source: branches/lib/HELP_SOURCE/source/ed4_flags.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: 4.3 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           Species flags
12
13OCCURRENCE      ARB_EDIT4/Properties/Select species flags
14
15DESCRIPTION     This module allows to show clickable flags between the species name
16                and the sequence display area.
17
18                These flags display the values of selected database fields interpreted
19                as bool (ie. "on"/"off") and by clicking them, you are able to toggle
20                the values of these database fields (between 0 and 1).
21
22                The following list shows how different field contents are mapped to flag states:
23
24                    Field content                       Flag state
25                    ---------------------------------------------
26                    field missing                       off
27                    '0'                                 off
28                    integer<>0                          on
29                    non-numeric text                    off
30                    floating point [0.0 .. 0.5[         off
31                    floating point [0.5 .. inf]         on
32
33                You can display up to 5 database fields at the same time.
34
35                The setup of displayed flags is stored together with your database
36                (not inside edit4-properties). This means: if you save your database while
37                flags are shown in EDIT4, another user will see these flags after opening
38                the editor on that database.
39                You can use the config-manager icon to store the current setup inside
40                properties and to restore it for a different database.
41
42                The size of the clickable boxes depends on the size of the space available,
43                which is determined by other settings, eg.
44                 - by the size of several fonts,
45                 - by the lengths of the customized flag abbreviations or
46                 - by sequence-sequence-spacing.
47
48NOTES           To display more than just a bool value use LINK{ed4_nds.hlp} with an ACI like
49
50                   readdb(name);" | ";readdb(nuc)
51
52                Flags work for SAIs as well.
53
54EXAMPLES        Example workflow using species flags:
55
56                Imagine your goal is to check and probably correct the alignment of several species.
57
58                1. use LINK{sp_search.hlp} to query those species for which you like to
59                   check the alignment (e.g. by searching for low qualities reported by LINK{seq_quality.hlp})
60
61                2. use LINK{write_field_list.hlp} to write '1' into the field 'tocheck' for queried species
62
63                3. load these species into the editor and configure to show the following fields as flags:
64
65                   - 'tocheck'
66                   - 'bad_alignment' (new field)
67                   - 'bad_sequence' (new field)
68
69                   The latter two fields should not exist for this use case to work as intended.
70
71                4. Go through your sequences and decide for each
72
73                   * whether the sequence data has sufficient quality (if not -> check 'bad_sequence')
74                   * whether the sequence alignment needs to be improved (if yes -> check 'bad alignment')
75
76                   After each decision made, clear the 'tocheck' flag of that sequence.
77
78                   (when done with all sequences, you might want to remove the 'tocheck' field
79                   from the database)
80
81                5. Use Search to find all species with 'bad_sequence' set to 1 and mark these species.
82                   Either remove them from your tree(s) or completely remove them from the database.
83
84                   (now the 'bad_sequence' field is obsolete and may be removed)
85
86                6. Restart the editor with all species which have 'bad_alignment' set to 1 (plus all
87                   species needed to fix their alignment).
88
89                   Change flag setup to show the following flags:
90
91                   - 'bad_alignment'
92                   - 'fixed' (new field)
93
94                7. Go through the alignment, fix the alignment of every species which has 'bad_alignment' set
95                   and set the 'fixed' flag to mark your progress.
96
97                (now all flags entries may be removed)
98
99
100WARNINGS        None
101
102BUGS            No bugs known
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