Choose this command to produce a new database index file. From the submenu select the type of database you want to index. For detailed information, please see help topics ‘Pattern Databases’ and ‘Block Databases’.
• Open Database File… (or ⌘-O)
This command displays a directory dialog box which lets you select an existing database index file on the disk. This command is not available if the maximum number of windows is already open.
Technical information: Only files of type 'MCPX' and 'MCPB' are shown in the directory dialog box so you cannot open normal text files such as the original database text files inadvertently.
Make sure that index and database files are in the same folder if you want to have access to entry documentation. See help topics ‘Pattern Databases’ and ‘Block Databases’ for details.
You may have more than one database file open at the same time (e.g. PROSITE and BLOCKS or your own private databases), but not the same file twice.
After reading the index file, the database entries are displayed in a database browser window (see help topic ‘Windows’).
• Load Sequence File… (or ⌘-L)
This menu command allows you to open a file that contains sequence data. MacPattern can process a variety of different formats; see help topic ‘Sequence File Formats’ for more information.
Only one sequence file can be open at a time. The sequence file, however, may contain more than one sequence. MacPattern does not allow you to select individual sequences from multi-sequence data files. Instead, MacPattern uses all sequences from a sequence file for the analysis.
After you have chosen a file from the standard directory dialog box MacPattern tries to determine the format of the sequences by checking the beginning of the first entry. It then opens a sequence window which displays the sequence format. All sequences in a file must have the same format.
• Close (or ⌘-W)
This command closes the active window and is the same as clicking in the active window’s close box. If the content of this window has been modified since it was last saved, a dialog box will ask you if you want to save the changes, discard them, or cancel the Close command. If the checkbox labelled “Confirm changes” in the “General Options” dialog box is not checked or if you hold down the Shift key when you close a window, changes are discarded silently.
Note: To quickly close all windows simultaneously hold down the Options key while choosing Close or clicking into a window’s close box.
• Save… (or ⌘-S)
This command saves the content of the active window to disk. The action taken depends on the type of window:
If it contains the output of a sequence analysis (results window) or documentation about a database entry (database entry window), the content will be saved as a text file which can be opened by any word processor for further manipulation. You can choose the creator of the text file from the Options menu.
If the front window is a database browser window, Save will save the current set status, i.e. information about the entry sets, the currently active set and which entries are selected (see help topic ‘Entry Sets’).
This command is not available if the front window is a sequence window because this window type cannot be modified.
• Revert
This command is only available if the active window is a database browser window. It reverts the set status of the database index file to the last saved values (see help topic ‘Entry Sets’) and discards any changes since then.
• Page Setup…
Presents the standard page setup dialog which lets you select paper size, orientation and several printer-specific options. See your Macintosh owner’s manual for details.
• Print… (or ⌘-P)
This command lets you print the content of the active window. The Print command is not available for sequence windows and database browser windows. Each page of the printout has a header with the window name and the page number and a footer showing the program name and the current date and time. To interrupt printing, press ‚åò-Period or Escape.
• Quit (or ⌘-Q)
This command terminates MacPattern and gets you back to the Finder. If the “Confirm changes” option from the “General Options” dialog box is on, then for each window whose content has changed since it was last saved, MacPattern asks you to save or discard changes or to interrupt the Quit command. Changes are discarded without prompting if the Shift key is held down when Quit is chosen.
