source: branches/lib/HELP_SOURCE/source/pa_locopti.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: 1.2 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      pa_optimizer.hlp
5
6#       sub topics:
7SUB     pa_globopti.hlp
8
9# format described in ../help.readme
10
11
12TITLE           Local optimization
13
14OCCURRENCE      ARB_PARSIMONY/Tree/Tree Optimization/Recursive NNI
15                ARB_PARSIMONY/<NNI-mode-button>
16
17DESCRIPTION     Locally optimizes (parts of) the current tree.
18
19                When called from the 'Tree optimization' window, the optimization is always
20                applied to the whole tree. When called via LINK{mode_nni.hlp}, it depends on
21                where you click to.
22                The settings from LINK{pa_optimizer.hlp} are used to select
23                the branches to optimize (e.g. marked and/or visible only).
24
25                At each such branch, this optimization attempts one NNI (see LINK{nni.hlp}).
26                If the tree topology improves by that modification, it will be kept.
27                Otherwise it will be undone.
28
29                If a better topology has been found, the recursion starts again (and again...)
30                until no NNI further improved the tree (see LINK{mode_nni.hlp} for exceptions).
31
32NOTES           None
33
34EXAMPLES        None
35
36WARNINGS        None
37
38BUGS            No bugs known
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