X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=9ede0f55d69b2d3e54d49167bcb6d988aaafa64e;hb=3bf2b5ea57b1d77d6e2e7adc11a50387e5376dc0;hp=9dd740b3a470d2363b49acb823a5183d4c5cf8fc;hpb=c5fc6f81bb87ee53a081ed9d0ec452c051da2e70;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 9dd740b..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; @@ -33,21 +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.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 @@ -184,6 +231,7 @@ public class FileLoader implements Runnable protected AlignFrame _LoadFileWaitTillLoaded() { this.run(); + return alignFrame; } @@ -246,6 +294,7 @@ public class FileLoader implements Runnable ? "Copied From Clipboard" : file; Runtime rt = Runtime.getRuntime(); + try { if (Desktop.instance != null) @@ -260,6 +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); @@ -281,6 +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 @@ -305,7 +360,9 @@ public class FileLoader implements Runnable "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 { @@ -333,16 +390,29 @@ 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 { - al = fa.readFile(file, 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) @@ -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 { @@ -422,13 +489,14 @@ 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 })); @@ -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) { } @@ -569,6 +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; } /** @@ -594,4 +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; + } + }