source: branches/lib/HELP_SOURCE/source/sp_mark.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: 1.8 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4
5#       sub topics:
6SUB     mark.hlp
7SUB     sp_info.hlp
8
9# format described in ../help.readme
10
11
12TITLE           Marking species
13
14OCCURRENCE      ARB_NT/Species/Mark species/...
15
16DESCRIPTION     Provides several ways to mark species.
17
18                Three general methods are available:
19                         * mark
20                         * unmark
21                         * invert
22
23                Each of these methods can be applied to one of
24                three basic sets, namely
25                     * all species in the database
26                     * all species in the current tree or
27                     * all species NOT in the current tree
28
29                These three sets can be intersected with one of the more specific
30                sets, which are provided by the submenu entries at the bottom of
31                the 'Mark species' menu, namely
32                    * all complete species (see LINK{partial_sequences.hlp}),
33                    * all partial species or
34                    * all species with data in the current alignment.
35
36NOTES           To check the number of marked species
37                - look at the button in the ARB_NT top area displaying the number of all marked species or
38                - choose one of the various 'Count marks of .. species ..' from the 'Mark species' menu.
39
40                The "current tree" mentioned above is the tree currently displayed in the main window.
41                When you have multiple ARB_NT windows open (see LINK{newwindow.hlp}), make sure
42                you use the menu of the intended ARB_NT window.
43
44                When using one or two sets (tree, complete, partial or alignment), all species
45                not included in the set (or in both sets) will not be affected/counted.
46
47EXAMPLES        None
48
49WARNINGS        None
50
51BUGS            No bugs known
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