Options Menu

 

• Output File Creator

The Macintosh Finder allows you to open documents easily by double-clicking their icons. Each file on a Macintosh disk is characterised by a “creator signature” which is invisible to the user but which allows the Finder to link documents to the application program that has created them. You can pick one of several popular word processors from the Output File Creator submenu to set the creator signature of text files created by MacPattern, so that you can open and further manipulate them with standard Macintosh word processors. You may also select a word processor not on this list by choosing Other... from the submenu and locating the editor of choice with the directory dialog box that appears.

• General Options…

This command lets you set the following options:

Confirm changes before closing a window

When a window is closed or the Quit command is chosen from the File menu, MacPattern checks whether the content of the active window has changed since it was last saved. In this case, a dialog box will appear and ask you to save the changes, discard them or cancel the Close or Quit command. Turn this option off or hold down the Shift key when you close a window to circumvent this dialog. Changes are then discarded without confirmation.

Translation of nucleotide sequences

This option allows you to control MacPattern’s handling of nucleotide sequences. If “one strand” or “both strands” is selected, MacPattern will translate nucleotide sequences automatically in three or six reading frames, respectively. If “none” is selected, nucleotide sequences are not translated. This is useful if you want to analyse nucleotide sequences with your own nucleotide patterns, or if a protein sequence resembles a nucleotide sequence so much that MacPattern tries to translate it. The default is to translate only one strand.

Reopen index files on startup

If this option is checked, the PROSITE and BLOCKS index files that are currently open when the Quit command is chosen are automatically opened again when you start MacPattern next time. Note that this option is only available when you run System 7.

• Save Preferences

This command saves your current settings to a preferences file in the Preferences Folder (or the System Folder under System 6). Every time you start up MacPattern it will read this file and use the saved settings. The values stored in the preferences file include the following:

- The options set by the General Options dialog.
- The output file creator
- Information whether to display entry names or accession numbers in the pattern and 
  block browser windows.
- The number of blocks to show in a block search.

Note: To return to “factory” settings just delete the MacPattern Prefs file from your System or Preferences Folder.