source: branches/lib/HELP_SOURCE/source/sequence_colors.hlp

Last change on this file was 19532, checked in by westram, 4 months ago
  • reintegrates 'help' into 'trunk'
    • tweak arb documentation:
      • automatically link
        • ticket references to arb bug tracker (only affects html version).
        • found URLs.
      • page titles
        • warn about long titles.
        • introduce SUBTITLEs (automatically triggered by multi-line titles in source files).
        • increase allowed length (limited by subwindow width).
      • cleanup header sections in all helpfiles.
      • fix and/or update several help files.
      • document syntax of help sources.
      • build issues:
        • when xml validation fails, next build no longer uses invalid xml ⇒ keeps failing.
        • remove output files on error (including files below ARBHOME/lib).
        • pipe output through logs to ensure proper wrapping in Entering/Leaving lines.
    • moves Tree admin + NDS menu entries to top of menu
  • adds: log:branches/help@18783:19531
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 2.2 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      e4.hlp
5
6#       sub topics:
7
8# format described in ../help.readme
9
10
11TITLE           Sequence color mapping
12
13OCCURRENCE      ARB_EDIT4/Properties/Sequence color mapping
14
15DESCRIPTION     The ARB_EDIT4 editor uses two tables to translate the
16                original sequence into a colored displayed sequence:
17
18                First Step:
19
20                      Each character in each sequence is translated into
21                      a new character and a color index (0..9) using the definitions
22                      from the 'Sequence color mapping' subwindow.
23
24                      - There are different sets (1..8) of color shemes,
25                        using two columns for each set.
26
27                      - At the top of the window you may choose which set is used
28                        for translation of nucleotides and aminoacids.
29
30                      - The first column shows the characters which should be
31                        translated/replaced.
32
33                      - The Nth + 1 column holds the translation instruction for set N.
34                        Each of its fields has two characters:
35
36                        - the character which should replace the original value,
37                          or '=' if no translation should be performed.
38
39                        - a color index for this character, between 0 and 9.
40
41                        The default for the translation instruction is '=0'
42
43                Second Step:
44
45                       Each of the color indices (0..9) corresponds to one of
46                       the colors defined in <Properties/Change colors & fonts>,
47                       namely to
48
49                              index     corresponding color
50                              0         SEQUENCES
51                              1         HELIX(1)
52                              2         COLOR 2
53                              3         COLOR 3
54                              .         .
55                              .         .
56                              9         COLOR 9
57
58
59EXAMPLES        You may use this feature to show:
60
61                - A simplified version of your amino acid alignment.
62                - Only YR instead of ACGTU
63                - Only ambiguous symbols
64                - etc.
65
66BUGS            No bugs known
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