X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=1fa6957f61a551fa54a591b9812fac82594ddf66;hb=d5acde3c12dac7b95d5623c024054bb4bc9cce1d;hp=3ad74c71ff2bed320f08579b9f1081459f15751f;hpb=483e7163b1fb8d4bcb9393014816c944befce328;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 3ad74c7..1fa6957 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -27,19 +27,28 @@ import jalview.api.FeaturesSourceI; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; +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.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.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; @@ -47,15 +56,35 @@ import javax.swing.SwingUtilities; public class FileLoader implements Runnable { + private File selectedFile; + String file; DataSourceType protocol; FileFormatI format; - AlignmentFileI 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; @@ -86,14 +115,18 @@ public class FileLoader implements Runnable this.raiseGUI = raiseGUI; } - public void LoadFile(AlignViewport viewport, String file, + 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, DataSourceType protocol, + public void loadFile(String file, DataSourceType protocol, FileFormatI format) { this.file = file; @@ -120,7 +153,7 @@ public class FileLoader implements Runnable */ public void LoadFile(String file, DataSourceType protocol) { - LoadFile(file, protocol, null); + loadFile(file, protocol, null); } /** @@ -133,7 +166,7 @@ public class FileLoader implements Runnable public AlignFrame LoadFileWaitTillLoaded(String file, DataSourceType sourceType) { - return LoadFileWaitTillLoaded(file, sourceType, null); + return loadFileWaitTillLoaded(file, sourceType, null); } /** @@ -144,13 +177,26 @@ public class FileLoader implements Runnable * @param format * @return alignFrame constructed from file contents */ - public AlignFrame LoadFileWaitTillLoaded(String file, + public AlignFrame loadFileWaitTillLoaded(String file, DataSourceType sourceType, FileFormatI format) { - this.file = file; - this.protocol = sourceType; - 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(); } /** @@ -160,54 +206,45 @@ public class FileLoader implements Runnable * @param format * @return alignFrame constructed from file contents */ - public AlignFrame LoadFileWaitTillLoaded(AlignmentFileI source, + public AlignFrame loadFileWaitTillLoaded(AlignmentFileReaderI source, FileFormatI format) { - this.source = source; - - file = source.getInFile(); - protocol = source.getDataSourceType(); - 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(); + 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; } + 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; @@ -217,7 +254,7 @@ public class FileLoader implements Runnable while (st.hasMoreTokens()) { - recent.addElement(st.nextElement().toString().trim()); + recent.addElement(st.nextToken().trim()); } } @@ -237,21 +274,22 @@ public class FileLoader implements Runnable if (protocol == DataSourceType.FILE) { - Cache.setProperty("DEFAULT_FILE_FORMAT", format.toString()); + Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName()); } } @Override public void run() { - String title = protocol == DataSourceType.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) { @@ -261,6 +299,9 @@ public class FileLoader implements Runnable 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); @@ -270,16 +311,15 @@ public class FileLoader implements Runnable if (format == null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); System.err.println("The input file \"" + file + "\" has null or unidentifiable data content!"); if (!Jalview.isHeadlessMode()) { - JvOptionPane.showInternalMessageDialog( - Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.getString("label.couldnt_read_data") + " in " + file + "\n" - + AppletFormatAdapter.SUPPORTED_FORMATS, + + AppletFormatAdapter.getSupportedFormats(), MessageManager.getString("label.couldnt_read_data"), JvOptionPane.WARNING_MESSAGE); } @@ -287,7 +327,7 @@ public class FileLoader implements Runnable } // 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 @@ -303,35 +343,69 @@ public class FileLoader implements Runnable 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; - try + String error = AppletFormatAdapter.getSupportedFormats(); + try + { + if (source != null) { - if (source != null) - { - // read from the provided source + // 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) + { + 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); + 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(); } + } catch (java.io.IOException ex) + { + error = ex.getMessage(); + } if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence()) { @@ -348,8 +422,8 @@ public class FileLoader implements Runnable { // register PDB entries with desktop's structure selection // manager - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).registerPDBEntry(pdbe); + Desktop.getStructureSelectionManager() + .registerPDBEntry(pdbe); } } } @@ -371,8 +445,8 @@ public class FileLoader implements Runnable if (source instanceof ComplexAlignFile) { - ColumnSelection colSel = ((ComplexAlignFile) source) - .getColumnSelection(); + HiddenColumns colSel = ((ComplexAlignFile) source) + .getHiddenColumns(); SequenceI[] hiddenSeqs = ((ComplexAlignFile) source) .getHiddenSequences(); String colourSchemeName = ((ComplexAlignFile) source) @@ -384,8 +458,8 @@ public class FileLoader implements Runnable alignFrame.getViewport().setFeaturesDisplayed(fd); alignFrame.getViewport().setShowSequenceFeatures( ((ComplexAlignFile) source).isShowSeqFeatures()); - ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme( - colourSchemeName, al); + ColourSchemeI cs = ColourSchemeMapper + .getJalviewColourScheme(colourSchemeName, al); if (cs != null) { alignFrame.changeColour(cs); @@ -404,15 +478,16 @@ public class FileLoader implements Runnable if (!(protocol == DataSourceType.PASTE)) { alignFrame.setFileName(file, format); + alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS } if (proxyColourScheme != null) { alignFrame.getViewport() .applyFeaturesStyle(proxyColourScheme); } - alignFrame.statusBar.setText(MessageManager.formatMessage( - "label.successfully_loaded_file", - new String[] { title })); + alignFrame.setStatus(MessageManager.formatMessage( + "label.successfully_loaded_file", new String[] + { title })); if (raiseGUI) { @@ -421,14 +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) { } @@ -436,27 +516,25 @@ public class FileLoader implements Runnable } else { - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); } - final String errorMessage = MessageManager - .getString("label.couldnt_load_file") - + " " - + title - + "\n" + error; + 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) + if (raiseGUI && Desktop.getDesktopPane() != null) { javax.swing.SwingUtilities.invokeLater(new Runnable() { @Override public void run() { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - errorMessage, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), + errorMessage, + MessageManager .getString("label.error_loading_file"), JvOptionPane.WARNING_MESSAGE); } @@ -482,11 +560,11 @@ public class FileLoader implements 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.showInternalMessageDialog(Desktop.getDesktopPane(), + MessageManager.formatMessage( + "label.problems_opening_file", new String[] + { file }), + MessageManager.getString("label.file_open_error"), JvOptionPane.WARNING_MESSAGE); } }); @@ -504,11 +582,11 @@ public class FileLoader implements Runnable @Override public void run() { - JvOptionPane.showInternalMessageDialog( - Desktop.desktop, MessageManager.formatMessage( + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), + MessageManager.formatMessage( "warn.out_of_memory_loading_file", new String[] - { file }), MessageManager - .getString("label.out_of_memory"), + { file }), + MessageManager.getString("label.out_of_memory"), JvOptionPane.WARNING_MESSAGE); } }); @@ -526,7 +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) { @@ -548,25 +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 */ - @Override - 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)); } }