X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=b16c37f83ce16b5e3088d9443e3a865d3d133947;hb=efee78d45ceeb879d98fedd399a71d84a5ecd5f8;hp=eda3899a13306555a3c15bc0fa13cdb268bd2415;hpb=c945c9641de88cad01b09b3db19e45667dfe751e;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index eda3899..b16c37f 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; @@ -33,27 +40,15 @@ 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.BufferedReader; -import java.io.ByteArrayInputStream; -import java.io.File; -import java.io.FileNotFoundException; -import java.io.FileReader; -import java.io.IOException; -import java.io.InputStream; -import java.io.InputStreamReader; -import java.util.StringTokenizer; -import java.util.Vector; - -import javax.swing.SwingUtilities; - public class FileLoader implements Runnable { String file; @@ -79,6 +74,8 @@ public class FileLoader implements Runnable private File selectedFile; + private static boolean useDefaultFileFormat = false; + /** * default constructor always raised errors in GUI dialog boxes */ @@ -101,31 +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(); + } } /** @@ -170,6 +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 @@ -196,6 +231,7 @@ public class FileLoader implements Runnable protected AlignFrame _LoadFileWaitTillLoaded() { this.run(); + return alignFrame; } @@ -258,6 +294,7 @@ public class FileLoader implements Runnable ? "Copied From Clipboard" : file; Runtime rt = Runtime.getRuntime(); + try { if (Desktop.instance != null) @@ -272,7 +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 @@ -285,9 +323,9 @@ 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()) + if (!Jalview.isHeadlessMode() && !Jalview.isBatchMode()) { JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.couldnt_read_data") @@ -296,6 +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 @@ -316,11 +356,14 @@ 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. } - alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file); + // BH 2018 switch to File object here instead of filename + alignFrame = new Jalview2XML(raiseGUI && !Jalview.isBatchMode()) + .loadJalviewAlign( + selectedFile == null ? file : selectedFile); } else { @@ -348,22 +391,29 @@ public class FileLoader implements Runnable file.lastIndexOf(".")); String tempStructureFileStr = createNamedJvTempFile( urlLeafName, structExt); - UrlDownloadClient.download(file, tempStructureFileStr); - al = fa.readFile(tempStructureFileStr, DataSourceType.FILE, - format); + + // 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(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) @@ -397,12 +447,9 @@ 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 { @@ -443,13 +490,14 @@ 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( + alignFrame.setStatus(MessageManager.formatMessage( "label.successfully_loaded_file", new String[] { title })); @@ -462,12 +510,18 @@ 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) { } @@ -484,7 +538,7 @@ public class FileLoader implements Runnable "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 && !Jalview.isBatchMode() && Desktop.desktop != null) { javax.swing.SwingUtilities.invokeLater(new Runnable() { @@ -501,7 +555,7 @@ public class FileLoader implements Runnable } else { - System.err.println(errorMessage); + jalview.bin.Console.errPrintln(errorMessage); } } } @@ -510,9 +564,10 @@ 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) + if (raiseGUI && !Jalview.isBatchMode()) { javax.swing.SwingUtilities.invokeLater(new Runnable() { @@ -534,7 +589,7 @@ public class FileLoader implements Runnable er.printStackTrace(); alignFrame = null; - if (raiseGUI) + if (raiseGUI && !Jalview.isBatchMode()) { javax.swing.SwingUtilities.invokeLater(new Runnable() { @@ -550,7 +605,8 @@ 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(); @@ -569,7 +625,7 @@ 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)"); @@ -578,7 +634,7 @@ 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)"); @@ -590,6 +646,9 @@ public class FileLoader implements Runnable Desktop.instance.stopLoading(); } + this.setShouldBeSaved(); + // after first file loaded we revert to assuming a default file format + useDefaultFileFormat = true; } /** @@ -615,21 +674,34 @@ public class FileLoader implements Runnable return tempStructFile.toString(); } - /** - * - * @param file a File, or a String which is a name of a file - * @return - * @throws FileNotFoundException + /* + * set whether quit should ask to save when just loaded this source */ - @SuppressWarnings("unused") - public static BufferedReader getBuffereReader(Object file) throws FileNotFoundException { - if (file instanceof String) - return new BufferedReader(new FileReader((String) file)); - - byte[] bytes = /** @j2sNative file._bytes || */ null; - if (bytes != null) - return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes))); - return new BufferedReader(new FileReader((File) file)); + private void setShouldBeSaved() + { + if (protocol == null) + return; + AlignFrame af = this.alignFrame; + if (af == null) + return; + AlignViewport avp = af.getViewport(); + if (avp == null) + return; + boolean upToDate = !protocol.isDynamic(); + if (protocol.isUrl() && !Cache + .getDefault(PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS, true)) + { + upToDate = true; + } + avp.setSavedUpToDate(upToDate, + upToDate ? null : QuitHandler.Message.UNSAVED_ALIGNMENTS); + } + + public static final String PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS = "PROMPT_SAVE_UNCHANGED_URL_ALIGNMENTS"; + + public static boolean getUseDefaultFileFormat() + { + return useDefaultFileFormat; } }