From: gmungoc Date: Thu, 17 Oct 2019 15:10:43 +0000 (+0100) Subject: JAL-3436 save filePath from fileObject, tidy updateRecentlyOpened X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6463d6e0b78c66ca70ebe73c9f0f115185d1e681;p=jalview.git JAL-3436 save filePath from fileObject, tidy updateRecentlyOpened --- diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 2ef31a2..2371be3 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1053,86 +1053,86 @@ public class AlignFrame extends GAlignFrame @Override public void reload_actionPerformed(ActionEvent e) { - System.out.println("AlignFrame.reload " + fileName); - if (fileName != null) - { - // TODO: JAL-1108 - ensure all associated frames are closed regardless of - // originating file's format - // TODO: work out how to recover feature settings for correct view(s) when - // file is reloaded. - if (FileFormat.Jalview.equals(currentFileFormat)) + if (fileName == null) + { + return; + } + // TODO: JAL-1108 - ensure all associated frames are closed regardless of + // originating file's format + // TODO: work out how to recover feature settings for correct view(s) when + // file is reloaded. + if (FileFormat.Jalview.equals(currentFileFormat)) + { + JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); + for (int i = 0; i < frames.length; i++) { - JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames(); - for (int i = 0; i < frames.length; i++) + if (frames[i] instanceof AlignFrame && frames[i] != this + && ((AlignFrame) frames[i]).fileName != null + && ((AlignFrame) frames[i]).fileName.equals(fileName)) { - if (frames[i] instanceof AlignFrame && frames[i] != this - && ((AlignFrame) frames[i]).fileName != null - && ((AlignFrame) frames[i]).fileName.equals(fileName)) + try + { + frames[i].setSelected(true); + Desktop.getInstance().closeAssociatedWindows(); + } catch (java.beans.PropertyVetoException ex) { - try - { - frames[i].setSelected(true); - Desktop.getInstance().closeAssociatedWindows(); - } catch (java.beans.PropertyVetoException ex) - { - } } - } - Desktop.getInstance().closeAssociatedWindows(); - FileLoader loader = new FileLoader(); - DataSourceType protocol = fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE; - loader.loadFile(viewport, - (fileObject == null ? fileName : fileObject), protocol, - currentFileFormat); } - else - { - Rectangle bounds = this.getBounds(); + Desktop.getInstance().closeAssociatedWindows(); - FileLoader loader = new FileLoader(); + FileLoader loader = new FileLoader(); + DataSourceType protocol = fileName.startsWith("http:") + ? DataSourceType.URL + : DataSourceType.FILE; + loader.loadFile(viewport, + (fileObject == null ? fileName : fileObject), protocol, + currentFileFormat); + } + else + { + Rectangle bounds = this.getBounds(); - AlignFrame newframe = null; + FileLoader loader = new FileLoader(); - if (fileObject == null) - { + AlignFrame newframe = null; - DataSourceType protocol = (fileName.startsWith("http:") - ? DataSourceType.URL - : DataSourceType.FILE); - newframe = loader.loadFileWaitTillLoaded(fileName, protocol, - currentFileFormat); - } - else - { - newframe = loader.loadFileWaitTillLoaded(fileObject, - DataSourceType.FILE, currentFileFormat); - } + if (fileObject == null) + { - newframe.setBounds(bounds); - if (featureSettings != null && featureSettings.isShowing()) + DataSourceType protocol = (fileName.startsWith("http:") + ? DataSourceType.URL + : DataSourceType.FILE); + newframe = loader.loadFileWaitTillLoaded(fileName, protocol, + currentFileFormat); + } + else + { + newframe = loader.loadFileWaitTillLoaded(fileObject, + DataSourceType.FILE, currentFileFormat); + } + + newframe.setBounds(bounds); + if (featureSettings != null && featureSettings.isShowing()) + { + final Rectangle fspos = featureSettings.frame.getBounds(); + // TODO: need a 'show feature settings' function that takes bounds - + // need to refactor Desktop.addFrame + newframe.featureSettings_actionPerformed(null); + final FeatureSettings nfs = newframe.featureSettings; + SwingUtilities.invokeLater(new Runnable() { - final Rectangle fspos = featureSettings.frame.getBounds(); - // TODO: need a 'show feature settings' function that takes bounds - - // need to refactor Desktop.addFrame - newframe.featureSettings_actionPerformed(null); - final FeatureSettings nfs = newframe.featureSettings; - SwingUtilities.invokeLater(new Runnable() + @Override + public void run() { - @Override - public void run() - { - nfs.frame.setBounds(fspos); - } - }); - this.featureSettings.close(); - this.featureSettings = null; - } - this.closeMenuItem_actionPerformed(true); + nfs.frame.setBounds(fspos); + } + }); + this.featureSettings.close(); + this.featureSettings = null; } + this.closeMenuItem_actionPerformed(true); } } diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 1fa6957..684e59a 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -49,13 +49,27 @@ 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; @@ -146,17 +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 @@ -187,36 +190,23 @@ public class FileLoader implements Runnable /** * 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) { - setFileFields(null, file, null, sourceType, format); + setFileFields(null, fileObject, fileObject.getPath(), sourceType, 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) - { - setFileFields(source, null, source.getInFile(), - source.getDataSourceType(), 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 */ @@ -226,35 +216,45 @@ public class FileLoader implements Runnable 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 recent = new Vector<>(); + List recent = new ArrayList<>(); if (protocol == DataSourceType.PASTE) { // do nothing if the file was pasted in as text... there is no filename to // refer to it as. return; } - if (file != null - && file.indexOf(System.getProperty("java.io.tmpdir")) > -1) + 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"; + String type = protocol == DataSourceType.FILE ? RECENT_FILE_PROPERTY + : RECENT_URL_PROPERTY; String historyItems = Cache.getProperty(type); - StringTokenizer st; - if (historyItems != null) { - st = new StringTokenizer(historyItems, "\t"); + String[] tokens = historyItems.split("\\t"); - while (st.hasMoreTokens()) + for (String token : tokens) { - recent.addElement(st.nextToken().trim()); + recent.add(token.trim()); } } @@ -263,18 +263,18 @@ public class FileLoader implements Runnable recent.remove(file); } - StringBuffer newHistory = new StringBuffer(file); - for (int i = 0; i < recent.size() && i < 10; i++) + StringBuilder newHistory = new StringBuilder(file); + for (int i = 0; i < recent.size() && i < MAX_HISTORY - 1; i++) { - newHistory.append("\t"); - newHistory.append(recent.elementAt(i)); + newHistory.append(TAB); + newHistory.append(recent.get(i)); } Cache.setProperty(type, newHistory.toString()); if (protocol == DataSourceType.FILE) { - Cache.setProperty("DEFAULT_FILE_FORMAT", format.getName()); + Cache.setProperty(DEFAULT_FILE_FORMAT_PROPERTY, format.getName()); } }