source: trunk/HELP_SOURCE/source/ad_align.hlp

Last change on this file was 19532, checked in by westram, 5 weeks 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: 2.0 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      security.hlp
5
6#       sub topics:
7SUB     insdel.hlp
8
9
10
11
12
13TITLE           Alignment Administration
14
15OCCURRENCE      ARB_NT/Sequence/Admin
16                ARB_MERGE/Check alignments/MODIFY
17
18DESCRIPTION  This module allows handling and modification of 'alignments'
19             (see LINK{glossary.hlp}).
20
21                Select an alignment from the 'Alignments' subwindow
22
23                Define the type of sequences (DNA, RNA, protein):
24
25                        Press the <Type of Sequences> button and choose from the
26                        displayed menu.
27
28                Set protection:
29
30                        Press the <Default Write Protection> button and choose
31                        from the displayed menu.
32
33                Press the respective buttons to perform further functions:
34
35                      DELETE:     Delete an alignment and its sequence data
36                      RENAME:     Rename an alignment
37                      CREATE:     Create a new alignment (no data)
38                      COPY:       Copy an alignment
39                      CHECK LEN:  Find the longest sequence and set the
40                                  'Maximum Seq. Length' displayed in the
41                                  corresponding subwindow
42                      FORMAT:     Append '.' to sequences up to 'Maximum Seq.
43                                  Length'.
44
45                Auto format: Whether to ask, format or skip w/o asking
46                             whenever an unformatted alignment is detected.
47
48NOTES           Some functions require setting a protection level equal to or
49                higher than that of the 'alignment'.
50
51                There is one special alignment called "ali_genom" used for full
52                genome sequences. You can't format that alignment because it is
53                necessary to ensure that it's alignment positions match those
54                used in the gene entries. For the same reason you should never
55                ever put any gap into that alignment.
56
57EXAMPLES        None
58
59WARNINGS        Be careful when deleting or changing the name of an alignment
60                while other programs are using it (eg. parsimony programs ..)
61
62BUGS            No bugs known
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