X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;fp=src%2Fjalview%2Fio%2FFileLoader.java;h=26641b10ea1c0ce51ded38d125a44dec3483bfba;hb=f063821ed0be9c1581af74643a1aa5798731af65;hp=3ad74c71ff2bed320f08579b9f1081459f15751f;hpb=fd18e2c73cd015d4e38ad91da0e5d7532ff0ef42;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 3ad74c7..26641b1 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; @@ -204,6 +208,12 @@ 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"; @@ -237,14 +247,15 @@ public class FileLoader implements Runnable if (protocol == DataSourceType.FILE) { - Cache.setProperty("DEFAULT_FILE_FORMAT", format.toString()); + Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName()); } } @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 @@ -275,11 +286,10 @@ 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.SUPPORTED_FORMATS, + + AppletFormatAdapter.getSupportedFormats(), MessageManager.getString("label.couldnt_read_data"), JvOptionPane.WARNING_MESSAGE); } @@ -303,35 +313,54 @@ 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); } else { - String error = AppletFormatAdapter.SUPPORTED_FORMATS; - try + String error = AppletFormatAdapter.getSupportedFormats(); + try + { + if (source != null) { - if (source != null) - { - // read from the provided source + // read from the provided source al = new FormatAdapter().readFromFile(source, format); + } + else + { + + // open a new source and read from it + FormatAdapter fa = new FormatAdapter(); + 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 { - - // 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. } - } catch (java.io.IOException ex) - { - error = ex.getMessage(); } + } catch (java.io.IOException ex) + { + error = ex.getMessage(); + } if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence()) { @@ -348,8 +377,9 @@ 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); } } } @@ -371,8 +401,8 @@ 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 +414,8 @@ 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 +441,8 @@ 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 +457,8 @@ 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 +471,8 @@ 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 +483,8 @@ 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 +510,11 @@ 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 +532,11 @@ 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); } }); @@ -555,6 +583,29 @@ public class FileLoader implements Runnable } + /** + * This method creates the file - + * {tmpdir}/jalview/{current_timestamp}/fileName.exetnsion using the supplied + * file name and extension + * + * @param fileName + * the name of the temp file to be created + * @param extension + * the extension of the temp file to be created + * @return + */ + private static String createNamedJvTempFile(String fileName, + String extension) throws IOException + { + 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(); + } + /* * (non-Javadoc) *