X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=9ede0f55d69b2d3e54d49167bcb6d988aaafa64e;hb=3bf2b5ea57b1d77d6e2e7adc11a50387e5376dc0;hp=8b753e695f89700efa8b4524ab568d65e8e40dac;hpb=c4e4696dec425130ba431f458ce7acf204448641;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 8b753e6..9ede0f5 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -20,6 +20,13 @@ */ package jalview.io; +import java.io.File; +import java.io.IOException; +import java.util.StringTokenizer; +import java.util.Vector; + +import javax.swing.SwingUtilities; + import jalview.api.ComplexAlignFile; import jalview.api.FeatureSettingsModelI; import jalview.api.FeaturesDisplayedI; @@ -27,27 +34,21 @@ 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.gui.QuitHandler; 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; @@ -71,6 +72,10 @@ public class FileLoader implements Runnable boolean raiseGUI = true; + private File selectedFile; + + private static boolean useDefaultFileFormat = false; + /** * default constructor always raised errors in GUI dialog boxes */ @@ -90,30 +95,54 @@ 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) { + LoadFile(viewport, file, protocol, format, true); + } + + public void LoadFile(AlignViewport viewport, Object file, + DataSourceType protocol, FileFormatI format, boolean async) + { this.viewport = viewport; - LoadFile(file, protocol, format); + if (file instanceof File) + { + this.selectedFile = (File) file; + file = selectedFile.getPath(); + } + LoadFile(file.toString(), protocol, format, async); } public void LoadFile(String file, DataSourceType protocol, FileFormatI format) { + LoadFile(file, protocol, format, true); + } + + public void LoadFile(String file, DataSourceType protocol, + FileFormatI format, boolean async) + { this.file = file; this.protocol = protocol; this.format = format; - final Thread loader = new Thread(this); - - SwingUtilities.invokeLater(new Runnable() + if (async) { - @Override - public void run() + final Thread loader = new Thread(this); + + SwingUtilities.invokeLater(new Runnable() { - loader.start(); - } - }); + @Override + public void run() + { + loader.start(); + } + }); + } + else + { + this.run(); + } } /** @@ -158,6 +187,24 @@ public class FileLoader implements Runnable } /** + * 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) + { + this.selectedFile = file; + this.file = file.getPath(); + this.protocol = sourceType; + this.format = format; + return _LoadFileWaitTillLoaded(); + } + + /** * Load alignment from FileParse source of type format and wait till loaded * * @param source @@ -176,42 +223,37 @@ public class FileLoader implements Runnable } /** - * 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() { - 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; @@ -221,7 +263,7 @@ public class FileLoader implements Runnable while (st.hasMoreTokens()) { - recent.addElement(st.nextElement().toString().trim()); + recent.addElement(st.nextToken().trim()); } } @@ -248,9 +290,11 @@ public class FileLoader implements Runnable @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) @@ -265,6 +309,10 @@ 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); @@ -279,14 +327,15 @@ public class FileLoader implements Runnable + "\" has null or unidentifiable data content!"); if (!Jalview.isHeadlessMode()) { - JvOptionPane.showInternalMessageDialog( - Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.couldnt_read_data") + " in " + file + "\n" + AppletFormatAdapter.getSupportedFormats(), MessageManager.getString("label.couldnt_read_data"), JvOptionPane.WARNING_MESSAGE); } + // don't set shouldBeSaved if didn't load anything + // this.setShouldBeSaved(); return; } // TODO: cache any stream datasources as a temporary file (eg. PDBs @@ -307,11 +356,13 @@ 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 + alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign( + selectedFile == null ? file : selectedFile); } else { @@ -333,18 +384,36 @@ public class FileLoader implements Runnable if (downloadStructureFile) { String structExt = format.getExtensions().split(",")[0]; - String urlLeafName = file.substring(file.lastIndexOf(System - .getProperty("file.separator")), file - .lastIndexOf(".")); + 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; + + // BH - switching to File object here so as to hold + // ._bytes array directly + File tempFile = new File(tempStructureFileStr); + UrlDownloadClient.download(file, tempFile); + + al = fa.readFile(tempFile, DataSourceType.FILE, format); + source = fa.getAlignFile(); + } + else + { + if (selectedFile == null) + { + al = fa.readFile(null, file, protocol, format); + + } + else + { + al = fa.readFile(selectedFile, null, protocol, format); + } + source = fa.getAlignFile(); // keep reference for later if + + // necessary. } - al = fa.readFile(file, protocol, format); - source = fa.getAlignFile(); // keep reference for later if - // necessary. } } catch (java.io.IOException ex) { @@ -366,8 +435,9 @@ public class FileLoader implements Runnable { // register PDB entries with desktop's structure selection // manager - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).registerPDBEntry(pdbe); + StructureSelectionManager + .getStructureSelectionManager(Desktop.instance) + .registerPDBEntry(pdbe); } } } @@ -376,12 +446,9 @@ public class FileLoader implements Runnable .getFeatureColourScheme(); if (viewport != null) { - if (proxyColourScheme != null) - { - viewport.applyFeaturesStyle(proxyColourScheme); - } // append to existing alignment viewport.addAlignment(al, title); + viewport.applyFeaturesStyle(proxyColourScheme); } else { @@ -389,8 +456,8 @@ 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) @@ -402,8 +469,8 @@ 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); @@ -422,15 +489,16 @@ 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) { @@ -441,12 +509,18 @@ public class FileLoader implements Runnable // that perform queries to find the 'current working alignment' Desktop.addInternalFrame(alignFrame, title, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + + /* + * for an Overview automatically opened with alignment, + * set its title now alignFrame title has been set + */ + alignFrame.alignPanel.setOverviewTitle(alignFrame); } try { - alignFrame.setMaximum(jalview.bin.Cache.getDefault( - "SHOW_FULLSCREEN", false)); + alignFrame.setMaximum( + Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { } @@ -459,11 +533,8 @@ public class FileLoader implements Runnable Desktop.instance.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) @@ -474,7 +545,8 @@ public class FileLoader implements Runnable public void run() { JvOptionPane.showInternalMessageDialog(Desktop.desktop, - errorMessage, MessageManager + errorMessage, + MessageManager .getString("label.error_loading_file"), JvOptionPane.WARNING_MESSAGE); } @@ -500,11 +572,11 @@ 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.desktop, + MessageManager.formatMessage( + "label.problems_opening_file", new String[] + { file }), + MessageManager.getString("label.file_open_error"), JvOptionPane.WARNING_MESSAGE); } }); @@ -522,11 +594,11 @@ public class FileLoader implements Runnable @Override public void run() { - JvOptionPane.showInternalMessageDialog( - Desktop.desktop, MessageManager.formatMessage( + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + 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); } }); @@ -571,6 +643,9 @@ public class FileLoader implements Runnable Desktop.instance.stopLoading(); } + this.setShouldBeSaved(); + // after first file loaded we revert to assuming a default file format + useDefaultFileFormat = true; } /** @@ -590,24 +665,32 @@ public class FileLoader implements Runnable 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); + File tempStructFile = new File( + jvTempDir + seprator + fileName + "." + extension); tempStructFile.mkdirs(); return tempStructFile.toString(); } /* - * (non-Javadoc) - * - * @see java.lang.Object#finalize() + * set whether quit should ask to save when just loaded this source */ - @Override - protected void finalize() throws Throwable + private void setShouldBeSaved() + { + if (protocol == null) + return; + AlignFrame af = this.alignFrame; + if (af == null) + return; + AlignViewport avp = af.getViewport(); + if (avp == null) + return; + avp.setSavedUpToDate(!protocol.isDynamic(), + QuitHandler.Message.UNSAVED_ALIGNMENTS); + } + + public static boolean getUseDefaultFileFormat() { - source = null; - alignFrame = null; - viewport = null; - super.finalize(); + return useDefaultFileFormat; } }