X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=bf79fa4c0c0c4fcc4e49db3663f672d18af6dee4;hb=1ef93cb2817f75699773f049b8d25e5b509c2830;hp=3d2ddedfee15fb8180f4a3c86671fa088c831fe0;hpb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 3d2dded..bf79fa4 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -41,6 +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; @@ -73,6 +74,8 @@ public class FileLoader implements Runnable private File selectedFile; + private static boolean useDefaultFileFormat = false; + /** * default constructor always raised errors in GUI dialog boxes */ @@ -95,31 +98,51 @@ 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) { + 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(); + } } /** @@ -271,6 +294,7 @@ public class FileLoader implements Runnable ? "Copied From Clipboard" : file; Runtime rt = Runtime.getRuntime(); + try { if (Desktop.instance != null) @@ -285,7 +309,8 @@ public class FileLoader implements Runnable format = new IdentifyFile().identify(source, false); // identify stream and rewind rather than close } - else if (selectedFile != null) { + else if (selectedFile != null) + { format = new IdentifyFile().identify(selectedFile, protocol); } else @@ -298,7 +323,7 @@ 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()) { @@ -309,6 +334,8 @@ 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 @@ -329,12 +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( + jalview.bin.Console.errPrintln( "IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream."); // We read the data anyway - it might make sense. } // BH 2018 switch to File object here instead of filename - alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile); + alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign( + selectedFile == null ? file : selectedFile); } else { @@ -362,27 +390,29 @@ public class FileLoader implements Runnable file.lastIndexOf(".")); String tempStructureFileStr = createNamedJvTempFile( urlLeafName, structExt); - + // 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); + + al = fa.readFile(tempFile, DataSourceType.FILE, format); source = fa.getAlignFile(); } else { - if (selectedFile == null) { - al = fa.readFile(file, protocol, format); - - } else { - al = fa.readFile(selectedFile, protocol, format); - } + 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. + + // necessary. } } } catch (java.io.IOException ex) @@ -479,12 +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(Cache - .getDefault("SHOW_FULLSCREEN", false)); + alignFrame.setMaximum( + Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { } @@ -518,7 +554,7 @@ public class FileLoader implements Runnable } else { - System.err.println(errorMessage); + jalview.bin.Console.errPrintln(errorMessage); } } } @@ -527,7 +563,7 @@ 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) { @@ -567,7 +603,7 @@ 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(); @@ -586,7 +622,7 @@ 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)"); @@ -595,7 +631,7 @@ 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)"); @@ -607,6 +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; } /** @@ -632,4 +671,26 @@ 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); + } + + public static boolean getUseDefaultFileFormat() + { + return useDefaultFileFormat; + } + }