Rename user "default" directory method name for clarity

igvteam · Jan 16, 2025 · e7bcd3e · e7bcd3e
1 parent fda2603
commit e7bcd3e
Show file tree

Hide file tree

Showing 8 changed files with 12 additions and 14 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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);