Directory HELP_SOURCE/source/

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westram 2024-10-01 18:45 Rev.: 19499

* implements #863
* add new ACI command "dupidx" (active in group search).
* update group-enumeration presets: use '~' instead of '_'. use new ACI command 'dupidx'.

9 lines of code changed in 2 files:

• HELP_SOURCE/source: group_rename.hlp (new)

westram 2023-09-13 18:33 Rev.: 19489

* reintegrates 'macros' into 'trunk'
* implements #856
* adds: log:branches/macros@19482:19488

72 lines of code changed in 3 files:

• HELP_SOURCE/source: macro.hlp (new), macro_interruption.hlp (new 58)

westram 2023-07-04 12:14 Rev.: 19425

* reintegrates 'ali' into 'trunk'
- refactorings + fixes related to SEQ_QUALITY + HELIX
* adds: log:branches/ali@19407:19424

15 lines of code changed in 3 files:

• HELP_SOURCE/source: seq_quality.hlp (+3 -1), species_configs.hlp (new)

westram 2023-06-25 16:59 Rev.: 19411

* update documentation of SEQ_QUALITY:
- non-evaluated fields
- usage of default helix base pairings.

0 lines of code changed in 2 files:

• HELP_SOURCE/source: seq_quality.hlp (new)

westram 2023-06-25 16:30 Rev.: 19407

* reintegrates 'ali' into 'trunk'
- use bond settings from EDIT4 in SECEDIT
- fix refresh logic
- refactor underlying code
* adds: log:branches/ali@19393:19406

19 lines of code changed in 3 files:

• HELP_SOURCE/source: helixsym.hlp (+3 -1), sec_bonddef.hlp (+16 -8)

westram 2023-06-15 15:31 Rev.: 19393

* reintegrates 'ali' into 'trunk'
- refactored misused enum
- support for helix pairs:
* drop non-standard defs
* add more user defs
- change defaults
- add several predefined configs (esp. for IUPAC ambiguity codes)
* adds: log:branches/ali@19376:19392

2 lines of code changed in 2 files:

• HELP_SOURCE/source: helixsym.hlp (+2 -2)

westram 2023-06-03 13:36 Rev.: 19376

* reintegrates 'ali' into 'trunk'
- completes #854
* adds: log:branches/ali@19363:19375

17 lines of code changed in 1 file:

• HELP_SOURCE/source: bad_alignment.hlp (+17 -1)

westram 2023-05-25 14:50 Rev.: 19363

* reintegrates 'ali' into 'trunk'
* basically implements #854
* adds: log:branches/ali@19357:19362

35 lines of code changed in 1 file:

• HELP_SOURCE/source: bad_alignment.hlp (new 35)

westram 2022-11-30 20:16 Rev.: 19353

* added script to delete unlisted trees.

0 lines of code changed in 2 files:

• HELP_SOURCE/source: treeadm.hlp (new)

westram 2022-11-30 20:12 Rev.: 19352

* added script to delete unlisted species selections.

0 lines of code changed in 2 files:

• HELP_SOURCE/source: mg_species_configs.hlp (new)

westram 2022-11-30 20:00 Rev.: 19351

* added script to delete unlisted SAIs.

0 lines of code changed in 2 files:

• HELP_SOURCE/source: ad_extended.hlp (changed)

westram 2022-11-17 12:29 Rev.: 19348

* emphasize reference- and ptserver-database have to be the same database!

18 lines of code changed in 1 file:

• HELP_SOURCE/source: sina_main.hlp (+18 -6)

westram 2022-10-22 19:30 Rev.: 19283

* allow to define a separator used to generate clusternames
- old hardcoded default was '_' (which interferes with groupname conventions)
- new customisable default is '-'
- use custom separator
* in get_upgroup_info().
* for matchrate.
- correctly handle empty separator.
* change other hardcoded characters
- avoid '_' in {{{WHOLE_TREE}}} (now uses {{{<WHOLE TREE>}}}).
- neighter use '/' nor '-' when inserting relative notation (old: {{{3-4/7}}} new {{{3.4[7]}}}).
* part of #832

2 lines of code changed in 1 file:

• HELP_SOURCE/source: cluster_group.hlp (+2)

westram 2022-10-22 19:17 Rev.: 19280

* document collaboration between 'create groups' with 'append original' and 'delete groups'.

0 lines of code changed in 2 files:

• HELP_SOURCE/source: cluster_group.hlp (new)

westram 2022-09-08 13:45 Rev.: 19270

* document default of sina binary (was changed with [19240]).
* add warning.

2 lines of code changed in 1 file:

• HELP_SOURCE/source: sina_main.hlp (+2 -1)

westram 2022-09-05 16:02 Rev.: 19262

* add 'View sysinfo' entry to arb 'Tools' menu.
- shows 'sys.info' generated by arb_launcher.
* document 'ARB session log archive'.

10 lines of code changed in 2 files:

• HELP_SOURCE/source: console.hlp (new)

westram 2022-09-01 16:19 Rev.: 19245

* reintegrates 'sina' into 'trunk'
- build/deliver sina together with arb
* adds: log:branches/sina@18984:19043,19046:19069,19072:19244

286 lines of code changed in 4 files:

• HELP_SOURCE/source: markbyref.hlp (+3 -2), sina_main.hlp (+283 -53)

westram 2022-08-06 19:25 Rev.: 19222

* reintegrates 'split' into 'trunk'
- completes #846
* adds: log:branches/split@19169:19221

4 lines of code changed in 1 file:

• HELP_SOURCE/source: split.hlp (+4)

westram 2022-07-21 14:01 Rev.: 19167

* reintegrates 'split' into 'trunk'
* adds: log:branches/split@19102:19166

24 lines of code changed in 1 file:

• HELP_SOURCE/source: split.hlp (+24 -5)

westram 2022-06-29 14:54 Rev.: 19100

* reintegrates 'split' into 'trunk'
- implemented beta version of alignment splitter
* adds: log:branches/split@19077:19099

51 lines of code changed in 5 files:

• HELP_SOURCE/source: concatenate.hlp (new), merge_species.hlp (+1 -1), split.hlp (new 44)

westram 2022-05-06 10:44 Rev.: 19022

* add example macro for database maintainers
- allows to delete all fields except those listed in the script
- script needs to be edited (to allow execution and to maintain field list)
* mention script in "Delete Fields" help.

0 lines of code changed in 2 files:

• HELP_SOURCE/source: spaf_delete.hlp (new)

westram 2022-03-30 11:48 Rev.: 18974

* {{{next_expand_mode}}} now also expands all groups containing unmarked species:
- can be applied to subtrees by key 'x'.
- update documentation.
- impl: also count **unmarked** species in {{{AWT_graphic_tree_group_state}}}.

4 lines of code changed in 2 files:

• HELP_SOURCE/source: nt_keys.hlp (new)

westram 2022-03-30 11:44 Rev.: 18973

* implement 'expand unmarked'
- call from 'collapse' menu.
- document.

1 lines of code changed in 2 files:

• HELP_SOURCE/source: tree_group.hlp (new)

westram 2022-02-28 14:58 Rev.: 18937

* mention various 'count species' menu entries.
* remove unused .hlp (count now refers to same helpfile as mark).

0 lines of code changed in 3 files:

• HELP_SOURCE/source: sp_count_mrk.hlp (del), sp_mark.hlp (new)

westram 2021-12-20 18:44 Rev.: 18883

* reintegrates 'nds' into 'trunk'
- fixes #841
* adds: log:branches/nds@18843:18882

33 lines of code changed in 4 files:

• HELP_SOURCE/source: props_nds.hlp (new), tr_export.hlp (+31 -18)

westram 2021-12-17 16:32 Rev.: 18863

* document 'Import fields from calc-sheet'.
* link to 'Export fields (to calc-sheet using NDS)'.
* add another pointer, where to add helpfiles for GDE menus.

2 lines of code changed in 2 files:

• HELP_SOURCE/source: arb_export_nds.hlp (+2)