source: branches/lib/HELP_SOURCE/source/markbyref.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
File size: 2.1 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6#SUB     subtopic.hlp
7
8# format described in ../help.readme
9
10
11TITLE           Mark by reference
12
13OCCURRENCE      ARB_NT/Species/Mark by reference
14
15DESCRIPTION     Allows to mark all species referred to in the content of a field.
16
17                Select whether to check all or marked species.
18
19                Enter the name of a field containing references.
20
21                      A reference is a single species ID ('name') or a
22                      comma-, semicolon- or space-separated list of species IDs.
23
24                Choose whether
25                       - to abort if the field is missing or
26                       - to continue w/o warning
27
28                Enter an ACI expression (see LINK{aci.hlp}) to postprocess
29                the field content. The result must be a reference or
30                reference-list (see above).
31
32                The default ACI is '/[0-9.]+[%]*://'. This works with the information
33                written by LINK{next_neighbours_listed.hlp} if score information has been added.
34
35                For the 'used_rels' field written by the fast-aligner (see LINK{faligner.hlp}) or by
36                sina (see LINK{sina_main.hlp}) you might use '/:[0-9]+//'.
37
38                Predefined configurations for these two use-cases are available using the
39                config manager button.
40
41                Below the ACI there are 3 lines showing
42                    - the LINK{selected.hlp}
43                    - the content of the specified field
44                    - the result after processing it through the ACI
45
46                Use the result line to check whether the specified ACI does generate a valid
47                ID or list of IDs.
48
49                Choose whether
50                       - to abort if an unknown reference is found or
51                       - to continue w/o warning
52
53                Click 'Mark referenced' to mark all species which are referenced
54                by the examined set of species.
55
56NOTES           None
57
58EXAMPLES        None
59
60WARNINGS        Under development
61
62BUGS            No bugs known
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