JAL-3141 Changed suffix position to after the extension (removed extension detection...

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index aefcf08..1a1fa45 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -1616,7 +1616,7 @@ public class Desktop extends jalview.jbgui.GDesktop
     // autoSave indicates we already have a file and don't need to ask
     boolean autoSave = projectFile != null && !saveAs && BackupFiles.getEnabled();
 
-    System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"', saveAs="+saveAs+", Backups "+(BackupFiles.getEnabled()?"enabled":"disabled"));
+    //System.out.println("autoSave="+autoSave+", projectFile='"+projectFile+"', saveAs="+saveAs+", Backups "+(BackupFiles.getEnabled()?"enabled":"disabled"));
 
     boolean approveSave = false;
     if (!autoSave)

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 7258957..5740759 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -555,7 +555,7 @@ public class Preferences extends GPreferences
     enableBackupFiles
             .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
     suffixTemplate.setText(Cache.getDefault(BackupFiles.SUFFIX,
-            "-v" + BackupFiles.NUM_PLACEHOLDER));
+            "-bak" + BackupFiles.NUM_PLACEHOLDER));
     suffixDigitsSpinner
             .setValue(Cache.getDefault(BackupFiles.SUFFIX_DIGITS, 3));
     suffixReverse.setSelected(

diff --git a/src/jalview/io/BackupFilenameFilter.java b/src/jalview/io/BackupFilenameFilter.java
index db1645a..916d660 100644 (file)
--- a/src/jalview/io/BackupFilenameFilter.java
+++ b/src/jalview/io/BackupFilenameFilter.java
@@ -13,21 +13,16 @@ public class BackupFilenameFilter implements FilenameFilter
 
   public int digits;
 
-  public String extension;
-
-  public BackupFilenameFilter(String base, String template, int digits,
-          String extension)
+  public BackupFilenameFilter(String base, String template, int digits)
   {
     this.base = base;
     this.template = template;
     this.digits = digits;
-    this.extension = extension;
   }
 
   @Override
   public boolean accept(File dir, String filename)
   {
-    boolean ret = false;
     try
     {
       File file = new File(
@@ -44,18 +39,17 @@ public class BackupFilenameFilter implements FilenameFilter
     }
 
     BackupFilenameParts bffp = new BackupFilenameParts(filename, base,
-            template, digits, extension);
-    ret = bffp.isBackupFile();
-    return ret;
+            template, digits);
+    return bffp.isBackupFile();
   }
 
   public static String getBackupFilename(int index, String base,
-          String template, int digits, String extension)
+          String template, int digits)
   {
     String numString = String.format("%0" + digits + "d", index);
     String backupSuffix = template.replaceAll(BackupFiles.NUM_PLACEHOLDER,
             numString);
-    String backupfilename = base + backupSuffix + extension;
+    String backupfilename = base + backupSuffix;
     return backupfilename;
   }
 

diff --git a/src/jalview/io/BackupFilenameParts.java b/src/jalview/io/BackupFilenameParts.java
index b9f766e..93aa602 100644 (file)
--- a/src/jalview/io/BackupFilenameParts.java
+++ b/src/jalview/io/BackupFilenameParts.java
@@ -14,28 +14,23 @@ public class BackupFilenameParts
 
   String templateEnd;
 
-  String extension;
-
   boolean isBackupFile;
 
-  public BackupFilenameParts(File file, String base, String template, int digits,
-          String extension)
+  public BackupFilenameParts(File file, String base, String template, int digits)
   {
-    this(file.getName(), base, template, digits, extension);
+    this(file.getName(), base, template, digits);
   }
 
   public BackupFilenameParts(String filename, String base, String template,
-          int digits, String extension)
+          int digits)
   {
     this.isBackupFile = false;
 
     // calculate minimum length of a backup filename
     int minlength = base.length() + template.length()
-            - BackupFiles.NUM_PLACEHOLDER.length() + digits
-            + extension.length();
+            - BackupFiles.NUM_PLACEHOLDER.length() + digits ;
 
-    if (!(filename.startsWith(base) && filename.endsWith(extension)
-            && filename.length() >= minlength))
+    if (!(filename.startsWith(base) && filename.length() >= minlength))
     {
       // non-starter
       return;
@@ -52,13 +47,13 @@ public class BackupFilenameParts
     }
     
     int startLength = base.length() + templateStart.length();
-    int endLength = templateEnd.length() + extension.length();
+    int endLength = templateEnd.length();
     String numString = filename.substring(startLength,
             filename.length() - endLength);
 
     if (filename.length() >= startLength + digits + endLength
             && filename.startsWith(base + templateStart)
-            && filename.endsWith(templateEnd + extension)
+            && filename.endsWith(templateEnd)
             && numString.matches("[0-9]+"))
     {
       this.base = base;

diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java
index 7a026f9..1553a41 100644 (file)
--- a/src/jalview/io/BackupFiles.java
+++ b/src/jalview/io/BackupFiles.java
@@ -16,7 +16,7 @@ import java.util.TreeMap;
  * BackupFiles used for manipulating (naming rolling/deleting) backup/version files when an alignment or project file is saved.
  * User configurable options are:
  * BACKUPFILES_ENABLED - boolean flag as to whether to use this mechanism or act as before, including overwriting files as saved.
- * BACKUPFILES_SUFFIX - a template to insert just before the file extension.  Use '%n' to be replaced by a 0-led SUFFIX_DIGITS long integer.
+ * BACKUPFILES_SUFFIX - a template to insert after the file extension.  Use '%n' to be replaced by a 0-led SUFFIX_DIGITS long integer.
  * BACKUPFILES_NO_MAX - flag to turn off setting a maximum number of backup files to keep.
  * BACKUPFILES_ROLL_MAX - the maximum number of backupfiles to keep for any one alignment or project file.
  * BACKUPFILES_SUFFIX_DIGITS - the number of digits to insert replace %n with (e.g. BACKUPFILES_SUFFIX_DIGITS = 3 would make "001", "002", etc)
@@ -48,6 +48,8 @@ public class BackupFiles
 
   private static final String DEFAULT_TEMP_FILE = "jalview_temp_file_" + NS;
 
+  private static final String TEMP_FILE_EXT = ".tmp";
+
   // file - File object to be backed up and then updated (written over)
   private File file;
 
@@ -90,7 +92,7 @@ public class BackupFiles
   // REVERSE_ORDER
   public BackupFiles(File file)
   {
-    this(file, "-v" + NUM_PLACEHOLDER, false, 4, 3, false);
+    this(file, ".v" + NUM_PLACEHOLDER, false, 4, 3, false);
   }
 
   public BackupFiles(File file,
@@ -115,11 +117,11 @@ public class BackupFiles
       {
         String tempfilename = file.getName();
         File tempdir = file.getParentFile();
-        temp = File.createTempFile(tempfilename, ".tmp", tempdir);
+        temp = File.createTempFile(tempfilename, TEMP_FILE_EXT, tempdir);
       }
       else
       {
-        temp = File.createTempFile(DEFAULT_TEMP_FILE, ".tmp");
+        temp = File.createTempFile(DEFAULT_TEMP_FILE, TEMP_FILE_EXT);
       }
     } catch (IOException e)
     {
@@ -200,6 +202,7 @@ public class BackupFiles
 
   public boolean renameTempFile()
   {
+    System.out.println("RENAMING TEMP FILE '"+tempFile.getName() + "' TO '"+file.getName()+"'"); // DELETEME
     return tempFile.renameTo(file);
   }
 
@@ -231,15 +234,6 @@ public class BackupFiles
     }
     String filename = file.getName();
     String basename = filename;
-    String extension = "";
-    int dotcharpos = filename.lastIndexOf('.');
-    // don't split filenames with the last '.' at the very beginning or
-    // very end of the filename
-    if ((dotcharpos > 0) && (dotcharpos < filename.length() - 1))
-    {
-      basename = filename.substring(0, dotcharpos);
-      extension = filename.substring(dotcharpos); // NOTE this includes the '.'
-    }
 
     boolean ret = true;
     // Create/move backups up one
@@ -248,8 +242,7 @@ public class BackupFiles
     
     // find existing backup files
     BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix,
-            digits,
-            extension);
+            digits);
     File[] backupFiles = dirFile.listFiles(bff);
     int nextIndexNum = 0;
     String confirmDeleteExtraInfo = null;
@@ -261,7 +254,7 @@ public class BackupFiles
     }
     else
     {
-      TreeMap<Integer, File> bfTreeMap = sortBackupFilesAsTreeMap(backupFiles, basename, extension);
+      TreeMap<Integer, File> bfTreeMap = sortBackupFilesAsTreeMap(backupFiles, basename);
 
       if (reverseOrder)
       {
@@ -290,7 +283,7 @@ public class BackupFiles
           // int n = tempMax - m;
           String backupfilename = dir + File.separatorChar
                   + BackupFilenameFilter.getBackupFilename(n, basename,
-                          suffix, digits, extension);
+                          suffix, digits);
           File backupfile_n = new File(backupfilename);
 
           if (!backupfile_n.exists())
@@ -305,7 +298,7 @@ public class BackupFiles
             // move the largest (max) rolled file to a temp file and add to the delete list
             try
             {
-              File temp = File.createTempFile(backupfilename, ".tmp",
+              File temp = File.createTempFile(backupfilename, TEMP_FILE_EXT,
                     dirFile);
               backupfile_n.renameTo(temp);
 
@@ -362,7 +355,7 @@ public class BackupFiles
     // Let's make the new backup file!! yay, got there at last!
     String latestBackupFilename = dir + File.separatorChar
             + BackupFilenameFilter.getBackupFilename(nextIndexNum, basename,
-                    suffix, digits, extension);
+                    suffix, digits);
     File latestBackupFile = new File(latestBackupFilename);
     ret = ret && file.renameTo(latestBackupFile);
 
@@ -419,14 +412,14 @@ public class BackupFiles
     }
   }
 
-  private TreeMap sortBackupFilesAsTreeMap(File[] backupFiles, String basename, String extension) {
+  private TreeMap sortBackupFilesAsTreeMap(File[] backupFiles, String basename) {
       // sort the backup files (based on integer found in the suffix) using a
       // precomputed Hashmap for speed
       Map<Integer, File> bfHashMap = new HashMap<>();
       for (int i = 0; i < backupFiles.length; i++)
       {
           File f = backupFiles[i];
-          BackupFilenameParts bfp = new BackupFilenameParts(f, basename, suffix, digits, extension);
+          BackupFilenameParts bfp = new BackupFilenameParts(f, basename, suffix, digits);
           bfHashMap.put(bfp.indexNum(), f);
       }
       TreeMap<Integer, File> bfTreeMap = new TreeMap<>();
@@ -497,18 +490,9 @@ public class BackupFiles
 
     String filename = file.getName();
     String basename = filename;
-    String extension = "";
-    int dotcharpos = filename.lastIndexOf('.');
-    // don't split of filenames with the last '.' at the very beginning or
-    // very end of the filename
-    if ((dotcharpos > 0) && (dotcharpos < filename.length() - 1))
-    {
-      basename = filename.substring(0, dotcharpos);
-      extension = filename.substring(dotcharpos); // NOTE this includes the '.'
-    }
     
     // find existing backup files
-    BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix, digits, extension);
+    BackupFilenameFilter bff = new BackupFilenameFilter(basename, suffix, digits);
     backupFiles = dirFile.listFiles(bff); // is clone needed?
     
     // sort the backup files (based on integer found in the suffix) using a
@@ -518,7 +502,7 @@ public class BackupFiles
     {
       File f = backupFiles[i];
       BackupFilenameParts bfp = new BackupFilenameParts(f, basename, suffix,
-              digits, extension);
+              digits);
       bfHashMap.put(bfp.indexNum(), f);
     }
     TreeMap<Integer, File> bfTreeMap = new TreeMap<>();