X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=bd8bc534e718429ac4a2b840343120a1ee0f5e43;hb=10eedfb43dacd4cf32d4b5fe27d8d5987c70eaf8;hp=9ac56b5334f1064e552de1c3687ed502466b20d1;hpb=dc1ad37588e94cbc9ebbfaab2e9e49407f464310;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 9ac56b5..bd8bc53 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -21,7 +21,10 @@ 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; @@ -31,26 +34,30 @@ 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 jalview.ws.utils.UrlDownloadClient; +import java.io.File; +import java.io.IOException; import java.util.StringTokenizer; import java.util.Vector; -import javax.swing.JOptionPane; 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 @@ -84,13 +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; @@ -100,6 +108,7 @@ public class FileLoader implements Runnable SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { loader.start(); @@ -113,7 +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); } @@ -122,27 +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(); } @@ -154,12 +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(); } @@ -191,13 +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); @@ -226,17 +243,18 @@ 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 @@ -250,32 +268,30 @@ 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 || format.equalsIgnoreCase("EMPTY DATA FILE")) + 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( + JvOptionPane.showInternalMessageDialog( Desktop.desktop, MessageManager.getString("label.couldnt_read_data") + " in " + file + "\n" - + AppletFormatAdapter.SUPPORTED_FORMATS, + + AppletFormatAdapter.getSupportedFormats(), MessageManager.getString("label.couldnt_read_data"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } return; } @@ -292,7 +308,7 @@ public class FileLoader implements Runnable loadtime = -System.currentTimeMillis(); AlignmentI al = null; - if (format.equalsIgnoreCase("Jalview")) + if (FileFormat.Jalview.equals(format)) { if (source != null) { @@ -305,37 +321,40 @@ public class FileLoader implements Runnable } 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) - { - // 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. + // 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]; + String urlLeafName = file.substring(file.lastIndexOf(System + .getProperty("file.separator")), file + .lastIndexOf(".")); + String tempStructureFileStr = createNamedJvTempFile( + urlLeafName, structExt); + UrlDownloadClient.download(file, tempStructureFileStr); + file = tempStructureFileStr; + protocol = DataSourceType.FILE; } - } catch (java.io.IOException ex) - { - error = ex.getMessage(); + al = fa.readFile(file, protocol, format); + source = fa.getAlignFile(); // keep reference for later if + // necessary. } - } - 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) && al.hasValidSequence()) @@ -359,8 +378,14 @@ public class FileLoader implements Runnable } } + FeatureSettingsModelI proxyColourScheme = source + .getFeatureColourScheme(); if (viewport != null) { + if (proxyColourScheme != null) + { + viewport.applyFeaturesStyle(proxyColourScheme); + } // append to existing alignment viewport.addAlignment(al, title); } @@ -374,18 +399,15 @@ public class FileLoader implements Runnable .getColumnSelection(); SequenceI[] hiddenSeqs = ((ComplexAlignFile) source) .getHiddenSequences(); - boolean showSeqFeatures = ((ComplexAlignFile) source) - .isShowSeqFeatures(); String colourSchemeName = ((ComplexAlignFile) source) .getGlobalColourScheme(); FeaturesDisplayedI fd = ((ComplexAlignFile) source) .getDisplayedFeatures(); alignFrame = new AlignFrame(al, hiddenSeqs, colSel, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - - alignFrame.getViewport().setShowSequenceFeatures( - showSeqFeatures); alignFrame.getViewport().setFeaturesDisplayed(fd); + alignFrame.getViewport().setShowSequenceFeatures( + ((ComplexAlignFile) source).isShowSeqFeatures()); ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme( colourSchemeName, al); if (cs != null) @@ -397,13 +419,21 @@ public class FileLoader implements Runnable { 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.equals(AppletFormatAdapter.PASTE)) + 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 })); @@ -446,12 +476,13 @@ public class FileLoader implements Runnable { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - JOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, errorMessage, MessageManager .getString("label.error_loading_file"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } @@ -472,14 +503,15 @@ public class FileLoader implements Runnable { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - javax.swing.JOptionPane.showInternalMessageDialog( + JvOptionPane.showInternalMessageDialog( Desktop.desktop, MessageManager.formatMessage( "label.problems_opening_file", new String[] { file }), MessageManager .getString("label.file_open_error"), - javax.swing.JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); } }); } @@ -493,14 +525,15 @@ public class FileLoader implements Runnable { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - javax.swing.JOptionPane.showInternalMessageDialog( + JvOptionPane.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.WARNING_MESSAGE); } }); } @@ -546,11 +579,35 @@ public class FileLoader implements Runnable } + /** + * This method creates the file - + * {tmpdir}/jalview/{current_timestamp}/fileName.exetnsion using the supplied + * file name and extension + * + * @param fileName + * the name of the temp file to be created + * @param extension + * the extension of the temp file to be created + * @return + */ + private static String createNamedJvTempFile(String fileName, + String extension) throws IOException + { + 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(); + } + /* * (non-Javadoc) * * @see java.lang.Object#finalize() */ + @Override protected void finalize() throws Throwable { source = null;