source: branches/lib/HELP_SOURCE/source/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: 1.6 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      species.hlp
5
6#       sub topics:
7SUB     ecoliref.hlp
8
9# format described in ../help.readme
10
11
12TITLE           SAI (Sequence associated information)
13
14DESCRIPTION     The main database divides all sequences into two groups:
15
16                    1. sequences of species -> stored in alignments of species
17                    2. all other sequences (masks, filters, profiles) -> stored in alignments of SAIs
18
19                You should keep the number of SAIs limited for you cannot search SAIs.
20
21SECTION         Edit SAIs
22
23                * LINK{ad_extended.hlp}
24                * LINK{e4_modsai.hlp}
25                * LINK{saicalc.hlp}
26
27SECTION         Visualize SAIs
28
29                * LINK{visualizeSAI.hlp}
30                * LINK{saiProbe.hlp}
31
32SECTION         IMPLEMENTED SAIs
33
34                ECOLI
35
36                        A copy of the E.coli sequence (see LINK{ecoliref.hlp}).
37
38                        It is used to convert the absolute alignment position into
39                        an E.coli-based position and vice versa.
40
41                        Note:
42                            * you may use any other sequence instead of ECOLI.
43                            * the name displayed in ARB_EDIT4 can be modified under Properties/NDS
44                            * see LINK{sp_sp_2_ext.hlp} for how to generate.
45
46                HELIX_NR
47
48                        Helix Numbering
49
50                HELIX
51
52                        and Helix template (see LINK{helix.hlp})
53
54                CONSENSUS
55
56                        custom consensus sequence (see LINK{consensus.hlp})
57
58SECTION         Additional information about SAI
59
60                * LINK{accessibility_sai.hlp}
61
62
63
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