source: branches/port5/HELP_SOURCE/oldhelp/sequence_colors.hlp

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UP      arb.hlp
UP      glossary.hlp
UP      e4.hlp

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#************* Title of helpfile !! and start of real helpfile ********
TITLE           Change Colors Of Sequences

OCCURRENCE      ARB_EDIT4

DESCRIPTION     The ARB_EDIT4 editor uses two tables to translate the
                original sequence into a colored displayed sequence:

                First Step:

                      Each character in each sequence is translated into
                      a new character and a color index (0..9) using the definitions
                      from the 'SEQUENCE COLORS' subwindow.

                      - There are different sets (S_0 .. S_#) of color shemes,
                        one column for each set.

                      - In the first row you may choose which set is used for translation.

                      - The first column shows the characters which should be
                        translated/replaced.

                      - The nth + 1 column holds the data for translation set n.
                        Each of its fields has two characters:

                           1. the character which should replace the original value,
                           or '=' if no translation should be performed.

                           2. A color index for this character, between 0 and 9.

                Second Step:

                       Each of the color indices (0..9) corresponds to one of
                       the colors defined in <Properties/Change colors & fonts>,
                       namely to

                              index     corresponding color
                              0         SEQUENCES
                              1         HELIX(1)
                              2         COLOR 2
                              3         COLOR 3
                              .         .
                              .         .
                              9         COLOR 9


EXAMPLES        You may use this feature to show:

                - A simplified version of your amino acid alignment.
                - Only YR instead of ACGTU
                - Only ambiguous symbols
                - ...

BUGS            No bugs known