source: branches/lib/HELP_SOURCE/source/ad_extended.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: 2.3 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4#       sub topics:
5
6SUB     extended.hlp
7SUB     security.hlp
8# format described in ../help.readme
9
10
11TITLE           SAI Administration
12
13OCCURRENCE      ARB_NT/SAI/Manage SAIs
14
15DESCRIPTION     This tool allows to delete, rename, copy and edit 'SAI' entries.
16                SAI is short for "sequence associated information".
17
18                The database entries contained in the selected SAI are displayed in the
19                'Info Box' subwindow.
20
21                Howto generate SAIs:
22
23                      Most SAIs will be generated by functions from the SAI menu in the ARB main window.
24
25                      It is as well possible to convert a species into an SAI (see LINK{sp_sp_2_ext.hlp}).
26                      SAIs can be converted into species entries by pressing the <COPY TO SPECIES> button.
27
28                      It is also possible to calculate SAI (from other SAI) using the LINK{saicalc.hlp}.
29
30                SAI grouping:
31
32                      Each SAI belongs to a group of SAIs. These groups appear in ARB_EDIT4.
33                      Use the 'ASSIGN GROUP' button to define the group membership of the
34                      select SAI.
35
36                SAI editing:
37
38                      Editing SAI data is possible using the sequence editor (see LINK{e4.hlp}).
39
40                      SAI may have alignment specific comments in each ali_xxx-CONTAINER.
41                      These comments are stored in the "_TYPE" field.
42                      The "EDIT COMMENT" button will always edit the comment associated with the
43                      alignment currently selected in the arb main window.
44
45                      Using the "Edit at top" entry, you may define, which SAI
46                      show up in the top area of the sequence editor by default.
47
48NOTES           It may be necessary to set the protection level equal or higher
49                than that assigned to the particular 'SAI' entry.
50
51                An example macro ("keep_listed_SAIs.amc") is delivered together with ARB,
52                which allows to delete all unwanted SAIs from a database, by defining
53                a list of all SAIs to keep.
54                That macro can be found using the file-prompter
55                under LINK{macro.hlp} (see EXAMPLES section there).
56
57EXAMPLES        None
58
59WARNINGS        None
60
61BUGS            No bugs known
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