Just download the new zip file, unzip it and copy the new directory in place of the old directory.
Uninstalling:
All versions of ApE after 1.08 store a user preference directory for each user that has ever run ApE. You can delete all of these directories if you uninstall ApE. In Windows 95/98 they are usually located in C:\WINDOWS\Profiles\[username]\Application Data, in Windows XP they are in C:\Documents and Settings\[username]\Application Data. On the Mac, they are in [user home]/Library/Preferences. In Linux the directories are in [user home]/.ApE/
For versions before 1.08:
Upgrading:
In most cases upgrading is simple. Just download the new file, and put the entire directory in place of the old ApE directory.
If you want to preserve customizations you have made in the previous version, you need to move some files from the old version to the new.
In windows or LINUX/UNIX:
Caution:The Windows .exe file overwrites all of the files in the ApE directory, so before you run it to unzip the new version change the directory name of your old ApE installation to something like "ApE_old".
After you have unzipped the new version, look in the sub-directory "Accessory Files" in both old and new directories.
You can copy the following files from your old version to your new:
"ApE_Defaults.txt": This contains all of your program default values that you set in Preferences. Rarely, the newer version of ApE contains preferences that were not present in the older version. In this case, you might have to edit the files by hand. Just open them in a text editor and add any lines from the new version that don't appear in the old version.
"DNA_ladders.txt": This contains all of the DNA ladders that you might have created.
"Enzymes\Default_Enzymes.txt": This file contains all of the enzyme definitions loaded when ApE starts up. In versions before 1.04a, this file was located in the Accessory files directory.
"Features\Default_Features.txt": This file contains all of the feature definitions loaded when ApE starts up. In versions before 1.04a, this file was located in the Accessory files directory. If you have chaged the default location of the feature directory in your preferences, you should move your feature directory so that it is in the same place that it was before the upgrade.
"Icons and Images" directory: If you have created custom icons or images for ApE, those files are located in this directory
In OS X:
The same files in the Windows and LINUX versions of ApE are all present in the OS X version, but they are in different places. Some are also slightly harder to get to.
In the same directory as the ApE application file, you can find the directory "Accessory Files". In this directory are the sub-directories "Enzymes" and "Features".
"Enzymes/Default_Enzymes.txt": This contains all of the enzyme definitions loaded when ApE starts up. In versions before 1.04a, this file was located in the "Accessory Files" directory inside the application bundle (see below for instructions on accessing this file). If you delete or move the "Enzymes" folder, ApE will use its internal Default_Enzymes file.
"Features/Default_Features.txt": This contains all of the feature definitions loaded when ApE starts up. If you have chaged the default location of the feature directory in your preferences, you should move your feature directory so that it is in the same place that it was before the upgrade. In versions before 1.04a, this file was located in the Accessory files directory inside the application bundle (see below for instructions on accessing this file). If ApE can't find the features file in the place you specified in your preferences, or in the "Features" directory in the ApE folder, it will use its internal Default_Features file.
Some files are stored inside the application bundle (i.e. the program itself). To get to these files hold down the "Ctrl" key and then hold the mose button down on the program file. In the popup menu, select "Show Package Contents". Inside the resulting directory, navigate to "Contents/Resources/Scripts/Accessory Files". There you will find:
"ApE_Defaults.txt": This contains all of your program default values that you set in Preferences. Rarely, the newer version of ApE contains preferences that were not present in the older version. In this case, you might have to edit the files by hand. Just open them in a text editor and add any lines from the new version that don't appear in the old version.
"DNA_ladders.txt": This contains all of the DNA ladders that you might have created.
"Icons and Images" directory: If you have created custom icons or images for ApE, those files are located in this directory
If you are upgrading to a recent version of ApE, after you have moved the files and run the program for the first time all of your user preferences files will have been copied into their appropriate locations.
Uninstalling:
For versions below 1.08, you can just delete the program directory. No files have been copied outside of the ApE directory.
Last modified: 2:04 PM 08/22/2005
