X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=684e59a79a568b8954ff2e6b308769fde552586b;hb=6463d6e0b78c66ca70ebe73c9f0f115185d1e681;hp=95f85e6336e9c259beaad99b8ea88da3d751bce7;hpb=042832306c7e7aa0484079f3bab1e141b2944de5;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 95f85e6..684e59a 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -37,11 +37,11 @@ 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.util.Platform; import jalview.ws.utils.UrlDownloadClient; +import java.awt.Dimension; import java.io.BufferedReader; import java.io.ByteArrayInputStream; import java.io.File; @@ -49,23 +49,56 @@ import java.io.FileNotFoundException; import java.io.FileReader; import java.io.IOException; import java.io.InputStreamReader; -import java.util.StringTokenizer; -import java.util.Vector; +import java.util.ArrayList; +import java.util.List; import javax.swing.SwingUtilities; public class FileLoader implements Runnable { + private static final String DEFAULT_FILE_FORMAT_PROPERTY = "DEFAULT_FILE_FORMAT"; + + private static final String RECENT_URL_PROPERTY = "RECENT_URL"; + + private static final String RECENT_FILE_PROPERTY = "RECENT_FILE"; + + private static final String TAB = "\t"; + + /* + * maximum number of items in file/url history lists; + * pseudo-constant (not final) so amendable by Groovy if wanted + */ + private static int MAX_HISTORY = 11; + + private File selectedFile; + String file; DataSourceType protocol; FileFormatI format; - AlignmentFileReaderI source = null; // alternative specification of where data - // comes + AlignmentFileReaderI source; // alternative specification of where data + // comes from - // from + /** + * It is critical that all these fields are set, as this instance is reused. + * + * @param source + * @param file + * @param inFile + * @param dataSourceType + * @param format + */ + private void setFileFields(AlignmentFileReaderI source, File file, + String inFile, DataSourceType dataSourceType, FileFormatI format) + { + this.source = source; + this.file = inFile; + this.selectedFile = file; + this.protocol = dataSourceType; + this.format = format; + } AlignViewport viewport; @@ -77,8 +110,6 @@ public class FileLoader implements Runnable boolean raiseGUI = true; - private File selectedFile; - /** * default constructor always raised errors in GUI dialog boxes */ @@ -98,7 +129,7 @@ public class FileLoader implements Runnable this.raiseGUI = raiseGUI; } - public void LoadFile(AlignViewport viewport, Object file, + public void loadFile(AlignViewport viewport, Object file, DataSourceType protocol, FileFormatI format) { this.viewport = viewport; @@ -106,10 +137,10 @@ public class FileLoader implements Runnable this.selectedFile = (File) file; file = selectedFile.getPath(); } - LoadFile(file.toString(), protocol, format); + loadFile(file.toString(), protocol, format); } - public void LoadFile(String file, DataSourceType protocol, + public void loadFile(String file, DataSourceType protocol, FileFormatI format) { this.file = file; @@ -129,17 +160,6 @@ public class FileLoader implements Runnable } /** - * Load a (file, protocol) source of unknown type - * - * @param file - * @param protocol - */ - public void LoadFile(String file, DataSourceType protocol) - { - LoadFile(file, protocol, null); - } - - /** * Load alignment from (file, protocol) and wait till loaded * * @param file @@ -149,7 +169,7 @@ public class FileLoader implements Runnable public AlignFrame LoadFileWaitTillLoaded(String file, DataSourceType sourceType) { - return LoadFileWaitTillLoaded(file, sourceType, null); + return loadFileWaitTillLoaded(file, sourceType, null); } /** @@ -160,92 +180,81 @@ public class FileLoader implements Runnable * @param format * @return alignFrame constructed from file contents */ - public AlignFrame LoadFileWaitTillLoaded(String file, + public AlignFrame loadFileWaitTillLoaded(String file, DataSourceType sourceType, FileFormatI format) { - this.file = file; - this.protocol = sourceType; - this.format = format; - return _LoadFileWaitTillLoaded(); + setFileFields(null, null, file, sourceType, format); + return _loadFileWaitTillLoaded(); } /** * Load alignment from (file, protocol) of type format and wait till loaded * - * @param file + * @param fileObject * @param sourceType * @param format * @return alignFrame constructed from file contents + * @throws NullPointerException + * if {@code file} is null */ - public AlignFrame LoadFileWaitTillLoaded(File file, + public AlignFrame loadFileWaitTillLoaded(File fileObject, 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 - * @param format - * @return alignFrame constructed from file contents - */ - public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source, - FileFormatI format) - { - this.source = source; - - file = source.getInFile(); - protocol = source.getDataSourceType(); - this.format = format; - return _LoadFileWaitTillLoaded(); + setFileFields(null, fileObject, fileObject.getPath(), sourceType, format); + return _loadFileWaitTillLoaded(); } /** - * runs the 'run' method (in this thread), then return the alignFrame that's - * (hopefully) been read + * Runs the 'run' method (in this thread), then returns the alignFrame that + * (hopefully) has been constructed * * @return */ - protected AlignFrame _LoadFileWaitTillLoaded() + private AlignFrame _loadFileWaitTillLoaded() { this.run(); return alignFrame; } + /** + * Updates the Jalview properties file to add the last file or URL read to the + * tab-separated list in property RECENT_FILE or RECENT_URL respectively. The + * property is created if it does not already exist. The new entry is added as + * the first item (without duplication). If the list exceeds some maximum + * length (currently 10 entries), the oldest (last) entry is dropped. + *
+ * Files read from the temporary file directory are not added to the property. + *
+ * Property DEFAULT_FILE_FORMAT (e.g. "Fasta" etc) is also set if currently
+ * reading from file.
+ */
public void updateRecentlyOpened()
{
- Vector