This is the first window that opens when you start ACT.
If you select this menu item a file requester will be displayed which allows you to open the sequence files and the comparison files. If the files you select are read successfully, a new window will open, which shows the sequences and the comparison. See Chapter 3 to find out how to use the main window. The comparison file is described in the section called The MSPcrunch Comparison File Format.
The "more files ..." button expands the window so that more sequence and comparison files can be read.
This menu item will close all windows and then exit the program
Choosing this menu item will discard the current options settings and then re-read the options file. Note that changing the font size in the file and then selecting this menu item will only change the font size for new windows, not existing windows. Currently some options are unaffected by this menu item. See the section called Options File Format in Chapter 5 for more information about options.
This menu item will toggle "direct editing" option. It is off be default because it can have surprising results unless the user is expecting it. See the section called "Direct Editing" in Chapter 3 for more detail about this.
These options make all the NCBI Genetic Codes available. The default setting is the Standard Code. This setting effects the display of start codons (see the section called Start Codons in Chapter 3) and the "Suspicious Start Codons ..." feature filter (see the section called Suspicious Start Codons ... in Chapter 3).
This is an advanced option for sites that have set up the ability to submit searches via SSH to another machine.
This is an advanced option that can be used to try of warning message. This options is displayed if the java property (black_belt_mode) is specified on opening up ACT, i.e. art -Dblack_belt_mode=yes.
When this option is on and the "One Line Per Entry" is on (see the section called One Line Per Entry in Chapter 3) the line that the active entry is on will be highlighted in yellow.
Show the log of informational messages from ACT. Currently the log window is only used on UNIX and GNU/Linux systems to show the output of external programs. This menu item is only available when running ACT on UNIX or GNU/Linux systems. The logging is controlled by log4j. The log4j.properties file (etc/log4j.properties in the source distribution) sets the level of logging. This can be used to send the logging information to other places such as a file.
Hide the log of informational messages. This menu item is only available when running ACT on UNIX or GNU/Linux systems.