From 4c29c5b40db7b7d0ac1175e7ec1a3ef94936416a Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Mon, 22 Oct 2018 17:10:38 +0100
Subject: [PATCH] JAL-3141 Taken the backing up code out of FileChooser into
 its own class for more generic usage, and extra data
 safe-guarding functionality

---
 src/jalview/io/BackupFiles.java |   85 ++++++++++++++++++++++++++-------------
 1 file changed, 56 insertions(+), 29 deletions(-)

diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java
index 761ab80..2d75746 100644
--- a/src/jalview/io/BackupFiles.java
+++ b/src/jalview/io/BackupFiles.java
@@ -152,45 +152,72 @@ public class BackupFiles
     // Create/move backups up one
     String numString = null;
     File lastfile = null;
-    for (int m = 0; m < max; m++)
+
+    if (reverseOrder)
     {
-      int n = reverseOrder ? max - m : m + 1;
-      numString = String.format("%0" + digits + "d", n);
-      String backupSuffix = suffix.replaceAll("%n", numString);
-      String backupfilename = dir + File.separatorChar + basename
-              + backupSuffix + extension;
-      File backupfile_n = new File(backupfilename);
-
-      if (!backupfile_n.exists())
+      // backup style numbering
+      for (int m = 0; m < max; m++)
       {
-        lastfile = backupfile_n;
-        continue;
-      }
-
-      if (m == 0)
-      { // Move the max backup to /tmp instead of deleting (Just In
-        // Case)
-        String tmpfile = "tmp-" + backupfile_n.getName();
-        try
+        int n = max - m;
+        numString = String.format("%0" + digits + "d", n);
+        String backupSuffix = suffix.replaceAll("%n", numString);
+        String backupfilename = dir + File.separatorChar + basename
+                + backupSuffix + extension;
+        File backupfile_n = new File(backupfilename);
+
+        if (!backupfile_n.exists())
         {
-          File tmpFile = File.createTempFile(tmpfile, ".tmp");
-          ret = ret && backupfile_n.renameTo(tmpFile);
-        } catch (IOException e)
+          lastfile = backupfile_n;
+          continue;
+        }
+
+        if (m == 0)
+        { // Move the max backup to /tmp instead of deleting (Just In
+          // Case)
+          String tmpfile = "tmp-" + backupfile_n.getName();
+          try
+          {
+            File tmpFile = File.createTempFile(tmpfile, ".tmp");
+            ret = ret && backupfile_n.renameTo(tmpFile);
+          } catch (IOException e)
+          {
+            System.out.println(
+                    "Could not create temp file '" + tmpfile + ".tmp'");
+          }
+        }
+        else
         {
-          System.out.println(
-                  "Could not create temp file '" + tmpfile + ".tmp'");
+          // Just In Case
+          if (lastfile != null)
+          {
+            ret = ret && backupfile_n.renameTo(lastfile);
+          }
         }
+
+        lastfile = backupfile_n;
       }
-      else
+
+    }
+    else
+    {
+      // version style numbering (with file rolling though)
+
+      // check if all backup files exist
+      int largest = 0;
+      for (int m = 0; m < max; m++)
       {
-        // Just In Case
-        if (lastfile != null)
+        int n = m + 1;
+        numString = String.format("%0" + digits + "d", n);
+        String backupSuffix = suffix.replaceAll("%n", numString);
+        String backupfilename = dir + File.separatorChar + basename
+                + backupSuffix + extension;
+        File backupfile_n = new File(backupfilename);
+        if (backupfile_n.exists())
         {
-          ret = ret && backupfile_n.renameTo(lastfile);
+          largest = n;
         }
       }
-
-      lastfile = backupfile_n;
+      // MORE CODE HERE BEN!
     }
 
     // now actually backup the important file!
-- 
1.7.10.2