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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:
886 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 | |
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| 5 | # sub topics: |
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| 6 | SUB gene_species.hlp |
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| 7 | SUB translate_dna_2_pro.hlp |
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| 8 | |
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| 9 | # format described in ../help.readme |
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| 10 | |
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| 11 | |
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| 12 | TITLE Extract genes to gene-species |
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| 13 | |
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| 14 | OCCURRENCE ARB_NT/Genome/Extract marked genes/... |
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| 15 | ARB_GENE_MAP/Genome/Extract marked genes/... |
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| 16 | |
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| 17 | DESCRIPTION For every marked gene this command creates a so called |
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| 18 | 'gene-species' (see LINK{gene_species.hlp}). |
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| 19 | |
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| 20 | Just enter the name of the alignment you like to create or |
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| 21 | to add species to. |
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| 22 | |
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| 23 | NOTES Depending on the value of 'complement' of the gene the forward |
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| 24 | or the reverse-complement sequence is extracted |
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| 25 | |
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| 26 | The fields 'codon_start' and 'transl_table' are exported to the |
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| 27 | resulting gene-species. They will be used by 'ARB_NT/Sequence/Translate..' |
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| 28 | |
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| 29 | EXAMPLES None |
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| 30 | |
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| 31 | WARNINGS None |
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| 32 | |
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| 33 | BUGS No bugs known |
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