X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=2a18b0b7ad1d4fd53d2fc165ae264ae5d1a8f511;hb=1b459bcde7bbbd9149b2f94777d7336156861533;hp=f19788b963927d1e80a0ffb2cc56b1ed7031b88c;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index f19788b..2a18b0b 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -1,38 +1,63 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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. - * + * 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 . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; -import java.util.*; - -import javax.swing.*; - -import jalview.datamodel.*; -import jalview.gui.*; +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.HiddenColumns; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; +import jalview.gui.Desktop; +import jalview.gui.JvOptionPane; +import jalview.json.binding.biojson.v1.ColourSchemeMapper; +import jalview.project.Jalview2XML; +import jalview.schemes.ColourSchemeI; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; +import jalview.ws.utils.UrlDownloadClient; + +import java.io.File; +import java.io.IOException; +import java.util.StringTokenizer; +import java.util.Vector; + +import javax.swing.SwingUtilities; public class FileLoader implements Runnable { String file; - String protocol; + DataSourceType protocol; - String format; + FileFormatI format; - FileParse source = null; // alternative specification of where data comes + AlignmentFileReaderI source = null; // alternative specification of where data + // comes // from @@ -66,13 +91,14 @@ public class FileLoader implements Runnable } public void LoadFile(AlignViewport viewport, String file, - String protocol, String format) + 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; @@ -82,6 +108,7 @@ public class FileLoader implements Runnable SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { loader.start(); @@ -95,7 +122,7 @@ public class FileLoader implements Runnable * @param file * @param protocol */ - public void LoadFile(String file, String protocol) + public void LoadFile(String file, DataSourceType protocol) { LoadFile(file, protocol, null); } @@ -104,27 +131,28 @@ public class FileLoader implements Runnable * Load alignment from (file, protocol) and wait till loaded * * @param file - * @param protocol + * @param sourceType * @return alignFrame constructed from file contents */ - public AlignFrame LoadFileWaitTillLoaded(String file, String protocol) + public AlignFrame LoadFileWaitTillLoaded(String file, + DataSourceType sourceType) { - return LoadFileWaitTillLoaded(file, protocol, null); + return LoadFileWaitTillLoaded(file, sourceType, null); } /** * Load alignment from (file, protocol) of type format and wait till loaded * * @param file - * @param protocol + * @param sourceType * @param format * @return alignFrame constructed from file contents */ - public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, - String format) + public AlignFrame LoadFileWaitTillLoaded(String file, + DataSourceType sourceType, FileFormatI format) { this.file = file; - this.protocol = protocol; + this.protocol = sourceType; this.format = format; return _LoadFileWaitTillLoaded(); } @@ -136,11 +164,13 @@ public class FileLoader implements Runnable * @param format * @return alignFrame constructed from file contents */ - public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format) + public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source, + FileFormatI format) { this.source = source; + file = source.getInFile(); - protocol = source.type; + protocol = source.getDataSourceType(); this.format = format; return _LoadFileWaitTillLoaded(); } @@ -172,13 +202,19 @@ public class FileLoader implements Runnable public void updateRecentlyOpened() { Vector recent = new Vector(); - if (protocol.equals(FormatAdapter.PASTE)) + 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.equals(FormatAdapter.FILE) ? "RECENT_FILE" + if (file != null + && file.indexOf(System.getProperty("java.io.tmpdir")) > -1) + { + // ignore files loaded from the system's temporary directory + return; + } + String type = protocol == DataSourceType.FILE ? "RECENT_FILE" : "RECENT_URL"; String historyItems = jalview.bin.Cache.getProperty(type); @@ -207,17 +243,19 @@ public class FileLoader implements Runnable 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.getName()); } } + @Override public void run() { - String title = protocol.equals(AppletFormatAdapter.PASTE) ? "Copied From Clipboard" + String title = protocol == DataSourceType.PASTE + ? "Copied From Clipboard" : file; Runtime rt = Runtime.getRuntime(); try @@ -231,15 +269,31 @@ public class FileLoader implements Runnable // 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 + format = new IdentifyFile().identify(source, false); + // identify stream and rewind rather than close } else { - format = new IdentifyFile().Identify(file, protocol); + 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) @@ -252,83 +306,159 @@ public class FileLoader implements Runnable // load } loadtime = -System.currentTimeMillis(); - Alignment al = null; + AlignmentI al = null; - if (format.equalsIgnoreCase("Jalview")) + 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."); + 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); + alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file); } else { - String error = AppletFormatAdapter.SUPPORTED_FORMATS; - if (FormatAdapter.isValidFormat(format)) + String error = AppletFormatAdapter.getSupportedFormats(); + try { - try + if (source != null) { - 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(); + boolean downloadStructureFile = format.isStructureFile() + && protocol.equals(DataSourceType.URL); + if (downloadStructureFile) { - // read from the provided source - al = new FormatAdapter().readFromFile(source, format); + String structExt = format.getExtensions().split(",")[0]; + String urlLeafName = file.substring( + file.lastIndexOf( + System.getProperty("file.separator")), + file.lastIndexOf(".")); + String tempStructureFileStr = createNamedJvTempFile( + urlLeafName, structExt); + UrlDownloadClient.download(file, tempStructureFileStr); + al = fa.readFile(tempStructureFileStr, DataSourceType.FILE, + format); + source = fa.getAlignFile(); } 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. + source = fa.getAlignFile(); // keep reference for later if + // necessary. } - } catch (java.io.IOException ex) - { - error = ex.getMessage(); } + } catch (java.io.IOException ex) + { + error = ex.getMessage(); } - else + + if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence()) { - if (format != null && format.length() > 7) + // 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) + { + HiddenColumns colSel = ((ComplexAlignFile) source) + .getHiddenColumns(); + 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)); + alignFrame.setMaximum(jalview.bin.Cache + .getDefault("SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { } @@ -341,17 +471,22 @@ public class FileLoader implements Runnable Desktop.instance.stopLoading(); } - final String errorMessage = "Couldn't load file " + title + "\n" - + error; - if (raiseGUI) + 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() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - errorMessage, "Error loading file", - JOptionPane.WARNING_MESSAGE); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + errorMessage, + MessageManager + .getString("label.error_loading_file"), + JvOptionPane.WARNING_MESSAGE); } }); } @@ -372,12 +507,15 @@ public class FileLoader implements Runnable { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - javax.swing.JOptionPane.showInternalMessageDialog( - Desktop.desktop, "Encountered problems opening " + file - + "!!", "File open error", - javax.swing.JOptionPane.WARNING_MESSAGE); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.problems_opening_file", new String[] + { file }), + MessageManager.getString("label.file_open_error"), + JvOptionPane.WARNING_MESSAGE); } }); } @@ -391,17 +529,15 @@ public class FileLoader implements Runnable { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override 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); + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.formatMessage( + "warn.out_of_memory_loading_file", new String[] + { file }), + MessageManager.getString("label.out_of_memory"), + JvOptionPane.WARNING_MESSAGE); } }); } @@ -447,17 +583,27 @@ public class FileLoader implements Runnable } - /* - * (non-Javadoc) + /** + * This method creates the file - + * {tmpdir}/jalview/{current_timestamp}/fileName.exetnsion using the supplied + * file name and extension * - * @see java.lang.Object#finalize() + * @param fileName + * the name of the temp file to be created + * @param extension + * the extension of the temp file to be created + * @return */ - protected void finalize() throws Throwable + private static String createNamedJvTempFile(String fileName, + String extension) throws IOException { - source = null; - alignFrame = null; - viewport = null; - super.finalize(); + String seprator = System.getProperty("file.separator"); + String jvTempDir = System.getProperty("java.io.tmpdir") + "jalview" + + seprator + System.currentTimeMillis(); + File tempStructFile = new File( + jvTempDir + seprator + fileName + "." + extension); + tempStructFile.mkdirs(); + return tempStructFile.toString(); } }