source: branches/lib/HELP_SOURCE/source/topology_shader.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: 2.8 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      tree_shading.hlp
5
6#       sub topics:
7#SUB     subtopic.hlp
8
9# format described in ../help.readme
10
11
12TITLE           Topology shader
13
14OCCURRENCE      ARB_NT/Tree/Tree shading/Topology shader
15
16DESCRIPTION     This shader uses the tree currently displayed in the main
17                tree display as a reference to shade species.
18
19                Species at the top of that tree will be shaded with the "low" color,
20                species at the bottom with the "high" color of the active color-range.
21
22                The intented purpose of this shader is comparing two tree topologies.
23                To do that, display one of the trees in the main window, then open a
24                second treeview using "File/New Window" and display a different tree
25                in that window.
26
27                  * The tree in the main window will always be shaded continuously.
28
29                  * Shading of trees in other windows will be non-continuous where their
30                    topology differs from the topology shown in the main window.
31                    This facilitates the detection of topology differences.
32
33                The granularity of topology shading depends on the size of the reference tree.
34                Therefore modifying the settings in section 'Value phasing' is strongly
35                recommended while comparing topologies:
36
37                  * to detect local topology differences, increase the phasing frequency
38                    until adjacent species are displayed in distinguishable colors.
39                    Then use either of the phase-shift sliders to shift the shading.
40                  * to detect global topology differences, decrease the phasing frequency.
41
42NOTES           Whenever the tree in the main tree display changes, the shading is instantly
43                updated and refreshed in all tree displays.
44
45                You can use the logical zoom-mode in the main tree display while the
46                topology shader is active, to shade only the zoomed part of the tree.
47
48EXAMPLES        The range allowed for the phasing frequency is [0.01 .. 100].
49                The number of colors available for shading is currently limited to 4096.
50
51                When you compare trees with e.g. 500k Species,
52
53                  * using a frequency of 1.0 will shade approx. 120 adjacent species with the same color,
54                  * using a frequency of 0.1 will shade approx. 1200 adjacent species with the same color and
55                  * using a frequency of 10 will shade approx. 12 adjacent species with the same color.
56
57WARNINGS        This feature will cause frequent display updates. Using it while ARB is running
58                over a remote connection may be dissatisfying.
59
60BUGS            No bugs known
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