X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFileLoader.java;fp=src%2Fjalview%2Fio%2FFileLoader.java;h=4cf77de01e2ad9dd0e1dc54450da135cd7c5fd2c;hb=4a3def9f59cefe629c9a33d87483283aee085928;hp=8e7de3f932081a4203ee92fa5930870ca2ae77f6;hpb=914a9aaf5a2eeb3cdedf136c2e6b4b6e4b5d6174;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 8e7de3f..4cf77de 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; @@ -34,21 +41,14 @@ import jalview.ext.archaeopteryx.AptxInit; import jalview.gui.AlignFrame; import jalview.gui.AlignViewport; import jalview.gui.Desktop; -import jalview.gui.Jalview2XML; import jalview.gui.JvOptionPane; 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; @@ -72,6 +72,8 @@ public class FileLoader implements Runnable boolean raiseGUI = true; + private File selectedFile; + /** * default constructor always raised errors in GUI dialog boxes */ @@ -91,11 +93,16 @@ 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) { this.viewport = viewport; - LoadFile(file, protocol, format); + if (file instanceof File) + { + this.selectedFile = (File) file; + file = selectedFile.getPath(); + } + LoadFile(file.toString(), protocol, format); } public void LoadFile(String file, DataSourceType protocol, @@ -159,6 +166,24 @@ 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 @@ -177,33 +202,21 @@ 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, "LoadFileWithWaiting"); - loader.start(); - - while (loader.isAlive()) - { - try - { - Thread.sleep(500); - } catch (Exception ex) - { - } - } - + this.run(); return alignFrame; } // add support for recently opened Aptx trees 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 @@ -219,7 +232,7 @@ public class FileLoader implements Runnable String type = protocol == DataSourceType.FILE ? "RECENT_FILE" : "RECENT_URL"; - String historyItems = jalview.bin.Cache.getProperty(type); + String historyItems = Cache.getProperty(type); StringTokenizer st; @@ -229,7 +242,7 @@ public class FileLoader implements Runnable while (st.hasMoreTokens()) { - recent.addElement(st.nextElement().toString().trim()); + recent.addElement(st.nextToken().trim()); } } @@ -274,6 +287,10 @@ 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); @@ -319,7 +336,9 @@ 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 { @@ -347,16 +366,29 @@ 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(file, protocol, format); + + } + else + { + al = fa.readFile(selectedFile, protocol, format); + } source = fa.getAlignFile(); // keep reference for later if - // necessary. + + // necessary. } } } catch (java.io.IOException ex) @@ -390,12 +422,9 @@ 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 { @@ -436,6 +465,7 @@ public class FileLoader implements Runnable if (!(protocol == DataSourceType.PASTE)) { alignFrame.setFileName(file, format); + alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS } if (proxyColourScheme != null) { @@ -449,7 +479,7 @@ public class FileLoader implements Runnable alignFrame.getViewport()); } - alignFrame.statusBar.setText(MessageManager.formatMessage( + alignFrame.setStatus(MessageManager.formatMessage( "label.successfully_loaded_file", new String[] { title })); @@ -467,8 +497,8 @@ public class FileLoader implements Runnable try { - alignFrame.setMaximum(jalview.bin.Cache - .getDefault("SHOW_FULLSCREEN", false)); + alignFrame.setMaximum( + Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { }