X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=88f9ae5743f8895fc620859b529310ef3b9f0c18;hb=230fac58c5afe1843bf7177834fe1bd1d7e6f9d5;hp=6310cc456573b37a7ddc8aa70c6f9ea932daf965;hpb=a4fca83856b96df2fe8701bb5cc14c8d1d0a6b09;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 6310cc4..88f9ae5 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -1,48 +1,100 @@ /* - * 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.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.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.JOptionPane; +import javax.swing.SwingUtilities; + +public class FileLoader implements Runnable +{ + String file; -import javax.swing.*; + DataSourceType protocol; -import jalview.datamodel.*; -import jalview.gui.*; + FileFormatI format; + + AlignmentFileI source = null; // alternative specification of where data comes + + // from -public class FileLoader - implements Runnable -{ - String file; - String protocol; - String format; 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, + DataSourceType protocol, FileFormatI format) { this.viewport = viewport; LoadFile(file, protocol, format); } - public void LoadFile(String file, String protocol, String format) + public void LoadFile(String file, DataSourceType protocol, + FileFormatI format) { this.file = file; this.protocol = protocol; @@ -52,6 +104,7 @@ public class FileLoader SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { loader.start(); @@ -59,13 +112,73 @@ public class FileLoader }); } - public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, - String format) + /** + * 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 = protocol; + 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(AlignmentFileI 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(); @@ -74,9 +187,9 @@ public class FileLoader try { Thread.sleep(500); + } catch (Exception ex) + { } - catch (Exception ex) - {} } return alignFrame; @@ -85,9 +198,14 @@ public class FileLoader public void updateRecentlyOpened() { Vector recent = new Vector(); - - String type = protocol.equals(FormatAdapter.FILE) - ? "RECENT_FILE" : "RECENT_URL"; + 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); @@ -115,87 +233,203 @@ 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)) + if (protocol == DataSourceType.FILE) { - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format); + Cache.setProperty("DEFAULT_FILE_FORMAT", format.toString()); } } + @Override public void run() { - String title = protocol.equals(AppletFormatAdapter.PASTE) - ? "Copied From Clipboard" : file; - + 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); + } + + } - Alignment al = null; + if (format == null) + { + Desktop.instance.stopLoading(); + System.err.println("The input file \"" + file + + "\" has null or unidentifiable data content!"); + if (!Jalview.isHeadlessMode()) + { + javax.swing.JOptionPane.showInternalMessageDialog( + Desktop.desktop, + MessageManager.getString("label.couldnt_read_data") + + " in " + file + "\n" + + AppletFormatAdapter.SUPPORTED_FORMATS, + MessageManager.getString("label.couldnt_read_data"), + JOptionPane.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 (format.equalsIgnoreCase("Jalview")) + if (format == FileFormat.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) + + if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence()) + { + // construct and register dataset sequences + for (SequenceI sq : al.getSequences()) { - // ad hoc message in format. - error = format +"\n"+error; + 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); + } + } } - } - if ( (al != null) && (al.getHeight() > 0)) - { + FeatureSettingsModelI proxyColourScheme = source + .getFeatureColourScheme(); if (viewport != null) { - for (int i = 0; i < al.getHeight(); i++) + if (proxyColourScheme != null) { - viewport.getAlignment().addSequence(al.getSequenceAt(i)); + viewport.applyFeaturesStyle(proxyColourScheme); } - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - + // 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 (!protocol.equals(AppletFormatAdapter.PASTE)) + 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 })); - 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 { alignFrame.setMaximum(jalview.bin.Cache.getDefault( - "SHOW_FULLSCREEN", false)); - } - catch (java.beans.PropertyVetoException ex) + "SHOW_FULLSCREEN", false)); + } catch (java.beans.PropertyVetoException ex) { } } @@ -207,46 +441,113 @@ 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 = 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) { - public void run() + javax.swing.SwingUtilities.invokeLater(new Runnable() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - errorMessage, - "Error loading file", - JOptionPane.WARNING_MESSAGE); - } - }); + @Override + 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() + { + @Override + 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); - } - }); + @Override + 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 +555,18 @@ public class FileLoader } + /* + * (non-Javadoc) + * + * @see java.lang.Object#finalize() + */ + @Override + protected void finalize() throws Throwable + { + source = null; + alignFrame = null; + viewport = null; + super.finalize(); + } + }