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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:
1.4 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 arb_edit4.hlp |
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| 5 | UP extended.hlp |
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| 6 | |
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| 7 | # sub topics: |
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| 8 | SUB e4_get_species.hlp |
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| 9 | |
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| 10 | # format described in ../help.readme |
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| 11 | |
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| 12 | |
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| 13 | TITLE E. coli Reference |
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| 14 | |
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| 15 | OCCURRENCE ARB_EDIT4/Edit/Reload Ecoli sequence |
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| 16 | |
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| 17 | DESCRIPTION The SAI entry 'ECOLI' is used by the editor and other |
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| 18 | programs to detect and display the current cursor position |
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| 19 | with respect to the homologous position within the |
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| 20 | E. coli sequence. |
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| 21 | |
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| 22 | If you have no SAI 'ECOLI' yet this creates one: |
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| 23 | |
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| 24 | * Search your ecoli sequence and select it. |
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| 25 | * Go to species information window and |
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| 26 | * press SPECIES/COPY to create a copy of the LINK{selected.hlp}. |
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| 27 | This will create a species with ID 'xxx0' or similar, where 'xxx' is |
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| 28 | the ID of your selected species. |
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| 29 | * select the 'name' field and change it to 'ECOLI' |
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| 30 | * press 'SPECIES/Convert to SAI' |
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| 31 | |
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| 32 | NOTES After inserting or deleting gaps in the whole alignment (ARB_NT/ |
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| 33 | Sequence/Insert/Delete column) the reference SAI has to be |
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| 34 | reloaded by this function. |
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| 35 | |
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| 36 | You may as well choose any other sequence as reference sequence. |
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| 37 | |
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| 38 | See LINK{ed4_nds.hlp} to change the default name 'Ecoli'. |
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| 39 | |
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| 40 | BUGS No bugs known |
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