X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=1126de6a0a27c8191d3b6260f572b10c0ceebde7;hb=1595128a4bfc730f1e55c347f0a52eb0d491ca92;hp=bd8bc534e718429ac4a2b840343120a1ee0f5e43;hpb=10eedfb43dacd4cf32d4b5fe27d8d5987c70eaf8;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index bd8bc53..1126de6 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -27,15 +27,15 @@ import jalview.api.FeaturesSourceI; import jalview.bin.Cache; import jalview.bin.Jalview; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; 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; @@ -43,13 +43,16 @@ import jalview.ws.utils.UrlDownloadClient; import java.io.File; import java.io.IOException; +import java.util.ArrayList; +import java.util.List; import java.util.StringTokenizer; -import java.util.Vector; import javax.swing.SwingUtilities; public class FileLoader implements Runnable { + private static final String TAB = "\t"; + String file; DataSourceType protocol; @@ -193,68 +196,111 @@ public class FileLoader implements Runnable Thread.sleep(500); } catch (Exception ex) { + System.out.println( + "Exception caught while waiting for FileLoader thread"); + ex.printStackTrace(); } } return alignFrame; } - public void updateRecentlyOpened() + public void LoadFileOntoAlignmentWaitTillLoaded(AlignViewport viewport, + String file, DataSourceType sourceType, FileFormatI format) + { + this.viewport = viewport; + this.file = file; + this.protocol = sourceType; + this.format = format; + _LoadAlignmentFileWaitTillLoaded(); + } + + protected void _LoadAlignmentFileWaitTillLoaded() { - Vector recent = new Vector(); - if (protocol == DataSourceType.PASTE) + Thread loader = new Thread(this); + loader.start(); + + while (loader.isAlive()) { - // do nothing if the file was pasted in as text... there is no filename to - // refer to it as. - return; + try + { + Thread.sleep(500); + } catch (Exception ex) + { + } } - if (file != null - && file.indexOf(System.getProperty("java.io.tmpdir")) > -1) + } + + /** + * 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) { - // 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); + 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 null; + } - 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(); + if (!recent.contains(trimmed)) + { + 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 @@ -285,8 +331,7 @@ 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(), @@ -313,8 +358,8 @@ 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); @@ -339,18 +384,23 @@ 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); - file = tempStructureFileStr; - protocol = DataSourceType.FILE; + al = fa.readFile(tempStructureFileStr, DataSourceType.FILE, + format); + source = fa.getAlignFile(); + } + else + { + al = fa.readFile(file, protocol, format); + source = fa.getAlignFile(); // keep reference for later if + // necessary. } - al = fa.readFile(file, protocol, format); - source = fa.getAlignFile(); // keep reference for later if - // necessary. } } catch (java.io.IOException ex) { @@ -372,8 +422,9 @@ 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); } } } @@ -388,6 +439,28 @@ public class FileLoader implements Runnable } // append to existing alignment viewport.addAlignment(al, title); + if (source instanceof HMMFile) + { + // TODO: absorb into viewport.addAlignment above ? + 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(); + // update HMM colour options  + if (alignFrame != null) + { + alignFrame.buildColourMenu(); + } + } } else { @@ -395,8 +468,8 @@ public class FileLoader implements Runnable if (source instanceof ComplexAlignFile) { - ColumnSelection colSel = ((ComplexAlignFile) source) - .getColumnSelection(); + HiddenColumns colSel = ((ComplexAlignFile) source) + .getHiddenColumns(); SequenceI[] hiddenSeqs = ((ComplexAlignFile) source) .getHiddenSequences(); String colourSchemeName = ((ComplexAlignFile) source) @@ -408,8 +481,8 @@ 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); @@ -434,9 +507,9 @@ public class FileLoader implements Runnable 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) { @@ -451,8 +524,8 @@ 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) { } @@ -465,11 +538,8 @@ 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) @@ -480,7 +550,8 @@ public class FileLoader implements Runnable public void run() { JvOptionPane.showInternalMessageDialog(Desktop.desktop, - errorMessage, MessageManager + errorMessage, + MessageManager .getString("label.error_loading_file"), JvOptionPane.WARNING_MESSAGE); } @@ -493,7 +564,12 @@ 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) { @@ -506,11 +582,11 @@ 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); } }); @@ -528,11 +604,11 @@ 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); } }); @@ -596,24 +672,10 @@ 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(); - } - }