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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:
800 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 subtopic.hlp |
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| 7 | |
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| 8 | # format described in ../help.readme |
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| 9 | |
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| 10 | |
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| 11 | |
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| 12 | TITLE User Defined Distance Matrix |
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| 13 | |
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| 14 | OCCURRENCE ARB_DIST |
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| 15 | |
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| 16 | DESCRIPTION Allows the user to define distances between different bases. |
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| 17 | E.g. An A-T should get a smaller difference |
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| 18 | as an A-G, so the corresponding matrix elements should be set |
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| 19 | to 1.0 and 2.0. |
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| 20 | |
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| 21 | NOTE Before the algorithm starts, all matrix values will be |
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| 22 | multiplied by a factor, such that the average matrix value |
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| 23 | (except the diagonal) is approximately 1.0! |
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| 24 | |
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| 25 | To save a user matrix use <Properties/Save Properties> menu |
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| 26 | item. |
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| 27 | |
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| 28 | BUGS Works only with some distance corrections: |
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| 29 | |
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| 30 | none similarity jukes_cantor |
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| 31 | |
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| 32 | Works only with dna |
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| 33 | |
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| 34 | If enabled only ACGTU/GAPS bases are calculated. |
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| 35 | |
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