source: branches/lib/HELP_SOURCE/source/tr_export.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: 3.8 KB
Line 
1#       main topics:
2UP      arb.hlp
3UP      glossary.hlp
4UP      treeadm.hlp
5
6#       sub topics:
7#SUB     subtopic.hlp
8
9# format described in ../help.readme
10
11
12TITLE           Export tree to file
13
14OCCURRENCE      ARB_NT/Tree admin/Export
15
16DESCRIPTION     Writes a tree to file in Newick format
17
18                Press the 'EXPORT' button to display the 'TREE SAVE' window.
19
20                Select a tree file from the 'Directories and Files' subwindow or
21                type the file name to the 'FILE NAME' subwindow.
22
23        NEWICK TREE FORMAT
24
25               Nodetype
26
27                      Species ID
28
29                              This is the traditional format using species IDs as leaf names.
30
31                      NDS
32
33                              This uses the current NDS tree settings as leaf names,
34                              i.e. this mode can be used for EXPORT ONLY!
35                              (until #774 gets implemented).
36
37                              The "truncated" NDS mode respects the WIDTH entry in LINK{props_nds.hlp},
38                              as done by the arb tree display.
39                              This was the hardcoded behavior until arb-7.0.
40
41                              The newer "untruncated" NDS mode ignores the WIDTH field and
42                              always exports complete field contents.
43
44                              Group names are now as well generated via NDS in NDS mode.
45                              To export plain group names, use a group NDS with WIDTH=0 and
46                              ACI='taxonomy(1)' (which is the current default).
47
48               Label quoting
49
50                    choose whether and how to quote names for leafs and/or groups.
51                    Quoting names may be necessary to ensure other software is able
52                    to read the generated tree files.
53
54               Replace problem chars
55
56                    if checked, problematic characters in labels will be replaced (currently "()[]:;," plus
57                    used quote, if any).
58
59               Save group names
60
61                    if marked, groupnames (taxonomy) are written to the tree file.
62
63               Save branch lengths
64
65                    if marked, branchlengths are written to the tree file.
66
67               Save bootstraps
68
69                    if marked, bootstraps are written to the tree file.
70
71        ARB_XML TREE FORMAT
72
73                Simple XML Format (export only; experimental)
74
75                Hide folded groups
76
77                     If checked, folded groups will be exported as terminal node. Otherwise
78                     group contents will be written into tree file.
79
80
81NOTES           If you select both 'Save group names' and 'Save bootstraps', other programs may be
82                unable to load the tree or at least unable to interpret the bootstrap values correctly.
83
84                If a suffix is displayed in or typed to the 'SUFFIX' subwindow,
85                only the corresponding filenames will be displayed.
86                The suffix is automatically appended to the filename typed
87                to the 'File Name' subwindow.
88
89                The different export types cause the suffix to change:
90
91                    - '.tree' for normal newick
92                    - '.ntree' for newick using NDS
93                    - '.xml' for xml
94
95SECTION         Keeled groups
96
97                ARB will refuse to store LINK{keeled_groups.hlp} into a newick file.
98
99                To work around that restriction either
100                  - uncheck 'Save group names' or
101                  - read about howto fix keeled groups.
102
103WARNINGS        Tree data written with the 'NDS' option cannot be
104                reimported to the database without data loss!
105
106                It's possible to reload such a tree, but it's leafs
107                will not be linked to the correct species.
108
109BUGS            No bugs known
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