:outputfile
Output text file to deposit data about sequences,
alignments, block coordinates, gap sizes and gap
positions. Will delete any existing file with the
same name.
#

:proceed
Press "proceed" to start the analysis.
#

:zoomdone
zoomdone
#

:zoom
A new window will appear with sequences aligned
on the currently selected color. Sequence names
and coordinates corresponding to the framed
residues will be displayed in the left.
#

:motif
A new window will appear with the list of common
triplets of the active color, aligned the way
they occur in the selected peak. The number of
sequences that would have the listed triplet at
the right position in an implicit alignment is
also shown. 
#

:parameters
To set the maximum span of triplets to "i" and the
threshold for regarding a triplet as common to "j"
click with the left button over the "i,j" matrix
element. The framed number of common triplets will
result from this selection. You may confirm this
selection with a right click or you may select an
other parameter pair with a left mouse click. 
#

:print
After a click on this button file "visa.corners"
will contain the coordinates of the main canvas.
The utility "visadump.com" uses this data to create
a Postscipt page from the image on the canvas.
Zoom and motif frames are handled similarily, using
"zoom.corners" and "motif.corners" auxiliary files
and "zoomdump.com" and "motifdump.com" scripts.
#

:redisplay
A repaint event is activated by this button. Use 
this to make sure your screen reflects the latest
selections of peaks, options, alignments, etc.
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:align
You may select alignment on a single colored peak
or on all the colored peaks from this menu. You
may also untie an earlier alignment.
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:files
Define your sequence and data files in this window.
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:filesdone
Go, and [create] load the specified sequence and
data files.
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:seqfile
Define the file of sequences to be analyzed here.
If it is not a GCG dataset format file, use the
READSEQ utility and reformat it!
#

:patfile
Define the file of common triplets here. If you
have already created it earlier with the GCGPAT 
utility, check the LOAD box, otherwise click on
CREATE, and VISA will create and dump the necesary
data file.
#
 
:seqload
When this box is checked the named file will be
loaded. If you intend to replace the pattern file
only, uncheck the box.
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:patload
If you have not created your pattern file yet,
check box "create". If you already have a pattern
file that you want to load, check box "load".
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:namesframe
A new frame is activated that displays sequence
ID-s, sequence sizes and definition lines.
#

:namesdone
Remove this annotation window
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:options
You may set several options from the frame that
is activated by a click over this button.
#

:optionsdone
Implements all the changes that have been made 
in this options frame and removes the frame from
the screen.
#

:optionstoggle
Control flags for color assignments. OVERPAINT
enables consecutive selections to redefine the
color of a triplet. If not checked the original
color assignments remain in effect. EXPAND PAINT
will add new triplets to an existing colored
triplet list. If not checked, a new list is
created. When checked SUPPRESS makes the repaint
process suppress the display of non-colored
triplets.
#

:optionshorizontalscale
This option allows you to overwrite the automatic
scaling feature of VISA.
#

:optionsverticalscale
This option gives control over the vertical
scaling of the histograms.
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:optionspalette
You may choose between several preset palettes
and optimize the image on your specific display
and color printer hardware.
#

:optionsthreshold
A single color alignment locates the best match
for every sequence to the selected peak. The
score for this best match has to exceed the
threshold (percent of maximum score) specified
here in order be accepted as a meaningful match.
Spurious best matches in case of missing peak
will be rejected.
#

:optionsflip
Background and foreground colors can be flipped
by this option, light and dark colored peaks
may both dominate the  screen in this way.
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:colors
In order to select the active color click on one
of the colored boxes. This active color is used
to color a selected peak, and also by MOTIF and
ZOOM buttons.
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:decolor
Erases earlier color assignments.
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:ruler
A soft ruler is activated by this button. You may
drag this ruler into your main canvas to estimate
sequence lengths. 
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:quit
This is the safe exit from VISA.
#