X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=49571dc7d1b21bd6697e0088cc9e7424b7da7b78;hb=8a2a0cda7067530f8481c2aec203e18d555f2dfd;hp=c7ade20da180eea51bb50cc66d5e38c92caf4e8f;hpb=892e857760e779796e156b4fa36d97d8d31e73e1;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index c7ade20..49571dc 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -33,8 +33,6 @@ import jalview.api.FeaturesDisplayedI; import jalview.api.FeaturesSourceI; import jalview.bin.Cache; import jalview.bin.Jalview; -import jalview.datamodel.AlignmentAnnotation; -import jalview.datamodel.AlignmentAnnotation.TFType; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; @@ -43,6 +41,7 @@ import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; import jalview.gui.Desktop; import jalview.gui.JvOptionPane; +import jalview.gui.QuitHandler; import jalview.json.binding.biojson.v1.ColourSchemeMapper; import jalview.project.Jalview2XML; import jalview.schemes.ColourSchemeI; @@ -75,8 +74,6 @@ public class FileLoader implements Runnable private File selectedFile; - private AlignmentAnnotation.TFType temperatureFactorType = null; - /** * default constructor always raised errors in GUI dialog boxes */ @@ -99,32 +96,51 @@ public class FileLoader implements Runnable 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; if (file instanceof File) { this.selectedFile = (File) file; file = selectedFile.getPath(); } - LoadFile(file.toString(), protocol, format); + 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(); + } } /** @@ -162,26 +178,9 @@ public class FileLoader implements Runnable public AlignFrame LoadFileWaitTillLoaded(String file, DataSourceType sourceType, FileFormatI format) { - return LoadFileWaitTillLoaded(file, sourceType, format, null); - } - - /** - * Load alignment from (file, protocol) of type format with specified - * temperature factor type and wait till loaded - * - * @param file - * @param sourceType - * @param format - * @param tempfacType - * @return alignFrame constructed from file contents - */ - public AlignFrame LoadFileWaitTillLoaded(String file, - DataSourceType sourceType, FileFormatI format, AlignmentAnnotation.TFType tempfacType) - { this.file = file; this.protocol = sourceType; this.format = format; - this.temperatureFactorType = tempfacType; return _LoadFileWaitTillLoaded(); } @@ -322,7 +321,7 @@ public class FileLoader implements Runnable if (format == null) { Desktop.instance.stopLoading(); - System.err.println("The input file \"" + file + jalview.bin.Console.errPrintln("The input file \"" + file + "\" has null or unidentifiable data content!"); if (!Jalview.isHeadlessMode()) { @@ -333,6 +332,8 @@ public class FileLoader implements Runnable 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 @@ -353,7 +354,7 @@ public class FileLoader implements Runnable if (source != null) { // Tell the user (developer?) that this is going to cause a problem - System.err.println( + jalview.bin.Console.errPrintln( "IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream."); // We read the data anyway - it might make sense. } @@ -400,14 +401,12 @@ public class FileLoader implements Runnable { if (selectedFile == null) { - al = fa.readFile(null, file, protocol, format, - temperatureFactorType); + al = fa.readFile(null, file, protocol, format); } else { - al = fa.readFile(selectedFile, null, protocol, format, - temperatureFactorType); + al = fa.readFile(selectedFile, null, protocol, format); } source = fa.getAlignFile(); // keep reference for later if @@ -508,6 +507,12 @@ 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 @@ -547,7 +552,7 @@ public class FileLoader implements Runnable } else { - System.err.println(errorMessage); + jalview.bin.Console.errPrintln(errorMessage); } } } @@ -556,7 +561,7 @@ public class FileLoader implements Runnable } catch (Exception er) { - System.err.println("Exception whilst opening file '" + file); + jalview.bin.Console.errPrintln("Exception whilst opening file '" + file); er.printStackTrace(); if (raiseGUI) { @@ -596,7 +601,7 @@ public class FileLoader implements Runnable } }); } - System.err.println("Out of memory loading file " + file + "!!"); + jalview.bin.Console.errPrintln("Out of memory loading file " + file + "!!"); } loadtime += System.currentTimeMillis(); @@ -615,7 +620,7 @@ public class FileLoader implements Runnable { AlignmentI al = alignFrame.getViewport().getAlignment(); - System.out.println("Loaded '" + title + "' in " + jalview.bin.Console.outPrintln("Loaded '" + title + "' in " + (loadtime / 1000.0) + "s, took an additional " + (1.0 * memused / (1024.0 * 1024.0)) + " MB (" + al.getHeight() + " seqs by " + al.getWidth() + " cols)"); @@ -624,7 +629,7 @@ public class FileLoader implements Runnable { // report that we didn't load anything probably due to an out of memory // error - System.out.println("Failed to load '" + title + "' in " + jalview.bin.Console.outPrintln("Failed to load '" + title + "' in " + (loadtime / 1000.0) + "s, took an additional " + (1.0 * memused / (1024.0 * 1024.0)) + " MB (alignment is null)"); @@ -636,6 +641,7 @@ public class FileLoader implements Runnable Desktop.instance.stopLoading(); } + this.setShouldBeSaved(); } /** @@ -661,4 +667,21 @@ public class FileLoader implements Runnable return tempStructFile.toString(); } + /* + * set whether quit should ask to save when just loaded this source + */ + 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); + } + }