From e7bcd3e2bb21bc2ef23f4e7106fe69919265f659 Mon Sep 17 00:00:00 2001 From: jrobinso <933148+jrobinso@users.noreply.github.com> Date: Wed, 15 Jan 2025 23:12:50 -0800 Subject: [PATCH] Rename user "default" directory method name for clarity --- src/main/java/org/broad/igv/DirectoryManager.java | 6 +++--- src/main/java/org/broad/igv/lists/GeneListManagerUI.java | 2 +- src/main/java/org/broad/igv/prefs/IGVPreferences.java | 4 ++-- src/main/java/org/broad/igv/prefs/PreferencesEditor.java | 4 ++-- src/main/java/org/broad/igv/ui/IGVMenuBar.java | 3 +-- .../org/broad/igv/ui/action/ExportRegionsMenuAction.java | 2 +- src/main/java/org/broad/igv/ui/util/FileDialogUtils.java | 3 +-- src/main/java/org/broad/igv/util/blat/BlatQueryWindow.java | 2 +- 8 files changed, 12 insertions(+), 14 deletions(-) diff --git a/src/main/java/org/broad/igv/DirectoryManager.java b/src/main/java/org/broad/igv/DirectoryManager.java index 994c274c4b..af84bbb30d 100644 --- a/src/main/java/org/broad/igv/DirectoryManager.java +++ b/src/main/java/org/broad/igv/DirectoryManager.java @@ -61,7 +61,7 @@ public class DirectoryManager { final public static String IGV_DIR_USERPREF = "igvDir"; - private static File getUserHome() { + public static File getUserHome() { if (USER_HOME == null) { String userHomeString = System.getProperty("user.home"); USER_HOME = new File(userHomeString); @@ -73,7 +73,7 @@ private static File getUserHome() { * The user directory. On Mac and Linux this should be the user home directory. On Windows platforms this * is the "My Documents" directory. */ - public static synchronized File getUserDirectory() { + public static synchronized File getUserDefaultDirectory() { if (USER_DIRECTORY == null) { USER_DIRECTORY = FileSystemView.getFileSystemView().getDefaultDirectory(); //Mostly for testing, in some environments USER_DIRECTORY can be null @@ -96,7 +96,7 @@ public static File getIgvDirectory() { // Hack for known Java / Windows bug. Attempt to remvoe (possible) read-only bit from user directory if (System.getProperty("os.name").startsWith("Windows")) { try { - Runtime.getRuntime().exec("attrib -r \"" + getUserDirectory().getAbsolutePath() + "\""); + Runtime.getRuntime().exec("attrib -r \"" + getUserDefaultDirectory().getAbsolutePath() + "\""); } catch (Exception e) { // We tried } diff --git a/src/main/java/org/broad/igv/lists/GeneListManagerUI.java b/src/main/java/org/broad/igv/lists/GeneListManagerUI.java index da1c21e7ef..501a891077 100644 --- a/src/main/java/org/broad/igv/lists/GeneListManagerUI.java +++ b/src/main/java/org/broad/igv/lists/GeneListManagerUI.java @@ -338,7 +338,7 @@ private void importButtonActionPerformed(ActionEvent e) { */ private void exportButtonActionPerformed(ActionEvent e) { if (selectedGroup != null) { - File userDir = DirectoryManager.getUserDirectory(); + File userDir = DirectoryManager.getUserDefaultDirectory(); File initFile = new File(selectedGroup + ".gmt"); File glFile = FileDialogUtils.chooseFile("Save gene lists", userDir, initFile, FileDialogUtils.SAVE); if (glFile != null) { diff --git a/src/main/java/org/broad/igv/prefs/IGVPreferences.java b/src/main/java/org/broad/igv/prefs/IGVPreferences.java index 497b9e2ca6..9118c1afd5 100644 --- a/src/main/java/org/broad/igv/prefs/IGVPreferences.java +++ b/src/main/java/org/broad/igv/prefs/IGVPreferences.java @@ -526,7 +526,7 @@ public File getDefineGenomeInputDirectory() { File directory = null; - String lastFilePath = get(DEFINE_GENOME_INPUT_DIRECTORY_KEY, DirectoryManager.getUserDirectory().getAbsolutePath()); + String lastFilePath = get(DEFINE_GENOME_INPUT_DIRECTORY_KEY, DirectoryManager.getUserDefaultDirectory().getAbsolutePath()); if (lastFilePath != null) { directory = new File(lastFilePath); @@ -550,7 +550,7 @@ public File getLastGenomeImportDirectory() { File genomeImportDirectory = null; - String lastFilePath = get(LAST_GENOME_IMPORT_DIRECTORY, DirectoryManager.getUserDirectory().getAbsolutePath()); + String lastFilePath = get(LAST_GENOME_IMPORT_DIRECTORY, DirectoryManager.getUserDefaultDirectory().getAbsolutePath()); if (lastFilePath != null) { genomeImportDirectory = new File(lastFilePath); diff --git a/src/main/java/org/broad/igv/prefs/PreferencesEditor.java b/src/main/java/org/broad/igv/prefs/PreferencesEditor.java index fc30673000..4224aafb12 100644 --- a/src/main/java/org/broad/igv/prefs/PreferencesEditor.java +++ b/src/main/java/org/broad/igv/prefs/PreferencesEditor.java @@ -289,7 +289,7 @@ public void focusLost(FocusEvent e) { moveButton.addActionListener(event -> { UIUtilities.invokeOnEventThread(() -> { final File directory = DirectoryManager.getFastaCacheDirectory(); - final File newDirectory = FileDialogUtils.chooseDirectory("Select cache directory", DirectoryManager.getUserDirectory()); + final File newDirectory = FileDialogUtils.chooseDirectory("Select cache directory", DirectoryManager.getUserDefaultDirectory()); if (newDirectory != null && !newDirectory.equals(directory)) { DirectoryManager.moveDirectoryContents(directory, newDirectory); SwingUtilities.invokeLater(() -> currentDirectoryLabel.setText(newDirectory.getAbsolutePath())); @@ -320,7 +320,7 @@ public void focusLost(FocusEvent e) { moveButton.addActionListener(event -> { UIUtilities.invokeOnEventThread(() -> { final File igvDirectory = DirectoryManager.getIgvDirectory(); - final File newDirectory = FileDialogUtils.chooseDirectory("Select IGV directory", DirectoryManager.getUserDirectory()); + final File newDirectory = FileDialogUtils.chooseDirectory("Select IGV directory", DirectoryManager.getUserDefaultDirectory()); if (newDirectory != null && !newDirectory.equals(igvDirectory)) { DirectoryManager.moveIGVDirectory(newDirectory); SwingUtilities.invokeLater(() -> currentDirectoryLabel.setText(newDirectory.getAbsolutePath())); diff --git a/src/main/java/org/broad/igv/ui/IGVMenuBar.java b/src/main/java/org/broad/igv/ui/IGVMenuBar.java index bb59c34f06..6ec97373f7 100644 --- a/src/main/java/org/broad/igv/ui/IGVMenuBar.java +++ b/src/main/java/org/broad/igv/ui/IGVMenuBar.java @@ -67,7 +67,6 @@ import javax.swing.*; import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; import javax.swing.plaf.basic.BasicBorders; import java.awt.*; import java.awt.event.ActionEvent; @@ -474,7 +473,7 @@ private JMenu createGenomesMenu() { try { File importDirectory = PreferencesManager.getPreferences().getLastGenomeImportDirectory(); if (importDirectory == null) { - PreferencesManager.getPreferences().setLastGenomeImportDirectory(DirectoryManager.getUserDirectory()); + PreferencesManager.getPreferences().setLastGenomeImportDirectory(DirectoryManager.getUserDefaultDirectory()); } // Display the dialog File file = FileDialogUtils.chooseFile("Load Genome", importDirectory, FileDialog.LOAD); diff --git a/src/main/java/org/broad/igv/ui/action/ExportRegionsMenuAction.java b/src/main/java/org/broad/igv/ui/action/ExportRegionsMenuAction.java index acaa9cb540..a3effe511e 100644 --- a/src/main/java/org/broad/igv/ui/action/ExportRegionsMenuAction.java +++ b/src/main/java/org/broad/igv/ui/action/ExportRegionsMenuAction.java @@ -78,7 +78,7 @@ public final void exportRegionsOfInterest() { File exportRegionDirectory = PreferencesManager.getPreferences().getLastExportedRegionDirectory(); if (exportRegionDirectory == null) { - exportRegionDirectory = DirectoryManager.getUserDirectory(); + exportRegionDirectory = DirectoryManager.getUserDefaultDirectory(); } String title = "Export Regions of Interest ..."; diff --git a/src/main/java/org/broad/igv/ui/util/FileDialogUtils.java b/src/main/java/org/broad/igv/ui/util/FileDialogUtils.java index d7cb1b24e6..cf840252eb 100644 --- a/src/main/java/org/broad/igv/ui/util/FileDialogUtils.java +++ b/src/main/java/org/broad/igv/ui/util/FileDialogUtils.java @@ -33,7 +33,6 @@ import javax.swing.*; import java.awt.*; import java.io.File; -import java.io.FileFilter; import java.io.FilenameFilter; import java.lang.reflect.Method; @@ -54,7 +53,7 @@ public static File chooseFile(String title, File initialDirectory, int mode) { } public static File chooseFile(String title) { - return chooseFile(title, DirectoryManager.getUserDirectory(), null, FileDialog.LOAD); + return chooseFile(title, DirectoryManager.getUserDefaultDirectory(), null, FileDialog.LOAD); } public static File chooseFile(String title, File initialDirectory, File initialFile, int mode) { diff --git a/src/main/java/org/broad/igv/util/blat/BlatQueryWindow.java b/src/main/java/org/broad/igv/util/blat/BlatQueryWindow.java index b157a3c9f5..7c21315cf3 100644 --- a/src/main/java/org/broad/igv/util/blat/BlatQueryWindow.java +++ b/src/main/java/org/broad/igv/util/blat/BlatQueryWindow.java @@ -108,7 +108,7 @@ private void closeItemActionPerformed(ActionEvent e) { private void saveItemActionPerformed(ActionEvent e) { - File f = FileDialogUtils.chooseFile("Save BLAT results", DirectoryManager.getUserDirectory(), FileDialogUtils.SAVE); + File f = FileDialogUtils.chooseFile("Save BLAT results", DirectoryManager.getUserDefaultDirectory(), FileDialogUtils.SAVE); if (f != null) { try { model.save(f);