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

Last change on this file was 19575, checked in by westram, 3 weeks ago
  • reintegrates 'help' into 'trunk'
    • preformatted text gets checked for width now (to enforce it fits into the arb help window).
    • fixed help following these checks, using the following steps:
      • ignore problems in foreign documentation.
      • increase default help window width.
      • introduce control comments to
        • accept oversized preformatted sections.
        • enforce preformatted style for whole sections.
        • simply define single-line preformatted sections
          Used intensive for definition of internal script languages.
    • fixed several non-related problems found in documentation.
    • minor layout changes for HTML version of arb help (more compacted; highlight anchored/all sections).
    • refactor system interface (GUI version) and use it from help module.
  • adds: log:branches/help@19532:19574
File size: 2.5 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6SUB     move_groups.hlp
7
8# format described in ../help.readme
9
10
11TITLE           Compare taxonomy
12
13OCCURRENCE      ARB_NT/Tree/Compare taxonomy
14
15DESCRIPTION     This module helps to detect differences in taxonomy classification
16                defined by two trees.
17
18                The main feature of this module is triggered by the 'species with
19                taxonomy changed' button. It searches all species that are included in
20                both selected trees, checks if the taxonomy information differs between both trees
21                and targets those species, that differ by more than the specified number of
22                levels (see also examples below).
23
24                Use the toggle at the left side to choose whether the targeted species
25                should be marked, unmarked or get their marks inverted.
26
27                The remaining actions do not compare taxonomy information and are provided
28                for convenience here:
29                  * target species included in both trees
30                  * target species only included in one of the selected trees
31                  * target all species
32
33NOTES           Optionally the difference-level between classifications defined by left
34                and right tree can be written into a db-field of each targeted species.
35
36                 * to write the difference level to ALL species that exist in both
37                   selected trees, enter "-1" as minimum difference level.
38                 * if you're working on taxonomy, it may be useful to visualize the
39                   difference level using the LINK{field_shader.hlp}.
40
41SECTION         Examples for difference between classifications:
42
43# PREFORMATTED WIDTH 107
44                 in left tree:  Bacteria/Firmicutes_Bacilli
45                 in right tree: Bacteria/Firmicutes_Bacilli/Bacillales_Bacillaceae_2
46                 difference:    1 level
47
48                 in left tree:  Bacteria/Firmicutes_Clostridia_1/Clostridiales/Ruminococcaceae
49                 in right tree: Bacteria/Firmicutes_Clostridia_1
50                 difference:    2 levels
51
52                 in left tree:  Bacteria/Firmicutes_Clostridia_1/Clostridiales/Lachnospiraceae/uncultured
53                 in right tree: Bacteria/Firmicutes_Clostridia_1/Clostridiales/Lachnospiraceae/Oribacterium
54                 difference:    2 levels
55# PREFORMATTED RESET
56
57SECTION         RELATED
58
59                To compare topologies use LINK{compare_topo.hlp}.
60
61WARNINGS        None
62
63BUGS            No bugs known
Note: See TracBrowser for help on using the repository browser.