X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=1fa6957f61a551fa54a591b9812fac82594ddf66;hb=d5acde3c12dac7b95d5623c024054bb4bc9cce1d;hp=6329f5895714b0d4937284edd9111c76c3d15462;hpb=7ce1382b998c007a78c9b33a3dc331e966eebc4b;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 6329f58..1fa6957 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -20,33 +20,71 @@ */ 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.HiddenColumns; 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.gui.JvOptionPane; +import jalview.json.binding.biojson.v1.ColourSchemeMapper; +import jalview.project.Jalview2XML; +import jalview.schemes.ColourSchemeI; import jalview.util.MessageManager; - +import jalview.util.Platform; +import jalview.ws.utils.UrlDownloadClient; + +import java.awt.Dimension; +import java.io.BufferedReader; +import java.io.ByteArrayInputStream; +import java.io.File; +import java.io.FileNotFoundException; +import java.io.FileReader; +import java.io.IOException; +import java.io.InputStreamReader; import java.util.StringTokenizer; import java.util.Vector; -import javax.swing.JOptionPane; import javax.swing.SwingUtilities; public class FileLoader implements Runnable { + private File selectedFile; + String file; - String protocol; + DataSourceType protocol; - String format; + FileFormatI format; - FileParse source = null; // alternative specification of where data comes + AlignmentFileReaderI source; // alternative specification of where data + // comes from - // from + /** + * It is critical that all these fields are set, as this instance is reused. + * + * @param source + * @param file + * @param inFile + * @param dataSourceType + * @param format + */ + private void setFileFields(AlignmentFileReaderI source, File file, + String inFile, DataSourceType dataSourceType, FileFormatI format) + { + this.source = source; + this.file = inFile; + this.selectedFile = file; + this.protocol = dataSourceType; + this.format = format; + } AlignViewport viewport; @@ -77,14 +115,19 @@ public class FileLoader implements Runnable this.raiseGUI = raiseGUI; } - public void LoadFile(AlignViewport viewport, String file, - String protocol, String format) + public void loadFile(AlignViewport viewport, Object file, + DataSourceType protocol, FileFormatI format) { this.viewport = viewport; - LoadFile(file, protocol, format); + if (file instanceof File) { + this.selectedFile = (File) file; + file = selectedFile.getPath(); + } + loadFile(file.toString(), 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; @@ -94,6 +137,7 @@ public class FileLoader implements Runnable SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { loader.start(); @@ -107,38 +151,52 @@ 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); + loadFile(file, protocol, null); } /** * 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.format = format; - return _LoadFileWaitTillLoaded(); + setFileFields(null, null, file, sourceType, format); + return _loadFileWaitTillLoaded(); + } + + /** + * 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(File file, + DataSourceType sourceType, FileFormatI format) + { + setFileFields(null, file, null, sourceType, format); + return _loadFileWaitTillLoaded(); } /** @@ -148,53 +206,45 @@ 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; - this.format = format; - return _LoadFileWaitTillLoaded(); + setFileFields(source, null, source.getInFile(), + source.getDataSourceType(), format); + return _loadFileWaitTillLoaded(); } /** - * start thread and wait until finished, then return the alignFrame that's - * (hopefully) been read. + * runs the 'run' method (in this thread), then return the alignFrame that's + * (hopefully) been read * * @return */ - protected AlignFrame _LoadFileWaitTillLoaded() + private AlignFrame _loadFileWaitTillLoaded() { - Thread loader = new Thread(this); - loader.start(); - - while (loader.isAlive()) - { - try - { - Thread.sleep(500); - } catch (Exception ex) - { - } - } - + this.run(); return alignFrame; } public void updateRecentlyOpened() { - Vector recent = new Vector(); - if (protocol.equals(FormatAdapter.PASTE)) + 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.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); + String historyItems = Cache.getProperty(type); StringTokenizer st; @@ -204,7 +254,7 @@ public class FileLoader implements Runnable while (st.hasMoreTokens()) { - recent.addElement(st.nextElement().toString().trim()); + recent.addElement(st.nextToken().trim()); } } @@ -220,43 +270,64 @@ 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 { - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.startLoading(file); + Desktop.getInstance().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 + format = new IdentifyFile().identify(source, false); + // identify stream and rewind rather than close + } + else if (selectedFile != null) { + format = new IdentifyFile().identify(selectedFile, protocol); } else { - format = new IdentifyFile().Identify(file, protocol); + format = new IdentifyFile().identify(file, protocol); + } + + } + + if (format == null) + { + Desktop.getInstance().stopLoading(); + System.err.println("The input file \"" + file + + "\" has null or unidentifiable data content!"); + if (!Jalview.isHeadlessMode()) + { + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), + 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()) + if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage()) { System.gc(); memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free @@ -267,93 +338,156 @@ public class FileLoader implements Runnable loadtime = -System.currentTimeMillis(); 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); + // BH 2018 switch to File object here instead of filename + Platform.timeCheck(null, Platform.TIME_MARK); + alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile); + Platform.timeCheck("JVP loaded", Platform.TIME_MARK); + } else { - String error = AppletFormatAdapter.SUPPORTED_FORMATS; - if (FormatAdapter.isValidFormat(format)) + String error = AppletFormatAdapter.getSupportedFormats(); + try { - try + if (source != null) + { + // read from the provided source + al = new FormatAdapter().readFromFile(source, format); + } + else { - if (source != null) + + // 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]; + int pt = file.lastIndexOf(file.indexOf('/') >= 0 ? "/" + : System.getProperty("file.separator")); + String urlLeafName = file.substring(pt, + file.lastIndexOf(".")); + String tempStructureFileStr = createNamedJvTempFile( + urlLeafName, structExt); + + // BH - switching to File object here so as to hold + // .秘bytes array directly + File tempFile = new File(tempStructureFileStr); + UrlDownloadClient.download(file, tempFile); + + al = fa.readFile(tempFile, 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.getAlignFile(); // keep reference for later if necessary. + if (selectedFile == null) { + al = fa.readFile(file, protocol, format); + + } else { + al = fa.readFile(selectedFile, protocol, format); + } + source = fa.getAlignFile(); // keep reference for later if + + // necessary. } - } catch (java.io.IOException ex) - { - error = ex.getMessage(); } - } - else + } catch (java.io.IOException ex) { - if (format != null && format.length() > 7) - { - // ad hoc message in format. - error = format + "\n" + error; - } + error = ex.getMessage(); } - if ((al != null) && (al.getHeight() > 0)) + 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.getPDBId() != null) + if (sq.getAllPDBEntries() != null) { - for (PDBEntry pdbe : sq.getPDBId()) + for (PDBEntry pdbe : sq.getAllPDBEntries()) { - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).registerPDBEntry(pdbe); + // register PDB entries with desktop's structure selection + // manager + Desktop.getStructureSelectionManager() + .registerPDBEntry(pdbe); } } } + + FeatureSettingsModelI proxyColourScheme = source + .getFeatureColourScheme(); if (viewport != null) { + if (proxyColourScheme != null) + { + viewport.applyFeaturesStyle(proxyColourScheme); + } + // append to existing alignment viewport.addAlignment(al, title); } else { - alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + // otherwise construct the alignFrame - alignFrame.statusBar.setText(MessageManager.formatMessage( - "label.successfully_loaded_file", new String[] - { title })); - - if (!protocol.equals(AppletFormatAdapter.PASTE)) + if (source instanceof ComplexAlignFile) { - alignFrame.setFileName(file, format); + 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); + } } - if (source instanceof HtmlFile) + else { - ((HtmlFile) source).applySettingsToAlignFrame(alignFrame); + alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + if (source instanceof FeaturesSourceI) + { + alignFrame.getViewport().setShowSequenceFeatures(true); + } } - else if (source instanceof JSONFile) + // add metadata and update ui + if (!(protocol == DataSourceType.PASTE)) { - ((JSONFile) source).applySettingsToAlignFrame(alignFrame); + alignFrame.setFileName(file, format); + alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS } + if (proxyColourScheme != null) + { + alignFrame.getViewport() + .applyFeaturesStyle(proxyColourScheme); + } + alignFrame.setStatus(MessageManager.formatMessage( + "label.successfully_loaded_file", new String[] + { title })); if (raiseGUI) { @@ -362,14 +496,19 @@ public class FileLoader implements Runnable // 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, + + + Dimension dim = Platform.getDimIfEmbedded(alignFrame, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + alignFrame.setSize(dim); + Desktop.addInternalFrame(alignFrame, title, dim.width, + dim.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) { } @@ -377,23 +516,27 @@ public class FileLoader implements Runnable } else { - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().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.getDesktopPane() != null) { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - errorMessage, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), + errorMessage, + MessageManager .getString("label.error_loading_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } @@ -414,14 +557,15 @@ public class FileLoader implements Runnable { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - javax.swing.JOptionPane.showInternalMessageDialog( - Desktop.desktop, MessageManager.formatMessage( + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), + MessageManager.formatMessage( "label.problems_opening_file", new String[] - { file }), MessageManager - .getString("label.file_open_error"), - javax.swing.JOptionPane.WARNING_MESSAGE); + { file }), + MessageManager.getString("label.file_open_error"), + JvOptionPane.WARNING_MESSAGE); } }); } @@ -435,14 +579,15 @@ public class FileLoader implements Runnable { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @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); + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), + MessageManager.formatMessage( + "warn.out_of_memory_loading_file", new String[] + { file }), + MessageManager.getString("label.out_of_memory"), + JvOptionPane.WARNING_MESSAGE); } }); } @@ -459,7 +604,7 @@ public class FileLoader implements Runnable // memory // after // load - if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage()) + if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage()) { if (alignFrame != null) { @@ -481,24 +626,53 @@ public class FileLoader implements Runnable } } // remove the visual delay indicator - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); } } - /* - * (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(); + } + + /** + * + * @param file a File, or a String which is a name of a file + * @return + * @throws FileNotFoundException + */ + public static BufferedReader getBufferedReader(Object file) throws FileNotFoundException { + if (file instanceof String) + { + return new BufferedReader(new FileReader((String) file)); + } + byte[] bytes = Platform.getFileBytes((File) file); + if (bytes != null) + { + return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes))); + } + return new BufferedReader(new FileReader((File) file)); } }