X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFileLoader.java;h=834e0040edfc27c617480aa9ae2416f9c862af5f;hb=c49683bef626d9c1de9d06e5f11039e6d4df55c3;hp=2a18b0b7ad1d4fd53d2fc165ae264ae5d1a8f511;hpb=1b459bcde7bbbd9149b2f94777d7336156861533;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 2a18b0b..834e004 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -20,6 +20,14 @@ */ package jalview.io; +import java.awt.Dimension; +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; @@ -39,17 +47,14 @@ import jalview.project.Jalview2XML; import jalview.schemes.ColourSchemeI; import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; +import jalview.util.Platform; 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; - +import java.util.ArrayList; +import java.util.List; public class FileLoader implements Runnable { + private static final String TAB = "\t"; String file; DataSourceType protocol; @@ -71,6 +76,8 @@ public class FileLoader implements Runnable boolean raiseGUI = true; + private File selectedFile; + /** * default constructor always raised errors in GUI dialog boxes */ @@ -90,11 +97,16 @@ 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, @@ -158,6 +170,24 @@ 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 @@ -176,79 +206,90 @@ 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); - loader.start(); - - while (loader.isAlive()) - { - try - { - Thread.sleep(500); - } catch (Exception ex) - { - } - } + this.run(); return alignFrame; } - public void updateRecentlyOpened() + public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport, + String file, DataSourceType sourceType, FileFormatI format) { - Vector recent = new Vector(); + Vector recent = new Vector<>(); if (protocol == DataSourceType.PASTE) + this.viewport = viewport; + this.file = file; + this.protocol = sourceType; + this.format = format; + _LoadFileWaitTillLoaded(); + } + + + /** + * Updates (or creates) the tab-separated list of recently opened files held + * under the given property name by inserting the filePath at the front of the + * list. Duplicates are removed, and the list is limited to 11 entries. The + * method returns the updated value of the property. + * + * @param filePath + * @param sourceType + */ + public static String updateRecentlyOpened(String filePath, + DataSourceType sourceType) + { + if (sourceType != DataSourceType.FILE + && sourceType != DataSourceType.URL) { - // do nothing if the file was pasted in as text... there is no filename to - // refer to it as. - return; + return null; } - if (file != null - && file.indexOf(System.getProperty("java.io.tmpdir")) > -1) + String propertyName = sourceType == DataSourceType.FILE ? "RECENT_FILE" + : "RECENT_URL"; + String historyItems = Cache.getProperty(propertyName); + if (filePath != null + && filePath.indexOf(System.getProperty("java.io.tmpdir")) > -1) { // ignore files loaded from the system's temporary directory - return; + return null; } - String type = protocol == DataSourceType.FILE ? "RECENT_FILE" - : "RECENT_URL"; - String historyItems = jalview.bin.Cache.getProperty(type); - - StringTokenizer st; + List recent = new ArrayList<>(); if (historyItems != null) { - st = new StringTokenizer(historyItems, "\t"); + StringTokenizer st = new StringTokenizer(historyItems, TAB); while (st.hasMoreTokens()) { - recent.addElement(st.nextElement().toString().trim()); + String trimmed = st.nextToken().trim(); + recent.add(trimmed); } } - if (recent.contains(file)) + /* + * if file was already in the list, it moves to the top + */ + if (recent.contains(filePath)) { - recent.remove(file); + recent.remove(filePath); } - StringBuffer newHistory = new StringBuffer(file); + StringBuilder newHistory = new StringBuilder(filePath); for (int i = 0; i < recent.size() && i < 10; i++) { - newHistory.append("\t"); - newHistory.append(recent.elementAt(i)); + newHistory.append(TAB); + newHistory.append(recent.get(i)); } - Cache.setProperty(type, newHistory.toString()); + String newProperty = newHistory.toString(); + Cache.setProperty(propertyName, newProperty); - if (protocol == DataSourceType.FILE) - { - Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName()); - } + return newProperty; } @Override @@ -260,9 +301,9 @@ public class FileLoader implements Runnable Runtime rt = Runtime.getRuntime(); try { - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.startLoading(file); + Desktop.getInstance().startLoading(file); } if (format == null) { @@ -272,6 +313,10 @@ 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); @@ -281,12 +326,12 @@ public class FileLoader implements Runnable if (format == null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); System.err.println("The input file \"" + file + "\" has null or unidentifiable data content!"); if (!Jalview.isHeadlessMode()) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.getString("label.couldnt_read_data") + " in " + file + "\n" + AppletFormatAdapter.getSupportedFormats(), @@ -297,7 +342,7 @@ public class FileLoader implements Runnable } // TODO: cache any stream datasources as a temporary file (eg. PDBs // retrieved via URL) - if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage()) + if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage()) { System.gc(); memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free @@ -317,7 +362,9 @@ 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 { @@ -345,16 +392,29 @@ 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) @@ -378,7 +438,7 @@ public class FileLoader implements Runnable // register PDB entries with desktop's structure selection // manager StructureSelectionManager - .getStructureSelectionManager(Desktop.instance) + .getStructureSelectionManager(Desktop.getInstance()) .registerPDBEntry(pdbe); } } @@ -388,12 +448,29 @@ public class FileLoader implements Runnable .getFeatureColourScheme(); if (viewport != null) { + // TODO: test if this needs to be done after addAlignment ? (like in 2.11.2) if (proxyColourScheme != null) { viewport.applyFeaturesStyle(proxyColourScheme); } // append to existing alignment viewport.addAlignment(al, title); + if (source instanceof HMMFile) + { + AlignmentI alignment = viewport.getAlignment(); + SequenceI seq = alignment + .getSequenceAt(alignment.getHeight() - 1); + if (seq.hasHMMProfile()) + { + /* + * fudge: move HMM consensus sequence from last to first + */ + alignment.deleteSequence(alignment.getAbsoluteHeight() - 1); + alignment.insertSequenceAt(0, seq); + } + viewport.getAlignPanel().adjustAnnotationHeight(); + viewport.updateSequenceIdColours(); + } } else { @@ -433,14 +510,14 @@ public class FileLoader implements Runnable // add metadata and update ui if (!(protocol == DataSourceType.PASTE)) { - alignFrame.setFileName(file, format); + alignFrame.setFile(file, selectedFile, protocol, format); } if (proxyColourScheme != null) { alignFrame.getViewport() .applyFeaturesStyle(proxyColourScheme); } - alignFrame.statusBar.setText(MessageManager.formatMessage( + alignFrame.setStatus(MessageManager.formatMessage( "label.successfully_loaded_file", new String[] { title })); @@ -451,14 +528,18 @@ public class FileLoader implements Runnable // status in Jalview 3 // TODO: define 'virtual desktop' for benefit of headless scripts // that perform queries to find the 'current working alignment' - Desktop.addInternalFrame(alignFrame, title, + + Dimension dim = Platform.getDimIfEmbedded(alignFrame, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + alignFrame.setSize(dim); + Desktop.addInternalFrame(alignFrame, title, dim.width, + dim.height); } try { - alignFrame.setMaximum(jalview.bin.Cache - .getDefault("SHOW_FULLSCREEN", false)); + alignFrame.setMaximum( + Cache.getDefault("SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { } @@ -466,23 +547,23 @@ public class FileLoader implements Runnable } else { - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); } final String errorMessage = MessageManager.getString( "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 && Desktop.getDesktopPane() != null) { javax.swing.SwingUtilities.invokeLater(new Runnable() { @Override public void run() { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), errorMessage, MessageManager .getString("label.error_loading_file"), @@ -497,7 +578,12 @@ public class FileLoader implements Runnable } } - updateRecentlyOpened(); + updateRecentlyOpened(file, protocol); + + if (protocol == DataSourceType.FILE && format != null) + { + Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName()); + } } catch (Exception er) { @@ -510,7 +596,7 @@ public class FileLoader implements Runnable @Override public void run() { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.formatMessage( "label.problems_opening_file", new String[] { file }), @@ -532,7 +618,7 @@ public class FileLoader implements Runnable @Override public void run() { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(), MessageManager.formatMessage( "warn.out_of_memory_loading_file", new String[] { file }), @@ -554,7 +640,7 @@ public class FileLoader implements Runnable // memory // after // load - if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage()) + if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage()) { if (alignFrame != null) { @@ -576,9 +662,9 @@ public class FileLoader implements Runnable } } // remove the visual delay indicator - if (Desktop.instance != null) + if (Desktop.getInstance() != null) { - Desktop.instance.stopLoading(); + Desktop.getInstance().stopLoading(); } }