source: branches/lib/HELP_SOURCE/source/mode_move.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
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 2.3 KB
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1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      mode.hlp
5
6#       sub topics:
7#SUB     subtopic.hlp
8
9# format described in ../help.readme
10
11
12TITLE           MOVE MODE
13
14OCCURRENCE      ARB_NT and ARB_PARSIMONY: <MOVE> button in the left column
15
16DESCRIPTION     The 'MOVE MODE' allows to change the topology of the
17                displayed tree by moving subtrees.
18
19                Click on the <MOVE> button in the left column of
20                the main window.
21
22                Move subtree:
23
24                     Drag and drop a branch onto a target branch, to remove the branch
25                     from the tree and insert it next to the target branch.
26
27                Move Group Info:
28
29                     Use the right mouse button to move the group information only.
30                     When dropped onto another group, both group informations will be
31                     exchanged.
32
33SECTION         ARB_PARSIMONY specific
34
35                Within the 'ARB_PARSIMONY' window, this mode can be used to test
36                tree topologies with respect to maximum parsimony criteria by
37                moving subtrees. The current parsimony value is shown after the
38                'Current Par' prompt and can be compared with the 'Optimum Par'
39                value of the initial tree (see LINK{pa_value.hlp}).
40
41
42NOTES           If you move group info in a tree that contains LINK{keeled_groups.hlp},
43                you'll probably encounter a special error message,
44                stating that a group could not be moved because otherwise
45                groups would partly overlap, which is impossible.
46
47                A simple example would be the following tree (which has
48                invalid group definitions):
49
50                              G1 = !K1
51                             /
52                         R---
53                             \
54                              G2 = !K2
55
56
57                If all tags are groups here, the original groups for '!K1' and '!K2'
58                would be equivalent to
59
60                 * K1 = R+G2
61                 * K2 = R+G1
62
63                which is impossible (because K1 and K2 share R, but none of
64                them is completely contained in the other).
65
66EXAMPLES        None
67
68WARNINGS        It is recommended to copy the tree before using the 'MOVE MODE',
69                to avoid problems caused by that bug:
70
71BUGS            Undo 'Move Group Info' does not work (leads to loss of groupname).
72                See http://bugs.arb-home.de/ticket/496
73
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