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Last change
on this file was
19532,
checked in by westram, 4 months ago
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- reintegrates 'help' into 'trunk'
- tweak arb documentation:
- automatically link
- ticket references to arb
 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
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Property svn:eol-style set to
native
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Property svn:keywords set to
Author Date Id Revision
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File size:
1.3 KB
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| 1 | # main topics: |
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| 2 | UP arb.hlp |
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| 3 | UP glossary.hlp |
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| 4 | UP genes.hlp |
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| 5 | |
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| 6 | # sub topics: |
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| 7 | SUB alignment.hlp |
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| 8 | SUB mark.hlp |
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| 9 | SUB selected.hlp |
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| 10 | |
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| 11 | # format described in ../help.readme |
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| 12 | |
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| 13 | |
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| 14 | TITLE What are Species? |
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| 15 | |
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| 16 | DESCRIPTION One species is one database entry containing many database entries |
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| 17 | describing the species and one or more sequences (every sequence |
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| 18 | belongs to a different alignment). |
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| 19 | |
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| 20 | A species is not necessarily consistent with a taxonomic species. |
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| 21 | |
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| 22 | |
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| 23 | [Database field name] [Comment] |
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| 24 | |
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| 25 | name Unique identifier of the species |
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| 26 | (max 8 characters long) |
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| 27 | |
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| 28 | acc Accession number |
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| 29 | |
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| 30 | full_name (User defined) name of the species |
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| 31 | |
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| 32 | strain |
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| 33 | |
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| 34 | author |
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| 35 | |
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| 36 | journal |
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| 37 | |
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| 38 | ali_16s/data a 16s sequence (part of the 16s alignment) |
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| 39 | ali_23s/data a 23s sequence |
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| 40 | ali_.../data a ... sequence |
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| 41 | |
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| 42 | The description of the alignment, e.g. type or length, is not stored in every |
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| 43 | species but in an alignment description. |
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