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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:
1015 bytes
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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 species.hlp |
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| 5 | |
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| 6 | # sub topics: |
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| 7 | SUB mark_genes.hlp |
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| 8 | SUB selected_gene.hlp |
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| 9 | SUB gene_species.hlp |
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| 10 | SUB organisms.hlp |
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| 11 | |
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| 12 | # format described in ../help.readme |
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| 13 | |
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| 14 | |
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| 15 | TITLE What are Genes? |
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| 16 | |
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| 17 | DESCRIPTION One gene is one database entry containing subentries which |
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| 18 | describe the gene. Every gene belongs to a specific |
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| 19 | organism, but one organism may have many genes. |
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| 20 | |
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| 21 | Main (reserved) entries of a gene: |
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| 22 | |
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| 23 | name, pos_begin, pos_end, complement, |
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| 24 | pos_joined, pos_begin1, pos_end1, pos_begin2, pos_end2, ... |
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| 25 | pos_uncertain, |
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| 26 | codon_start, transl_table |
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| 27 | |
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| 28 | See LINK{gene_info.hlp} for details about these fields. |
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| 29 | |
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| 30 | NOTE The main-sequence of a organism(species) is stored in the |
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| 31 | alignment 'ali_genom'. You should not change this alignment. |
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| 32 | |
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| 33 | WARNINGS The alignment 'ali_genom' should NOT contain any gaps!!!! |
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| 34 | |
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| 35 | BUGS No known bugs |
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| 36 | |
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