JAL-3676 Documentation in Help for Java Console, Logging and Reporting Bugs

[jalview.git] / src / jalview / io / BackupFiles.java

diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java
index 4f86f3d..2acd6cc 100644 (file)
--- a/src/jalview/io/BackupFiles.java
+++ b/src/jalview/io/BackupFiles.java
@@ -131,7 +131,7 @@ public class BackupFiles
       {
         String tempfilename = file.getName();
         File tempdir = file.getParentFile();
-        Cache.log.debug(
+        Cache.log.trace(
                 "BACKUPFILES [file!=null] attempting to create temp file for "
                         + tempfilename + " in dir " + tempdir);
         temp = File.createTempFile(tempfilename,
@@ -141,7 +141,7 @@ public class BackupFiles
       }
       else
       {
-        Cache.log.debug(
+        Cache.log.trace(
                 "BACKUPFILES [file==null] attempting to create default temp file "
                         + DEFAULT_TEMP_FILE + " with extension "
                         + TEMP_FILE_EXT);
@@ -152,26 +152,27 @@ public class BackupFiles
       Cache.log
               .error("Could not create temp file to save to (IOException)");
       Cache.log.error(e.getMessage());
-      Cache.log.debug(e.getStackTrace());
+      Cache.log.debug(Cache.getStackTraceString(e));
     } catch (Exception e)
     {
       Cache.log.error("Exception ctreating temp file for saving");
-      Cache.log.debug(e.getStackTrace());
+      Cache.log.debug(Cache.getStackTraceString(e));
     }
     this.setTempFile(temp);
   }
 
   public static void classInit()
   {
-    Cache.log.debug("BACKUPFILES classInit");
+    Cache.initLogger();
+    Cache.log.trace("BACKUPFILES classInit");
     boolean e = Cache.getDefault(ENABLED, true);
     setEnabled(e);
-    Cache.log.debug("BACKUPFILES " + (e ? "enabled" : "disabled"));
+    Cache.log.trace("BACKUPFILES " + (e ? "enabled" : "disabled"));
     BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
             .getSavedBackupEntry();
-    Cache.log.debug("BACKUPFILES preset scheme " + bfpe.toString());
+    Cache.log.trace("BACKUPFILES preset scheme " + bfpe.toString());
     setConfirmDelete(bfpe.confirmDelete);
-    Cache.log.debug("BACKUPFILES confirm delete " + bfpe.confirmDelete);
+    Cache.log.trace("BACKUPFILES confirm delete " + bfpe.confirmDelete);
   }
 
   public static void setEnabled(boolean flag)
@@ -218,7 +219,7 @@ public class BackupFiles
       Cache.log.error(
               "IOException when getting Canonical Path of temp file '"
                       + this.getTempFile().getName() + "'");
-      Cache.log.debug(e.getStackTrace());
+      Cache.log.debug(Cache.getStackTraceString(e));
     }
     return path;
   }
@@ -262,7 +263,7 @@ public class BackupFiles
       return true;
     }
 
-    Cache.log.debug("BACKUPFILES rollBackupFiles starting");
+    Cache.log.trace("BACKUPFILES rollBackupFiles starting");
 
     String dir = "";
     File dirFile;
@@ -270,19 +271,19 @@ public class BackupFiles
     {
       dirFile = file.getParentFile();
       dir = dirFile.getCanonicalPath();
-      Cache.log.debug("BACKUPFILES dir: " + dir);
+      Cache.log.trace("BACKUPFILES dir: " + dir);
     } catch (Exception e)
     {
       Cache.log.error(
               "Could not get canonical path for file '" + file + "'");
       Cache.log.error(e.getMessage());
-      Cache.log.debug(e.getStackTrace());
+      Cache.log.debug(Cache.getStackTraceString(e));
       return false;
     }
     String filename = file.getName();
     String basename = filename;
 
-    Cache.log.debug("BACKUPFILES filename is " + filename);
+    Cache.log.trace("BACKUPFILES filename is " + filename);
     boolean ret = true;
     // Create/move backups up one
 
@@ -295,11 +296,11 @@ public class BackupFiles
     int nextIndexNum = 0;
 
     Cache.log
-            .debug("BACKUPFILES backupFiles.length: " + backupFiles.length);
+            .trace("BACKUPFILES backupFiles.length: " + backupFiles.length);
     if (backupFiles.length == 0)
     {
       // No other backup files. Just need to move existing file to backupfile_1
-      Cache.log.debug(
+      Cache.log.trace(
               "BACKUPFILES no existing backup files, setting index to 1");
       nextIndexNum = 1;
     }
@@ -313,7 +314,7 @@ public class BackupFiles
       if (reverseOrder)
       {
         // backup style numbering
-        Cache.log.debug("BACKUPFILES rolling files in reverse order");
+        Cache.log.trace("BACKUPFILES rolling files in reverse order");
 
         int tempMax = noMax ? -1 : max;
         // noMax == true means no limits
@@ -345,7 +346,7 @@ public class BackupFiles
             // no "oldest" file to delete
             previousFile = backupfile_n;
             fileToBeDeleted = null;
-            Cache.log.debug("BACKUPFILES No oldest file to delete");
+            Cache.log.trace("BACKUPFILES No oldest file to delete");
             continue;
           }
 
@@ -356,9 +357,9 @@ public class BackupFiles
             File replacementFile = backupfile_n;
             long fileToBeDeletedLMT = fileToBeDeleted.lastModified();
             long replacementFileLMT = replacementFile.lastModified();
-            Cache.log.debug("BACKUPFILES fileToBeDeleted is "
+            Cache.log.trace("BACKUPFILES fileToBeDeleted is "
                     + fileToBeDeleted.getAbsolutePath());
-            Cache.log.debug("BACKUPFILES replacementFile is "
+            Cache.log.trace("BACKUPFILES replacementFile is "
                     + backupfile_n.getAbsolutePath());
 
             try
@@ -383,7 +384,7 @@ public class BackupFiles
 
                 boolean delete = confirmNewerDeleteFile(fileToBeDeleted,
                         replacementFile, true);
-                Cache.log.debug("BACKUPFILES "
+                Cache.log.trace("BACKUPFILES "
                         + (delete ? "confirmed" : "not") + " deleting file "
                         + fileToBeDeleted.getAbsolutePath()
                         + " which is newer than "
@@ -416,7 +417,7 @@ public class BackupFiles
               Cache.log.error(
                       "Error occurred, probably making new temp file for '"
                               + fileToBeDeleted.getName() + "'");
-              Cache.log.error(e.getStackTrace());
+              Cache.log.error(Cache.getStackTraceString(e));
             }
 
             // reset
@@ -431,7 +432,9 @@ public class BackupFiles
           {
             if (previousFile != null)
             {
-              ret = ret && moveFileToFile(backupfile_n, previousFile);
+              // using boolean '&' instead of '&&' as don't want moveFileToFile
+              // attempt to be conditional (short-circuit)
+              ret = ret & moveFileToFile(backupfile_n, previousFile);
             }
           }
 
@@ -456,12 +459,12 @@ public class BackupFiles
           }
           bfsb.append(backupFiles[i].getName());
         }
-        Cache.log.debug("BACKUPFILES backupFiles: " + bfsb.toString());
+        Cache.log.trace("BACKUPFILES backupFiles: " + bfsb.toString());
 
         // noMax == true means keep all backup files
         if ((!noMax) && bfTreeMap.size() >= max)
         {
-          Cache.log.debug("BACKUPFILES noMax: " + noMax + ", " + "max: "
+          Cache.log.trace("BACKUPFILES noMax: " + noMax + ", " + "max: "
                   + max + ", " + "bfTreeMap.size(): " + bfTreeMap.size());
           // need to delete some files to keep number of backups to designated
           // max.
@@ -471,7 +474,7 @@ public class BackupFiles
           int numToDelete = suffix.indexOf(NUM_PLACEHOLDER) > -1
                   ? bfTreeMap.size() - max + 1
                   : 0;
-          Cache.log.debug("BACKUPFILES numToDelete: " + numToDelete);
+          Cache.log.trace("BACKUPFILES numToDelete: " + numToDelete);
           // the "replacement" file is the latest backup file being kept (it's
           // not replacing though)
           File replacementFile = numToDelete < backupFiles.length
@@ -484,7 +487,7 @@ public class BackupFiles
             File fileToBeDeleted = backupFiles[i];
             boolean delete = true;
 
-            Cache.log.debug(
+            Cache.log.trace(
                     "BACKUPFILES fileToBeDeleted: " + fileToBeDeleted);
 
             boolean newer = false;
@@ -547,9 +550,11 @@ public class BackupFiles
     String latestBackupFilename = dir + File.separatorChar
             + BackupFilenameParts.getBackupFilename(nextIndexNum, basename,
                     suffix, digits);
-    Cache.log.debug("BACKUPFILES Moving old file [" + file
+    Cache.log.trace("BACKUPFILES Moving old file [" + file
             + "] to latestBackupFilename [" + latestBackupFilename + "]");
-    ret |= moveFileToFile(file, new File(latestBackupFilename));
+    // using boolean '&' instead of '&&' as don't want moveFileToFile attempt to
+    // be conditional (short-circuit)
+    ret = ret & moveFileToFile(file, new File(latestBackupFilename));
     Cache.log.debug(
             "BACKUPFILES moving " + file + " to " + latestBackupFilename
                     + " was " + (ret ? "" : "NOT ") + "successful");
@@ -721,10 +726,10 @@ public class BackupFiles
         for (int i = 0; i < deleteFiles.size(); i++)
         {
           File fileToDelete = deleteFiles.get(i);
-          Cache.log.debug(
-                  "BACKUPFILES deleting fileToDelete:" + fileToDelete);
+          Cache.log.trace("BACKUPFILES about to delete fileToDelete:"
+                  + fileToDelete);
           fileToDelete.delete();
-          Cache.log.warn("deleting '" + fileToDelete.getName() + "'");
+          Cache.log.warn("deleted '" + fileToDelete.getName() + "'");
         }
       }
 
@@ -772,7 +777,6 @@ public class BackupFiles
     boolean okay = roll && rename;
     if (!okay)
     {
-      boolean yesno = false;
       StringBuilder messageSB = new StringBuilder();
       messageSB.append(MessageManager.getString(
               "label.backupfiles_confirm_save_file_backupfiles_roll_wrong"));
@@ -797,6 +801,12 @@ public class BackupFiles
                 "label.backupfiles_confirm_save_new_saved_file_not_ok"));
         // "The new saved file might not be okay."
       }
+      if (messageSB.length() > 0)
+      {
+        messageSB.append("\n");
+      }
+      messageSB
+              .append(MessageManager.getString("label.continue_operation"));
 
       int confirmButton = Platform.isHeadless() ? JvOptionPane.OK_OPTION
               : JvOptionPane.showConfirmDialog(Desktop.desktop,
@@ -886,30 +896,31 @@ public class BackupFiles
 
   public static boolean moveFileToFile(File oldFile, File newFile)
   {
+    Cache.initLogger();
     boolean ret = false;
     Path oldPath = Paths.get(oldFile.getAbsolutePath());
     Path newPath = Paths.get(newFile.getAbsolutePath());
     try
     {
       // delete destination file - not usually necessary but Just In Case...
-      Cache.log.debug("BACKUPFILES deleting " + newFile.getAbsolutePath());
+      Cache.log.trace("BACKUPFILES deleting " + newFile.getAbsolutePath());
       newFile.delete();
-      Cache.log.debug("BACKUPFILES moving " + oldFile.getAbsolutePath()
+      Cache.log.trace("BACKUPFILES moving " + oldFile.getAbsolutePath()
               + " to " + newFile.getAbsolutePath());
       Files.move(oldPath, newPath, StandardCopyOption.REPLACE_EXISTING);
       ret = true;
-      Cache.log.debug("BACKUPFILES move seems to have succeeded");
+      Cache.log.trace("BACKUPFILES move seems to have succeeded");
     } catch (IOException e)
     {
       Cache.log.warn("Could not move file '" + oldPath.toString() + "' to '"
               + newPath.toString() + "'");
       Cache.log.error(e.getMessage());
-      Cache.log.debug(e.getStackTrace());
+      Cache.log.debug(Cache.getStackTraceString(e));
       ret = false;
     } catch (Exception e)
     {
       Cache.log.error(e.getMessage());
-      Cache.log.debug(e.getStackTrace());
+      Cache.log.debug(Cache.getStackTraceString(e));
       ret = false;
     }
     return ret;