X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=31a4deb22b5f79281ec9f76e96fec6b7000f11e6;hb=c794c5033adeee182b03a5ea92c0a7495a29661f;hp=b861c077b16d85b8380139f2e4e4ef84509ee982;hpb=3328ff82d86879e92139b1b2c98a1653939ee353;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index b861c07..31a4deb 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; @@ -29,28 +36,25 @@ import jalview.bin.Jalview; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceGroup; 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.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; +import java.util.ArrayList; +import java.util.List; public class FileLoader implements Runnable { + private static final String TAB = "\t"; + String file; DataSourceType protocol; @@ -72,6 +76,8 @@ public class FileLoader implements Runnable boolean raiseGUI = true; + private File selectedFile; + /** * default constructor always raised errors in GUI dialog boxes */ @@ -91,11 +97,15 @@ 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 +169,24 @@ 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 @@ -177,85 +205,98 @@ 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 public void run() { - String title = protocol == DataSourceType.PASTE ? "Copied From Clipboard" + String title = protocol == DataSourceType.PASTE + ? "Copied From Clipboard" : file; Runtime rt = Runtime.getRuntime(); try @@ -272,6 +313,9 @@ 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); @@ -286,8 +330,7 @@ public class FileLoader implements Runnable + "\" has null or unidentifiable data content!"); if (!Jalview.isHeadlessMode()) { - JvOptionPane.showInternalMessageDialog( - Desktop.desktop, + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager.getString("label.couldnt_read_data") + " in " + file + "\n" + AppletFormatAdapter.getSupportedFormats(), @@ -314,11 +357,12 @@ public class FileLoader implements Runnable if (source != null) { // Tell the user (developer?) that this is going to cause a problem - System.err - .println("IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream."); + System.err.println( + "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 { @@ -340,20 +384,32 @@ public class FileLoader implements Runnable if (downloadStructureFile) { String structExt = format.getExtensions().split(",")[0]; - String urlLeafName = file.substring(file.lastIndexOf(System - .getProperty("file.separator")), file - .lastIndexOf(".")); + String urlLeafName = file.substring( + file.lastIndexOf( + System.getProperty("file.separator")), + file.lastIndexOf(".")); String tempStructureFileStr = createNamedJvTempFile( urlLeafName, structExt); - UrlDownloadClient.download(file, tempStructureFileStr); - al = fa.readFile(tempStructureFileStr, DataSourceType.FILE, + + // 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. } } @@ -377,8 +433,9 @@ public class FileLoader implements Runnable { // register PDB entries with desktop's structure selection // manager - StructureSelectionManager.getStructureSelectionManager( - Desktop.instance).registerPDBEntry(pdbe); + StructureSelectionManager + .getStructureSelectionManager(Desktop.instance) + .registerPDBEntry(pdbe); } } } @@ -397,38 +454,17 @@ public class FileLoader implements Runnable { AlignmentI alignment = viewport.getAlignment(); SequenceI seq = alignment - .getSequenceAt(alignment.getAbsoluteHeight() - 1); - alignment.deleteSequence(alignment.getAbsoluteHeight() - 1); - SequenceGroup sg = viewport.getSelectionGroup(); - if (sg != null) - { - seq.insertCharAt(0, sg.getStartRes(), '-'); - seq.insertCharAt(sg.getEndRes() + 1, - alignment.getWidth() - sg.getEndRes(), '-'); - SequenceI topSeq = sg.getSequencesInOrder(alignment)[0]; - int topIndex = alignment.findIndex(topSeq); - alignment.insertSequenceAt(topIndex, seq); - sg.setSeqrep(seq); - viewport.getSelectionGroup().addSequence(seq, false); - } - else + .getSequenceAt(alignment.getHeight() - 1); + if (seq.hasHMMProfile()) { - for (int i = 0; i < alignment.getAbsoluteHeight(); i++) - { - if (!alignment.getSequenceAt(i).isHMMConsensusSequence()) - { - alignment.getSequences().add(i, seq); - break; - } - } + /* + * fudge: move HMM consensus sequence from last to first + */ + alignment.deleteSequence(alignment.getAbsoluteHeight() - 1); + alignment.insertSequenceAt(0, seq); } - viewport.setAlignment(alignment); - viewport.initInformation(); - viewport.updateInformation(viewport.getAlignPanel()); viewport.getAlignPanel().adjustAnnotationHeight(); viewport.updateSequenceIdColours(); - viewport.getAlignPanel().paintAlignment(true); - viewport.alignmentChanged(viewport.getAlignPanel()); } } else @@ -450,8 +486,8 @@ public class FileLoader implements Runnable alignFrame.getViewport().setFeaturesDisplayed(fd); alignFrame.getViewport().setShowSequenceFeatures( ((ComplexAlignFile) source).isShowSeqFeatures()); - ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme( - colourSchemeName, al); + ColourSchemeI cs = ColourSchemeMapper + .getJalviewColourScheme(colourSchemeName, al); if (cs != null) { alignFrame.changeColour(cs); @@ -470,15 +506,16 @@ 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( - "label.successfully_loaded_file", - new String[] { title })); + alignFrame.setStatus(MessageManager.formatMessage( + "label.successfully_loaded_file", new String[] + { title })); if (raiseGUI) { @@ -493,8 +530,8 @@ public class FileLoader implements Runnable try { - alignFrame.setMaximum(jalview.bin.Cache.getDefault( - "SHOW_FULLSCREEN", false)); + alignFrame.setMaximum(jalview.bin.Cache + .getDefault("SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { } @@ -507,11 +544,8 @@ public class FileLoader implements Runnable Desktop.instance.stopLoading(); } - final String errorMessage = MessageManager - .getString("label.couldnt_load_file") - + " " - + title - + "\n" + error; + 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) @@ -522,7 +556,8 @@ public class FileLoader implements Runnable public void run() { JvOptionPane.showInternalMessageDialog(Desktop.desktop, - errorMessage, MessageManager + errorMessage, + MessageManager .getString("label.error_loading_file"), JvOptionPane.WARNING_MESSAGE); } @@ -535,7 +570,12 @@ 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) { @@ -548,11 +588,11 @@ public class FileLoader implements Runnable @Override public void run() { - JvOptionPane.showInternalMessageDialog( - Desktop.desktop, MessageManager.formatMessage( - "label.problems_opening_file", - new String[] { file }), MessageManager - .getString("label.file_open_error"), + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.problems_opening_file", new String[] + { file }), + MessageManager.getString("label.file_open_error"), JvOptionPane.WARNING_MESSAGE); } }); @@ -570,11 +610,11 @@ public class FileLoader implements Runnable @Override public void run() { - JvOptionPane.showInternalMessageDialog( - Desktop.desktop, MessageManager.formatMessage( + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.formatMessage( "warn.out_of_memory_loading_file", new String[] - { file }), MessageManager - .getString("label.out_of_memory"), + { file }), + MessageManager.getString("label.out_of_memory"), JvOptionPane.WARNING_MESSAGE); } }); @@ -638,24 +678,10 @@ public class FileLoader implements Runnable String seprator = System.getProperty("file.separator"); String jvTempDir = System.getProperty("java.io.tmpdir") + "jalview" + seprator + System.currentTimeMillis(); - File tempStructFile = new File(jvTempDir + seprator + fileName + "." - + extension); + File tempStructFile = new File( + jvTempDir + seprator + fileName + "." + extension); tempStructFile.mkdirs(); return tempStructFile.toString(); } - /* - * (non-Javadoc) - * - * @see java.lang.Object#finalize() - */ - @Override - protected void finalize() throws Throwable - { - source = null; - alignFrame = null; - viewport = null; - super.finalize(); - } - }