X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=798875f9c0aab3a2f6f1d6c61750ac6b72ff708d;hb=d25ed8f9fb513fe5c33823afbeeb557c73a8c27b;hp=f1373953f7bbc94dc3621a2194654cef307a189e;hpb=95ebbef7b78bf266a8252bd479510be3c80cd234;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index f137395..798875f 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -27,7 +27,7 @@ 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; @@ -39,7 +39,10 @@ import jalview.json.binding.biojson.v1.ColourSchemeMapper; 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; @@ -53,7 +56,8 @@ public class FileLoader implements Runnable FileFormatI format; - AlignmentFileI source = null; // alternative specification of where data comes + AlignmentFileReaderI source = null; // alternative specification of where data + // comes // from @@ -160,7 +164,7 @@ public class FileLoader implements Runnable * @param format * @return alignFrame constructed from file contents */ - public AlignFrame LoadFileWaitTillLoaded(AlignmentFileI source, + public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source, FileFormatI format) { this.source = source; @@ -195,6 +199,32 @@ public class FileLoader implements Runnable return alignFrame; } + 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() + { + Thread loader = new Thread(this); + loader.start(); + + while (loader.isAlive()) + { + try + { + Thread.sleep(500); + } catch (Exception ex) + { + } + } + } + public void updateRecentlyOpened() { Vector recent = new Vector(); @@ -204,6 +234,12 @@ public class FileLoader implements Runnable // refer to it as. return; } + if (file != null + && file.indexOf(System.getProperty("java.io.tmpdir")) > -1) + { + // ignore files loaded from the system's temporary directory + return; + } String type = protocol == DataSourceType.FILE ? "RECENT_FILE" : "RECENT_URL"; @@ -244,7 +280,8 @@ public class FileLoader implements Runnable @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 @@ -275,8 +312,7 @@ 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(), @@ -303,8 +339,8 @@ 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); @@ -324,9 +360,28 @@ public class FileLoader implements Runnable // open a new source and read from it FormatAdapter fa = new FormatAdapter(); - al = fa.readFile(file, protocol, format); - source = fa.getAlignFile(); // keep reference for later if - // necessary. + boolean downloadStructureFile = format.isStructureFile() + && protocol.equals(DataSourceType.URL); + if (downloadStructureFile) + { + String structExt = format.getExtensions().split(",")[0]; + 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, + format); + source = fa.getAlignFile(); + } + else + { + al = fa.readFile(file, protocol, format); + source = fa.getAlignFile(); // keep reference for later if + // necessary. + } } } catch (java.io.IOException ex) { @@ -348,8 +403,9 @@ 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); } } } @@ -364,6 +420,22 @@ public class FileLoader implements Runnable } // append to existing alignment viewport.addAlignment(al, title); + if (source instanceof HMMFile) + { + AlignmentI alignment = viewport.getAlignment(); + SequenceI seq = alignment + .getSequenceAt(alignment.getAbsoluteHeight() - 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 { @@ -371,8 +443,8 @@ 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) @@ -384,8 +456,8 @@ 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); @@ -411,8 +483,8 @@ public class FileLoader implements Runnable .applyFeaturesStyle(proxyColourScheme); } alignFrame.statusBar.setText(MessageManager.formatMessage( - "label.successfully_loaded_file", - new String[] { title })); + "label.successfully_loaded_file", new String[] + { title })); if (raiseGUI) { @@ -427,8 +499,8 @@ 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) { } @@ -441,11 +513,8 @@ 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) @@ -456,7 +525,8 @@ public class FileLoader implements Runnable public void run() { JvOptionPane.showInternalMessageDialog(Desktop.desktop, - errorMessage, MessageManager + errorMessage, + MessageManager .getString("label.error_loading_file"), JvOptionPane.WARNING_MESSAGE); } @@ -482,11 +552,11 @@ 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); } }); @@ -504,11 +574,11 @@ 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); } }); @@ -555,18 +625,27 @@ public class FileLoader implements Runnable } - /* - * (non-Javadoc) + /** + * This method creates the file - + * {tmpdir}/jalview/{current_timestamp}/fileName.exetnsion using the supplied + * file name and extension * - * @see java.lang.Object#finalize() + * @param fileName + * the name of the temp file to be created + * @param extension + * the extension of the temp file to be created + * @return */ - @Override - protected void finalize() throws Throwable + private static String createNamedJvTempFile(String fileName, + String extension) throws IOException { - source = null; - alignFrame = null; - viewport = null; - super.finalize(); + 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); + tempStructFile.mkdirs(); + return tempStructFile.toString(); } }