source: branches/lib/HELP_SOURCE/source/nt_tree_settings_bootstrap.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: 3.6 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      nt_tree_settings.hlp
5
6#       sub topics:
7SUB     multifurcate.hlp
8SUB     mode_length.hlp
9
10# format described in ../help.readme
11
12
13TITLE           Bootstrap display settings
14
15OCCURRENCE      ARB_NT/Properties/Tree options/Bootstrap settings
16
17DESCRIPTION     The following bootstrap related display settings are available:
18
19                - 'Show bootstraps' completely toggles whether bootstrap values etc.
20                  will be displayed in the tree view.
21
22                - 'Hide bootstrap below' and 'Hide bootstrap above' allow to configure
23                  which range of bootstrap values is shown in the tree.
24
25                  Generally, branches with less than 50% cannot be regarded as supported
26                  (see also section about 'Bootstrap circle size' below).
27
28                  If a bootstrap value is hidden => no circle/ellipse will be displayed.
29
30                  Please note that bootstrap values at branches with zero length will never be
31                  displayed in ARB.
32                  Such branches occur as parts of multifurcations and are regarded as "non-present".
33                  Nevertheless such bootstrap values are NOT removed from trees (i.e. they'll appear again when
34                  you export the tree).
35
36                - 'Bootstrap style' allows to select one of the following display styles:
37                   * 'percent%' (<1% .. 100%)
38                   * 'percent' (<1 .. 100)
39                   * 'float' (<0.01 .. 1.00)
40
41                - 'Show bootstrap circles' toggles the display of bootstrap circles (only
42                  available if the tree contains bootstrap values).
43
44                - 'Greylevel of circles' allows to configure the shading level of bootstrap
45                  circles/disks.
46
47                - If 'Use ellipse' is active, ellipses instead of circles are drawn in
48                  dendrogram tree.
49
50                - 'Bootstrap circle zoom factor' allows to increase/reduce the size
51                  of the bootstrap circles/ellipse
52
53                - 'Bootstrap radius limit' allows to limit the max. bootstrap circle/ellipse size.
54                  If a bootstrap exceeds this limit its circle/ellipse will be drawn in a different
55                  color.
56
57NOTES           These settings will be managed together with other tree settings (use config
58                icon in 'Tree settings' window)
59
60SECTION         Bootstrap circle size
61
62                The radius of the bootstrap circle depends on the bootstrap value itself,
63                on the length of the branch from the node towards the tree root and on the
64                configured zoom factor/limit.
65
66                For a zoom factor of 1, a bootstrap value of ~44% will show a circle/ellipse
67                which completely contains the whole branch.
68
69                Such a bootstrap value indicates a certain fuzziness and the
70                associated bootstrap circle attempts to graphically visualize
71                that fuzziness.
72
73                Branches covered or overlapped by circles can be
74                considered more or less unstable.
75
76                For increasing bootstrap values the radius goes towards zero; for smaller
77                bootstrap values the radius will get infinite - that is why ARB uses
78                a 'Bootstrap radius limit'.
79
80                The formula used to calculate the (unlimited) bootstrap circle radius is
81
82                        (1/sqrt(bootstrap/100) - 1) * 2*branchlength
83
84
85EXAMPLES        None
86
87WARNINGS        None
88
89BUGS            No bugs known
Note: See TracBrowser for help on using the repository browser.