
+ if (!Jalview.isHeadlessMode())
+ {
+ JvOptionPane.showInternalMessageDialog(
+ Desktop.desktop,
+ MessageManager.getString("label.couldnt_read_data")
+ + " in " + file + "\n"
+ + AppletFormatAdapter.getSupportedFormats(),
+ MessageManager.getString("label.couldnt_read_data"),
+ JvOptionPane.WARNING_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 (FileFormat.Jalview.equals(format))
+ {
+ 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.getSupportedFormats();
+ 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();
+ }
+
+ if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
+ {
+ // construct and register dataset sequences
+ for (SequenceI sq : al.getSequences())
+ {
+ while (sq.getDatasetSequence() != null)
+ {
+ sq = sq.getDatasetSequence();
+ }
+ if (sq.getAllPDBEntries() != null)
+ {
+ for (PDBEntry pdbe : sq.getAllPDBEntries())
+ {
+ // register PDB entries with desktop's structure selection
+ // manager
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerPDBEntry(pdbe);
+ }
+ }
+ }
+
+ FeatureSettingsModelI proxyColourScheme = source
+ .getFeatureColourScheme();
+ if (viewport != null)
+ {
+ if (proxyColourScheme != null)
+ {
+ viewport.applyFeaturesStyle(proxyColourScheme);
+ }
+ // 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();
+ String colourSchemeName = ((ComplexAlignFile) source)
+ .getGlobalColourScheme();
+ FeaturesDisplayedI fd = ((ComplexAlignFile) source)
+ .getDisplayedFeatures();
+ alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ alignFrame.getViewport().setFeaturesDisplayed(fd);
+ alignFrame.getViewport().setShowSequenceFeatures(
+ ((ComplexAlignFile) source).isShowSeqFeatures());
+ ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
+ colourSchemeName, al);
+ if (cs != null)
+ {
+ alignFrame.changeColour(cs);
+ }
+ }
+ else
+ {
+ alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ if (source instanceof FeaturesSourceI)
+ {
+ alignFrame.getViewport().setShowSequenceFeatures(true);
+ }
+ }
+ // add metadata and update ui
+ if (!(protocol == DataSourceType.PASTE))
+ {
+ alignFrame.setFileName(file, format);
+ }
+ if (proxyColourScheme != null)
+ {
+ alignFrame.getViewport()
+ .applyFeaturesStyle(proxyColourScheme);
+ }
+ 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(jalview.bin.Cache.getDefault(
+ "SHOW_FULLSCREEN", false));
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+ }
+ }
+ else
+ {
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.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)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ errorMessage, MessageManager
+ .getString("label.error_loading_file"),
+ JvOptionPane.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()
+ {
+ @Override
+ public void run()
+ {
+ JvOptionPane.showInternalMessageDialog(
+ Desktop.desktop, MessageManager.formatMessage(
+ "label.problems_opening_file",
+ new String[] { file }), MessageManager
+ .getString("label.file_open_error"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ alignFrame = null;
+ } catch (OutOfMemoryError er)
+ {
+
+ er.printStackTrace();
+ alignFrame = null;
+ if (raiseGUI)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ JvOptionPane.showInternalMessageDialog(
+ Desktop.desktop, MessageManager.formatMessage(
+ "warn.out_of_memory_loading_file", new String[]
+ { file }), MessageManager
+ .getString("label.out_of_memory"),
+ JvOptionPane.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()
+ */
+ @Override
+ protected void finalize() throws Throwable
+ {
+ source = null;
+ alignFrame = null;
+ viewport = null;
+ super.finalize();
+ }
+
+}