/trunk Developers: westram

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westram 2025-08-01 16:29 Rev.: 19512

* fix wrong group counts (slighly too many for some DBs).

1 lines of code changed in 1 file:

• PERL_SCRIPTS/DB: databaseReport.pl (+1 -1)

westram 2025-08-01 16:02 Rev.: 19511

* DRYed code to read entries
* simplified nested sort conditions

53 lines of code changed in 1 file:

• PERL_SCRIPTS/DB: databaseReport.pl (+53 -56)

westram 2025-08-01 12:09 Rev.: 19510

* fix int overflow while calculating steps for parsimony quick add (#807)
- thx to jan for providing a log for huge insertions

1 lines of code changed in 1 file:

• PARSIMONY: PARS_main.cxx (+1 -1)

westram 2025-07-29 11:17 Rev.: 19509

* script to analyze structure of different databases (generated reports are meant to be compared using diff viewers)

667 lines of code changed in 2 files:

• ARBDB: ad_config.cxx (+2)
• PERL_SCRIPTS/DB: databaseReport.pl (new 665)

westram 2025-07-19 12:32 Rev.: 19508

* fix {{{TEST_diff_files()}}} (failing under some conditions)
- pull-out {{{TEST_diff_behavior_using_binary_files()}}}.
- disabled test for public.
- commented (strange failure; purpose).
- remove duplicated assertion.
- run tests for different amounts of expected different lines.

41 lines of code changed in 1 file:

• CORE: arb_diff.cxx (+41 -15)

westram 2025-07-19 11:55 Rev.: 19507

* avoid building arb as root:
- may cause test failures (permissions checks apparently succeed unexpectedly when called as root)

11 lines of code changed in 2 files:

• Makefile (+9)
• CORE: arb_file.cxx (+2)

westram 2025-07-19 11:48 Rev.: 19506

* fix gcc10.x vectorization checks:
- update {{{LOOP_VECTORIZED}}} comment: fix one vectorization for gcc 10.x series. Depends on UNIT_TEST=0|1.
- document vectorization count may depend on UNIT_TEST.

4 lines of code changed in 2 files:

• ARBDB: adoptimize.cxx (+2 -2)
• SOURCE_TOOLS: vectorize.README (+2)

westram 2025-06-03 11:40 Rev.: 19505

* fix constexpr issues for compilation under OSX 15

10 lines of code changed in 2 files:

• CONVERTALN: global.h (+3 -1)
• TEMPLATES: cxxforward.h (+7 -1)

westram 2025-04-17 19:09 Rev.: 19504

* also add buttons to experiment and genes search.

48 lines of code changed in 2 files:

• GENOM: EXP_interface.cxx (+24 -22), GEN_interface.cxx (+24 -22)

westram 2025-04-17 19:00 Rev.: 19503

* add mark/unmark listed buttons to search+query.

84 lines of code changed in 4 files:

• SL/DB_QUERY: db_query.cxx (+16), db_query.h (+5 -1)
• SL/DB_UI: ui_species.cxx (+23 -21)
• lib/pictures: ad_query.fig (+40 -36)

westram 2025-04-17 15:31 Rev.: 19502

* import from calc-sheet now interprets lines ending with ',' as empty cell

10 lines of code changed in 1 file:

• PERL_SCRIPTS/ARBTOOLS: import_from_table.pl (+10 -9)

westram 2025-01-30 15:49 Rev.: 19501

* implements #865:
- allows to match species and table rows, using list entries (in cells and/or fields).

428 lines of code changed in 3 files:

• GDEHELP/HELP_WRITTEN: import_calc.help (+58 -4)
• GDEHELP/MENUS: import.menu (+21 -3)
• PERL_SCRIPTS/ARBTOOLS: import_from_table.pl (+349 -142)

westram 2025-01-30 13:19 Rev.: 19500

* rename {{{GBT_create_alignment}}} -> {{{GBT_create_new_alignment}}}.
* restore old {{{GBT_create_alignment}}} flavor used before r19146 for binary compatibility.

25 lines of code changed in 12 files:

• ARBDB: ad_t_prot.h (+2 -1), adali.cxx (+12 -2)
• AWTI: AWTI_import.cxx (+1 -1)
• EDIT4: ED4_ProteinViewer.cxx (+1 -1)
• GDE/SINA/builddir/src: query_arb.cpp (+1 -1)
• GENOM: GEN_map.cxx (+1 -1)
• NTREE: AP_consensus.cxx (+1 -1), NT_concatenate.cxx (+1 -1), NT_split_ali.cxx (+2 -2)
• SL/ALILINK: AdminGui.cxx (+1 -1), TranslateRealign.cxx (+1 -1)
• TEMPLATES: arb_unit_test.h (+1 -1)

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'.

72 lines of code changed in 5 files:

• HELP_SOURCE/source: group_rename.hlp (new)
• NTREE: NT_group_search.cxx (+6 -6), NT_tree_cmp.cxx (+5 -5)
• SL/GROUP_SEARCH: group_search.cxx (+52 -7)

westram 2024-04-09 14:39 Rev.: 19495

* rename {{{aw_file_selection}}} -> {{{aw_modal_file_selection}}} to emphasize that it will break macro-capability.
* use non-modal fileprompter to select reference database for sina.

35 lines of code changed in 5 files:

• AWT: AWT_config_manager.cxx (+2 -2)
• EDIT4: graph_aligner_gui.cxx (+27 -15)
• WINDOW: AW_cb_struct.cxx (+1 -1), AW_modal.cxx (+4 -2), aw_root.hxx (+1 -1)

westram 2024-02-05 12:50 Rev.: 19494

* collection of sysinfo terminated with error
- caused by undefined environment variable
- relevant info (like available memory) was not collected

2 lines of code changed in 1 file:

• SH: arb_launcher (+2 -2)

westram 2023-12-07 19:22 Rev.: 19493

* homebrew build looked for wrong lib-suffix. patch from jan. thx :)
* fixed a typo in {{{warn_undefined_symbols.pl}}}

4 lines of code changed in 2 files:

• PERL2ARB: Makefile.main (+3 -1), warn_undefined_symbols.pl (+1 -1)

westram 2023-11-23 12:44 Rev.: 19492

* mention {{{libgomp1}}} (required by FastTreeMP)

2 lines of code changed in 2 files:

• arb_INSTALL.txt (+1)
• SH: arb_installubuntu4arb.sh (+1)

westram 2023-11-18 10:15 Rev.: 19491

* after detecting perl/macro-incompatibility, show OS-specific advice.

10 lines of code changed in 1 file:

• SH: arb_macro_compatibility.sh (+10)

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

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

277 lines of code changed in 16 files:

• HELP_SOURCE/source: macro.hlp (+14 -13), macro_interruption.hlp (new 58)
• PERL2ARB: ARB.pm (+17)
• SL/MACROS: Makefile (+3), macro_gui.cxx (+65 -3), macros_local.hxx (+1), recmac.cxx (+21 -3), recmac.hxx (+2), trackers.cxx (+5), trackers.hxx (+2)
• WETC: Makefile (+1), WETC_main.cxx (+58 -11)
• WINDOW: aw_window.hxx (+5)
• lib/pictures: macro_interruption.fig (new 19), macro_select.fig (+6 -5)

(8976 more)