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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:
982 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 nt_align_select.hlp |
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| 7 | SUB ad_align.hlp |
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| 8 | SUB pfold.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 What is an Alignment? |
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| 14 | |
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| 15 | DESCRIPTION Different alignments assigned to the same species (eg. sequences |
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| 16 | of different genes) can be stored in one database. |
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| 17 | The name of the currently accessible alignment (ali_*) is shown |
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| 18 | in the 3rd broad rectangular button in the top area of the |
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| 19 | ARB_NT window. |
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| 20 | |
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| 21 | The sequences themselves are not stored in the 'ali_*' field of |
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| 22 | a species, but in the subfield 'data' of 'ali_*' |
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| 23 | 'ali_*' is a container field: it holds no data |
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| 24 | except other data fields (like a directory in a file system). |
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| 25 | |
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| 26 | NOTE There is a special alignment called 'ali_genom' which is used |
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| 27 | for full genome databases. |
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| 28 | It's called an alignment because it fits into our database structure, |
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| 29 | but it should NOT contain any gaps. |
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