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westram 2026-06-30 10:45 Rev.: 19916

* fix compile with clang 6 under linux
- parts of {{{TEST_naninf}}} also fails using clang under linux.
- parse real clang version from detailed version info
* AFAIK this effectively already happens under OSX (since change r12860).
- also set USE_OPENMP=0 for clang under linux.
- fix undefined code: variable length arrays (VLAs) cannot be initialized at declaration.
- use {{{-std=gnu++17}}} for clang.
- {{{str_iequal}}} + {{{count_spaces}}} fail to build as {{{constexpr}}} under clang.

40 lines of code changed in 5 files:

• Makefile (+4 -8)
• CONVERTALN: global.h (+2 -2)
• CORE: arb_diff.cxx (+3 -3)
• SL/TREE_READ: TreeRead.cxx (+6 -3)
• SOURCE_TOOLS: arb_compiler_version.pl (+25 -4)

westram 2026-06-30 10:22 Rev.: 19915

* stuff leaks in {{{TEST_SLOW_treeIO_stable}}} + {{{setBranchName_acceptingBootstrap}}}
- DRY code in latter

10 lines of code changed in 2 files:

• SL/TREE_READ: TreeRead.cxx (+6 -13)
• TOOLS: arb_consensus_tree.cxx (+4 -1)

westram 2026-06-30 10:13 Rev.: 19914

* partial merge from 'gcc' into 'trunk'
* adds: [19738/branches/gcc]

21 lines of code changed in 3 files:

• Makefile (+18 -9)
• PROBE: PT_new_design.cxx (+1 -1)
• TEMPLATES: cxxforward.h (+2 -2)

westram 2026-06-26 15:01 Rev.: 19910

* reintegrates 'tree' into 'trunk'
- fixes #787
- implements #668 + #845
- contains several changes related to #774
* adds:
- log:branches/revert@18784:18786
- log:branches/tree@18706:18758,18787:19813,19816:19909
- log:branches/update@19813:19814

7050 lines of code changed in 236 files:

• arb_CHANGES.txt (+4)
• ARBDB: TreeNode.cxx (+176 -26), TreeNode.h (+87 -20), ad_prot.h (+1), ad_t_prot.h (+4 -1), adlang1.cxx (+1 -1), adseqcompr.cxx (+2 -2), adstring.cxx (+5), adtree.cxx (+140 -52), arbdb.cxx (+1 -1), arbdbt.h (+1)
• CONSENSUS_TREE: Makefile (+2)
• CORE: arb_strbuf.h (+5)
• DIST: DI_clusters.cxx (+1 -1)
• HELP_SOURCE/source: nt_tree_settings_bootstrap.hlp (+1), tbl_boot2len.hlp (+10 -4), tr_export.hlp (+16 -3), tr_import.hlp (+14 -4)
• NTREE: Makefile (+5), NT_extern.cxx (+6 -5), NT_sort.cxx (+1 -1), NT_tree_cmp.cxx (+3 -3), ad_trees.cxx (+101 -26)
• PARSIMONY: PARS_dtree.cxx (+25 -25)
• PERL2ARB: typemap (+5 -1)
• SEQ_QUALITY: SQ_main.cxx (+1 -1)
• SL/AP_TREE: AP_Tree.cxx (+4 -2)
• SL/ARB_TREE: ARB_Tree.cxx (+2 -2), ARB_Tree.hxx (+3 -2)
• SL/NEIGHBOURJOIN: NJ.cxx (+1 -1)
• SL/PVP: pvp.cxx (+1 -1)
• SL/SPECSEL: selection_admin.cxx (+1 -1)
• SL/TREEDISP: TreeCallbacks.cxx (+30 -8), TreeDisplay.cxx (+46 -12), TreeDisplay.hxx (+1 -1)
• SL/TREE_READ: LabelTranslator.cxx (new 144), LabelTranslator.h (new 74), Makefile (+36), TreeRead.cxx (+558 -95), TreeRead.h (+5 -2), TreeTools.cxx (+12 -9)
• SL/TREE_WRITE: TreeWrite.cxx (+86 -25), TreeWrite.h (+11 -1)
• SOURCE_TOOLS: generate_all_links.sh (+2)
• STAT: ST_ml.cxx (+2 -2)
• TEMPLATES: ErrorOrType.h (+1), arb_unordered_set.h (new 33)
• TOOLS: Makefile (+12), arb_calc_pvp.cxx (+1 -1), arb_consensus_tree.cxx (+68 -14), arb_export_newick.cxx (+44 -15), arb_read_tree.cxx (+7 -7), arb_test.cxx (+11 -5)
• UNIT_TESTER: Makefile.setup.template (+3 -2), reporter.pl (+1 -1)
• UNIT_TESTER/run: group_xfer_21.log.expected (+1 -1)
• UNIT_TESTER/run/consense/1: consense1_expected.tree (+44 -44), consense1_single_expected.tree (+44 -44)
• UNIT_TESTER/run/consense/2: consense2_expected.tree (+116 -116)
• UNIT_TESTER/run/consense/3: consense3_expected.tree (+243 -243)
• UNIT_TESTER/run/consense/4: disjunct_merged_expected.tree (+30 -30), overlap_merged_expected.tree (+30 -30), overlap_mini_merged_expected.tree (+30 -30)
• UNIT_TESTER/run/consense/5: help_merged_expected.tree (+12 -12)
• UNIT_TESTER/run/consense/6: overlap_twothirds_merged_expected.tree (+30 -30)
• UNIT_TESTER/run/consense/7: overlap_mostly_expected.tree (+30 -30)
• UNIT_TESTER/run/consense/8: overlap2_mostly_expected.tree (new)
• UNIT_TESTER/run/pars: nucl-add-NNI.tree.expected (+28 -28), nucl-add-quick.tree.expected (+28 -28), nucl-addPart-CloButyP.tree.expected (new), nucl-addPart-CorGlutP-CloButyP.tree.expected (new), nucl-addPart-CorGlutP.tree.expected (+29 -29), nucl-addPart-bug609.tree.expected (+34 -34), nucl-addPartialAsFull-CorGlutP.tree.expected (+30 -30), nucl-calclength.tree.expected (+28 -28), nucl-initial.tree.expected (+27 -27), nucl-opti-NNI.tree.expected (+28 -28), nucl-opti-all-NNI.tree.expected (+28 -28), nucl-opti-global.tree.expected (+28 -28), nucl-opti-marked-global.tree.expected (+28 -28), nucl-opti-visible-global.tree.expected (+28 -28), nucl-readdall-NNI.tree.expected (+28 -28), nucl-readdall-quick.tree.expected (+28 -28), nucl-removed.tree.expected (+15 -15), prot-add-NNI.tree.expected (+20 -20), prot-add-quick.tree.expected (+20 -20), prot-addPart-MucRaceP-StrCoelP.tree.expected (+24 -24), prot-addPart-MucRaceP.tree.expected (new), prot-addPart-StrCoelP.tree.expected (new), prot-addPart-bug609.tree.expected (+26 -26), prot-addPartialAsFull-MucRaceP.tree.expected (+22 -22), prot-calclength.tree.expected (+14 -14), prot-initial.tree.expected (+20 -20), prot-mixed.tree.expected (+14 -14), prot-opti-NNI.tree.expected (+17 -17), prot-opti-all-NNI.tree.expected (+19 -19), prot-opti-global.tree.expected (+19 -19), prot-opti-marked-global.tree.expected (+20 -20), prot-removed.tree.expected (new)
• UNIT_TESTER/run/trees: acc.tree (new 32), acc_name_fullname-nondup.tree (new 24), acc_name_fullname.tree (new 46), bg_exp_p_Bs100GrpLen_1.tree (new 50), bg_exp_p_Bs100GrpLen_2.tree (new 50), bg_exp_p_Bs100Grp_1.tree (new 50), bg_exp_p_Bs100Grp_2.tree (new 50), bg_exp_p_Bs100Len_0.tree (new 50), bg_exp_p_Bs100Len_1.tree (new 50), bg_exp_p_Bs100Len_2.tree (new 50), bg_exp_p_Bs100_0.tree (new 50), bg_exp_p_Bs100_1.tree (new 50), bg_exp_p_Bs100_2.tree (new 50), bg_exp_p_BsGrpLen_0.tree (del), bg_exp_p_BsGrpLen_1.tree (new), bg_exp_p_BsGrpLen_2.tree (new), bg_exp_p_BsGrp_0.tree (del), bg_exp_p_BsGrp_1.tree (+4 -4), bg_exp_p_BsGrp_2.tree (+4 -4), bg_exp_p_BsLen_0.tree (+32 -32), bg_exp_p_BsLen_1.tree (new 50), bg_exp_p_BsLen_2.tree (new 50), bg_exp_p_Bs_0.tree (new), bg_exp_p_Bs_1.tree (new 50), bg_exp_p_Bs_2.tree (new 50), bg_exp_p_CusGrpLen_1.tree (new 50), bg_exp_p_CusGrpLen_2.tree (new 50), bg_exp_p_CusGrp_1.tree (new 50), bg_exp_p_CusGrp_2.tree (new 50), bg_exp_p_CusLen_1.tree (new 50), bg_exp_p_CusLen_2.tree (new 50), bg_exp_p_Cus_1.tree (new 50), bg_exp_p_Cus_2.tree (new 50), bg_exp_p_GrpLen_0.tree (+31 -31), bg_exp_p_Grp_0.tree (new), bg_exp_p_Len_0.tree (+31 -31), bg_exp_p_Rem100GrpLen_1.tree (new 50), bg_exp_p_Rem100GrpLen_2.tree (new 50), bg_exp_p_Rem100Grp_1.tree (new 50), bg_exp_p_Rem100Grp_2.tree (new 50), bg_exp_p_Rem100Len_1.tree (new 50), bg_exp_p_Rem100Len_2.tree (new 50), bg_exp_p_Rem100_1.tree (new 50), bg_exp_p_Rem100_2.tree (new 50), bg_exp_p_RemGrpLen_1.tree (new 50), bg_exp_p_RemGrpLen_2.tree (new 50), bg_exp_p_RemGrp_1.tree (new 50), bg_exp_p_RemGrp_2.tree (new 50), bg_exp_p_RemLen_1.tree (new 50), bg_exp_p_RemLen_2.tree (new 50), bg_exp_p_Rem_1.tree (new 50), bg_exp_p_Rem_2.tree (new 50), bg_exp_s_Bs100GrpLen_1.tree (new 35), bg_exp_s_Bs100GrpLen_2.tree (new 35), bg_exp_s_Bs100Grp_1.tree (new 35), bg_exp_s_Bs100Grp_2.tree (new 35), bg_exp_s_Bs100Len_0.tree (new 35), bg_exp_s_Bs100Len_1.tree (new 35), bg_exp_s_Bs100Len_2.tree (new 35), bg_exp_s_Bs100_0.tree (new 35), bg_exp_s_Bs100_1.tree (new 35), bg_exp_s_Bs100_2.tree (new 35), bg_exp_s_BsGrpLen_0.tree (del), bg_exp_s_BsGrpLen_1.tree (new), bg_exp_s_BsGrpLen_2.tree (+32 -32), bg_exp_s_BsGrp_0.tree (del), bg_exp_s_BsGrp_1.tree (new), bg_exp_s_BsGrp_2.tree (new), bg_exp_s_BsLen_0.tree (+32 -32), bg_exp_s_BsLen_1.tree (new 35), bg_exp_s_BsLen_2.tree (new 35), bg_exp_s_Bs_0.tree (+4 -4), bg_exp_s_Bs_1.tree (new 35), bg_exp_s_Bs_2.tree (new 35), bg_exp_s_CusGrpLen_1.tree (new 35), bg_exp_s_CusGrpLen_2.tree (new 35), bg_exp_s_CusGrp_1.tree (new 35), bg_exp_s_CusGrp_2.tree (new 35), bg_exp_s_CusLen_1.tree (new 35), bg_exp_s_CusLen_2.tree (new 35), bg_exp_s_Cus_1.tree (new 35), bg_exp_s_Cus_2.tree (new 35), bg_exp_s_GrpLen_0.tree (new), bg_exp_s_Grp_0.tree (+2 -2), bg_exp_s_Len_0.tree (new), bg_exp_s_Rem100GrpLen_1.tree (new 35), bg_exp_s_Rem100GrpLen_2.tree (new 35), bg_exp_s_Rem100Grp_1.tree (new 35), bg_exp_s_Rem100Grp_2.tree (new 35), bg_exp_s_Rem100Len_1.tree (new 35), bg_exp_s_Rem100Len_2.tree (new 35), bg_exp_s_Rem100_1.tree (new 35), bg_exp_s_Rem100_2.tree (new 35), bg_exp_s_RemGrpLen_1.tree (new 35), bg_exp_s_RemGrpLen_2.tree (new 35), bg_exp_s_RemGrp_1.tree (new 35), bg_exp_s_RemGrp_2.tree (new 35), bg_exp_s_RemLen_1.tree (new 35), bg_exp_s_RemLen_2.tree (new 35), bg_exp_s_Rem_1.tree (new 35), bg_exp_s_Rem_2.tree (new 35), bootstrap_groups.arb (new), full_name-unique.tree (new 22), full_name.tree (new 32)

westram 2026-05-21 16:02 Rev.: 19811

* updated PHYLIP urls
* store {{{Interpretation of "Newick's 8:45" Tree Format Standard}}}

210 lines of code changed in 6 files:

• GDE/PHYLIP/doc: draw.html (+2 -2), main.html (+10 -10)
• GDE/TREEPUZZLE/doc: manual.html (+1 -1)
• HELP_SOURCE/source: tr_import.hlp (+1 -1)
• SOURCE_TOOLS/docs: newick_845_doc.html (new 191), newick_doc.html (+5)

westram 2026-05-18 15:28 Rev.: 19808

* update changes.

1 lines of code changed in 1 file:

• arb_CHANGES.txt (+1)

westram 2026-05-18 14:04 Rev.: 19806

* reintegrates 'sina' into 'trunk'
- fixes #875
* adds: log:branches/sina@19802:19805

25 lines of code changed in 9 files:

• GDE/SINA/builddir/src: cseq.h (+10 -1), query_arb.cpp (+4), query_arb.h (+1 -1), rw_arb.cpp (+1), sina.cpp (+9 -4)

westram 2026-05-15 10:54 Rev.: 19762

* tweak error excerpt:
- suppress several unwanted lines.
- adds target {{{REEXTRACT}}} for testing.
- warn about empty excerpt

26 lines of code changed in 4 files:

• Makefile (+5 -1)
• PERL2ARB: Makefile.main (+1 -1)
• SOURCE_TOOLS: short_error_summary.pl (+19 -4)
• UNIT_TESTER: Makefile.suite (+1 -1)

westram 2026-05-14 19:07 Rev.: 19761

* do not list duplicated error lines in excerpt.

27 lines of code changed in 1 file:

• SOURCE_TOOLS: short_error_summary.pl (+27 -2)

westram 2026-03-26 15:15 Rev.: 19733

* fix perl compatibility script:
- close database from script.
- fix indentation.
- previously script failed in DEBUG mode under OSX
* assertion fails: {{{assertion 'openedDBs == closedDBs' failed in arbdb.cxx #435}}}
- did not happen under Linux

17 lines of code changed in 1 file:

• PERL_SCRIPTS/ARBTOOLS/TESTS: automatic.pl (+17 -14)

westram 2026-03-10 20:56 Rev.: 19731

* reintegrates 'species' into 'trunk'
- provides species selections in mergetool (#868)
* adds: log:branches/species@19693:19730

568 lines of code changed in 54 files:

• Makefile (+3), arb_CHANGES.txt (+2)
• ARBDB: ad_config.cxx (+1), gb_cb.h (+1 -1)
• ARB_GDE: GDE.cxx (+1 -1)
• DIST: DI_view_matrix.cxx (+4 -4)
• GENOM: EXP_interface.cxx (-2), GEN_interface.cxx (-2)
• GL/glAW: AW_window_ogl.cxx (+1 -2)
• HELP_SOURCE/source: mg_species.hlp (+17), mg_species_configs.hlp (+14 -11), nt_tree_select.hlp (+2 -2), species_configs.hlp (+28 -19), species_configs_highlight.hlp (+14 -9), species_configs_saveload.hlp (+1 -1), syncscroll.hlp (+2 -2)
• MERGE: MG_configs.cxx (+86 -85), MG_main.cxx (+2 -2), MG_species.cxx (+6 -4), Makefile (+3), merge.hxx (+4 -1), needs_libs (+1 -2)
• NTREE: Makefile (+14 -5), NT_branchAnalysis.cxx (+1 -1), NT_cb.cxx (+10 -6), NT_edconf.cxx (+44 -1036), NT_extern.cxx (+23 -55), NT_local_proto.h (+2 -3), NT_sort.cxx (+2 -1), NT_sync_scroll.cxx (+3 -5), ad_trees.cxx (+3 -3), needs_libs (+1)
• PHYLO: PH_display.cxx (+4 -4)
• SL/APP: app.cxx (+1 -1)
• SL/DB_QUERY: db_query.cxx (+32 -45), db_query.h (-2)
• SL/DB_UI: ui_species.cxx (-2)
• SL/MACROS: macro_gui.cxx (+1 -1)
• SL/TREEDISP: TreeDisplay.cxx (+19 -3), TreeDisplay.hxx (+16 -5)
• SOURCE_TOOLS: dep.4dummy (+3 -2), dep.alltargets (+1), dep.libtargets (+1), generate_all_links.sh (+1)
• WINDOW: AW_button.cxx (+1 -1), AW_root.cxx (+39), AW_window.cxx (+106 -120), aw_awar_defs.hxx (-1), aw_root.hxx (+1), aw_window.hxx (+15 -13)
• lib/pictures: ad_query.fig (-2), mark_configs.fig (+15 -15)
• lib/pictures/merge: configs.fig (+12 -12), species.fig (+4 -4)

westram 2026-03-10 13:11 Rev.: 19708

* update doc+gui:
- avoid terms "ARB_NT" (=former name of main arb window), "ARB_NTREE" and similar
* instead talk about "ARB main window"
- correct refs to 'ARB/Probes/PT_SERVER Admin'.
- update 'What are marked species?'.
- update protection level documentation (parts already done with previous commit).

469 lines of code changed in 230 files:

• arb_CHANGES.txt (+8 -8), arb_README.txt (+1 -1), arb_install.sh (+1 -1)
• ARBDB: adali.cxx (+1 -1)
• EDIT4: ED4_main.cxx (+1 -1)
• HELP_SOURCE/source: FORM.hlp (+1 -1), Protection.hlp (+3 -3), aci.hlp (+2 -4), acisrt.hlp (+1 -1), ad_align.hlp (+1 -1), ad_extended.hlp (+1 -1), alignment.hlp (+10 -10), arb_commands.hlp (+5 -6), arb_db.hlp (+1 -1), arb_edit4.hlp (+4 -4), arb_export.hlp (+1 -1), arb_export_nds.hlp (+1 -1), arb_import.hlp (+2 -2), arb_intro.hlp (+1 -2), arb_merge.hlp (+2 -2), arb_merge_into.hlp (+2 -2), arb_merge_outof.hlp (+2 -2), arb_merge_workflow.hlp (+6 -6), arb_ntree.hlp (+8 -5), arb_pars.hlp (+4 -4), arb_pars_init.hlp (+1 -1), asciiprint.hlp (+1 -1), awt_csp.hlp (+1 -1), bonds.hlp (+2 -2), branch_analysis.hlp (+2 -2), chimera_check.hlp (+1 -1), color_loadsave.hlp (+4 -4), color_props.hlp (+1 -1), color_ranges.hlp (+1 -1), colorize.hlp (+4 -4), compare_taxonomy.hlp (+1 -1), compare_topo.hlp (+1 -1), consense_algo.hlp (+2 -2), consense_tree.hlp (+1 -1), consensus.hlp (+1 -1), consensus_def.hlp (+1 -1), console.hlp (+2 -2), count_chars.hlp (+1 -1), csp_2_gnuplot.hlp (+1 -1), del_list.hlp (+7 -8), di_clusters.hlp (+1 -1), displayField.hlp (+1 -1), dist.hlp (+3 -3), e4.hlp (+2 -1), e4_block.hlp (+1 -1), experiment_info.hlp (+2 -2), experiment_search.hlp (+2 -2), export_format.hlp (+2 -2), export_test.hlp (+1 -1), field_shader.hlp (+1 -1), gen_create.hlp (+2 -2), gen_jump.hlp (+1 -1), gene_extract.hlp (+2 -2), gene_hide.hlp (+1 -1), gene_info.hlp (+3 -3), gene_map.hlp (+2 -2), gene_mark.hlp (+1 -1), gene_search.hlp (+4 -4), gene_species_field_transfer.hlp (+1 -1), gene_species_mark.hlp (+1 -1), group_rename.hlp (+1 -1), group_search.hlp (+1 -1), group_trees.hlp (+1 -1), helix.hlp (+4 -4), import_test.hlp (+1 -1), importift.hlp (+1 -1), input_mask.hlp (+3 -1), insdel.hlp (+1 -1), insdel_sai.hlp (+1 -1), iupac-codes.hlp (+1 -1), macro.hlp (+1 -1), macro_interruption.hlp (+1 -1), manage_test.hlp (+2 -2), mark.hlp (+23 -27), mark_duplicates.hlp (+1 -1), mark_list.hlp (+3 -3), markbyref.hlp (+1 -1), max_freq.hlp (+1 -1), merge_species.hlp (+2 -2), mod_field_list.hlp (+3 -3), mode.hlp (+2 -2), mode_group.hlp (+2 -2), mode_info.hlp (+2 -2), mode_length.hlp (+2 -2), mode_lzoom.hlp (+3 -3), mode_mark.hlp (+1 -1), mode_move.hlp (+1 -1), mode_pzoom.hlp (+3 -3), mode_rotate.hlp (+2 -2), mode_select.hlp (+1 -1), mode_setroot.hlp (+2 -2), mode_spread.hlp (+3 -3), mode_swap.hlp (+2 -2), mode_width.hlp (+2 -2), mode_www.hlp (+2 -2), move_groups.hlp (+1 -1), multifurcate.hlp (+1 -1), namesadmin.hlp (+1 -1), newwindow.hlp (+8 -7), next_neighbours.hlp (+1 -1), next_neighbours_common.hlp (+2 -2), next_neighbours_listed.hlp (+1 -1), no_tree.hlp (+5 -5), nt_align_select.hlp (+10 -10), nt_keys.hlp (+1 -1), nt_tree_marker_settings.hlp (+1 -1), nt_tree_select.hlp (+1 -1), nt_tree_settings.hlp (+1 -1), nt_tree_settings_bootstrap.hlp (+1 -1), nt_tree_settings_expert.hlp (+1 -1), optimize.hlp (+1 -2), organism_mark.hlp (+1 -1), pa_quick.hlp (+1 -1), pars.hlp (+2 -2), pd_match_iupac.hlp (+1 -1), pd_spec_param.hlp (+1 -1), pfold.hlp (+5 -5), pfold_sai.hlp (+1 -1), ph_export_markerline.hlp (+2 -2), phylo.hlp (+1 -1), pm_spec_param.hlp (+1 -1), pos_var_pars.hlp (+1 -1), primer.hlp (+1 -1), primer_new.hlp (+2 -2), primer_result.hlp (+1 -1), probe_param.hlp (+1 -1), probeadmin.hlp (+1 -1), probedesign.hlp (+1 -1), probedesignresult.hlp (+1 -1), probematch.hlp (+1 -1), probespec.hlp (+5 -4), props_nds.hlp (+3 -3), props_www.hlp (+3 -3), pt_server.hlp (+5 -5), quit.hlp (+3 -2), realign_dna.hlp (+1 -1), rename.hlp (+1 -1), rerepair.hlp (+2 -2), resortbyother.hlp (+1 -1), resorttree.hlp (+2 -2), rst_log_zoom.hlp (+4 -5), rst_phys_zoom.hlp (+1 -1), saiProbe.hlp (+1 -1), saicalc.hlp (+1 -1), save.hlp (+6 -6), savedef.hlp (+2 -1), search_duplicates.hlp (+2 -2), searching.hlp (+3 -3), sel_box.hlp (+1 -1), sel_fil.hlp (+5 -4), selected.hlp (+4 -6), selected_gene.hlp (+3 -3), seq_quality.hlp (+1 -1), set_color_of_listed.hlp (+3 -3), set_protection.hlp (+1 -1), sina_main.hlp (+1 -1), sp_IDs.hlp (+1 -1), sp_del_mrkd.hlp (+6 -5), sp_info.hlp (+4 -4), sp_info_locked.hlp (+1 -1), sp_mark.hlp (+5 -4), sp_search.hlp (+2 -3), sp_sort_fld.hlp (+1 -1), sp_sort_phyl.hlp (+2 -2), sp_sp_2_ext.hlp (+1 -1), spa_copy.hlp (+4 -4), spa_create.hlp (+1 -1), spa_delete.hlp (+5 -6), spa_rename.hlp (+4 -4), spaf_convert.hlp (+1 -1), spaf_delete.hlp (+3 -2), species_configs.hlp (+1 -1), species_configs_highlight.hlp (+1 -1), species_join.hlp (+2 -2), split.hlp (+1 -1), st_ml.hlp (+1 -1), submission.hlp (+1 -1), syncroots.hlp (+1 -1), syncscroll.hlp (+1 -1), tags.hlp (+1 -1), tbl_boot2len.hlp (+1 -1), tbl_justify.hlp (+1 -1), tbl_reset.hlp (+1 -1), tbl_scale.hlp (+1 -1), ted_boot.hlp (+1 -1), tkeep_mrkd.hlp (+1 -1), topology_shader.hlp (+1 -1), tr_export.hlp (+1 -1), tr_import.hlp (+1 -1), tr_jump.hlp (+5 -5), tr_type_dendro.hlp (+1 -1), tr_type_irs.hlp (+1 -1), tr_type_nds.hlp (+2 -2), tr_type_radial.hlp (+1 -1), track_ali_changes.hlp (+1 -1), translate_dna_2_pro.hlp (+1 -1), tree2file.hlp (+1 -1), tree2prt.hlp (+3 -3), tree_group.hlp (+1 -1), tree_pseudo.hlp (+1 -1), tree_shading.hlp (+1 -1), treeadm.hlp (+4 -4), trees.hlp (+2 -3), trm_boot.hlp (+1 -1), trm_del.hlp (+1 -1), trm_mrkd.hlp (+1 -1), undo.hlp (+1 -1), unmark_list.hlp (+3 -3), vn_delete.hlp (+1 -1), vn_import.hlp (+1 -1), vn_search.hlp (+1 -1), vn_suggest.hlp (+1 -1), write_field_list.hlp (+7 -8), xferset.hlp (+2 -2), xterm.hlp (+1 -1)
• MERGE: MG_main.cxx (+1 -1), MG_species.cxx (+2 -2)
• NTREE: NT_extern.cxx (+1 -1)
• PERL2ARB: ARB.pm (+1 -1)
• SERVERCNTRL: servercntrl.cxx (+2 -2)
• SH: arb (+1 -1), example_batch_probe_match.sh (+1 -1)
• SL/APP: db_browser.cxx (+1 -1)
• SL/TREE_READ: TreeRead.cxx (+1 -1)
• WINDOW: AW_help.cxx (+1 -1)

westram 2026-03-10 13:00 Rev.: 19707

* update doc
- improve doc of global protection level.
- eliminate references to 'Protection' menu (pre-svn)

28 lines of code changed in 6 files:

• HELP_SOURCE/source: Protection.hlp (+6 -3), del_list.hlp (+5 -5), gene_info.hlp (+4 -4), security.hlp (+5 -4), sp_info.hlp (+3 -4), write_field_list.hlp (+5 -5)

westram 2026-03-10 12:56 Rev.: 19706

* update doc+gui:
- mention focus strategies.
- use term 'SAI admin'.
- arb introduction (updated + linked missing modules).

73 lines of code changed in 6 files:

• HELP_SOURCE/source: arb.hlp (+51 -9), nt_keys.hlp (+11), pt_server.hlp (+8 -5)
• NTREE: NT_extern.cxx (+1 -1), ad_ext.cxx (+1 -1)
• SL/SAICALC: saicalc.cxx (+1 -1)

westram 2026-02-12 18:58 Rev.: 19691

* reintegrates 'macros' into 'trunk'
- fixes macro IDs for mergetool (completing #870).
* most common problem:
- several modules were reused (twice) for items of same type, but in different databases.
- auto-generated IDs were identical.
* adds: log:branches/macros@19667:19690

660 lines of code changed in 28 files:

• GENOM: EXP_interface.cxx (+3 -3), GEN_interface.cxx (+41 -53)
• HELP_SOURCE/source: color_loadsave.hlp (+1 -1), colorize.hlp (+1 -1)
• MERGE: MG_preserves.cxx (+46 -43), MG_species.cxx (+9 -2), MG_trees.cxx (+3 -3), Makefile (+2)
• NTREE: Makefile (+3), NT_edconf.cxx (+65 -59), NT_main.cxx (+3), ad_trees.cxx (+1 -1)
• SL/DB_QUERY: db_query.cxx (+98 -118)
• SL/DB_UI: ui_species.cxx (+82 -102)
• SL/GUI_TK: config_manager.cxx (+90 -12), config_manager.hxx (+2)
• SL/ITEMS: Makefile (+7), items.h (+11 -7), itemtools.cxx (+113 -15), species.cxx (+2 -1)
• SL/TREE_ADMIN: Makefile (+1), TreeAdmin.cxx (+15 -2), TreeAdmin.h (+1 -1)
• WINDOW: AW_preset.cxx (+16 -12), AW_root.cxx (+16 -2), AW_root_debug.cxx (+11), AW_window.cxx (+16 -7), Makefile (+1)

westram 2026-02-12 12:58 Rev.: 19666

* add support to rename/merge existing managed configs
* merge all existing "modify fields of listed" managers.

216 lines of code changed in 7 files:

• SL/DB_QUERY: db_query.cxx (+2 -3)
• SL/GUI_TK: Makefile (new), config_manager.cxx (+211 -9), config_manager.hxx (+2)

westram 2026-02-12 12:53 Rev.: 19665

* fix string splitting
- add test showing that splitting an empty string with mode {{{SPLIT_DROPEMPTY}}} results in an empty array.
- document effect of 'mode' on empty arrays / empty elements.
- check + fix all callers:
* explicitly drop empty tokens where they are expected not to occur.
* {{{parse_helix_list}}}: accept adding "" to helix list for empty list => raise error if no helices specified.
* {{{gb_hierarchy_location}}}: explicitly accept EMPTY path elements. used correctly to encode absolute vs relative paths.

23 lines of code changed in 9 files:

• ARBDB: ad_cb.cxx (+1 -1), ad_colorset.cxx (+1 -1)
• CORE: arb_strarray.cxx (+12 -1)
• EDIT4: ED4_detect_bad_ali.cxx (+2 -1)
• SL/SAICALC: saicalc.cxx (+1 -1)
• SL/XFERGUI: xfergui.cxx (+2 -2)
• SL/XFERSET: xferset.cxx (+2 -2)
• WINDOW: AW_modal.cxx (+1), AW_preset.cxx (+1)

westram 2026-02-12 12:40 Rev.: 19664

* modify {{{GBT_join_strings}}}:
- converting an array containing one empty string is an idiom. optimize for that.
* add {{{TEST_GBT_join_strings}}}.

27 lines of code changed in 1 file:

• CORE: arb_strarray.cxx (+27 -1)

westram 2026-01-27 15:54 Rev.: 19662

* reintegrates 'macros' into 'trunk'
- implements #870
* provide macro playback from CLI for merge tool
* adds: log:branches/macros@19656:19661

121 lines of code changed in 14 files:

• HELP_SOURCE/source: arb_merge.hlp (+1 -1), arb_merge_outof.hlp (+1 -1)
• MERGE: MG_main.cxx (+19 -13)
• NTREE: NT_extern.cxx (+4 -4), NT_main.cxx (+16 -12)
• SL/APP: app.hxx (+1 -1)
• SL/MACROS: MacroExitor.hxx (+1 -1), macro_gui.cxx (+2 -3), recmac.cxx (+2 -1), trackers.cxx (+1 -1)
• WINDOW: AW_window.cxx (+18 -6), aw_root.hxx (+1 -1)
• lib/macros: _dolog.amc (+4 -2), _dolog_merge.amc (new 50)

westram 2026-01-23 16:40 Rev.: 19654

* reintegrates 'macros' into 'trunk'
- improves program termination (#867)
* introduces {{{MacroExitor}}} classes
- handles confirmation (to quit)
- waits for macros to finish, then exits w/o confirmation
- provides specialized termination for different programs via derived classes
* has been implemented for "normal" arb and merge-tool.
* introduces {{{ARB_disconnect_from_db}}}
- generalizes code to terminate all interconnections between GUI, database and macro-ability
- allow to install atdisconnect-callbacks
* usable by modules operating on a database; allow to inform module that database will vanish.
- now used by all arb applications to disconnect from all their database(s), except the properties.
- fixes some broken behavior
* merge-tool
- crashed when quitting via macro
- wrong restarts, if originally started with arguments,
* importer
- failed to record/playback macros
- crashed in modules operating on the temporary import database
* database browser
- crashed on disappearing database
* adds: log:branches/macros@19620:19653

560 lines of code changed in 49 files:

• Makefile (+1)
• ARBDB: adindex.cxx (+1 -1), adsocket.cxx (+1 -1), gb_undo.h (+1 -1)
• AWTI: AWTI_import.cxx (+10 -8), awti_import.hxx (+2 -3), needs_libs (-1)
• DIST: DI_matr.cxx (+1 -6)
• EDIT4: ED4_base.cxx (+4 -2), ED4_main.cxx (+1 -2), ED4_no_class.cxx (+13 -22), ed4_class.hxx (+1)
• MERGE: MG_main.cxx (+53 -33), Makefile (+2), mg_merge.hxx (+1 -1)
• NTREE: Makefile (+1), NT_extern.cxx (+53 -136), NT_import.cxx (+1 -1), NT_local_proto.h (+4 -3), NT_main.cxx (+14 -8)
• PARSIMONY: PARS_main.cxx (+7 -10), ap_main_type.hxx (+1 -1)
• PHYLO: PH_main.cxx (+5 -12), phylo.hxx (+3)
• SL/APP: Makefile (+31), app.cxx (new 72), app.hxx (+9 -3), db_browser.cxx (new)
• SL/DB_SCANNER: db_scanner.cxx (+4 -2)
• SL/MACROS: MacroExitor.hxx (new 182), macro_gui.cxx (+18 -11), macros.hxx (+2 -2), trackers.cxx (+8 -2), trackers.hxx (+5 -1)
• SL/MASKS: Makefile (+1), input_mask.cxx (new), input_mask.hxx (-1), needs_libs (+1)
• SL/XFERGUI: xfergui.cxx (+2 -2)
• SOURCE_TOOLS: dep.4dummy (+2 -2), generate_all_links.sh (+1)
• WINDOW: AW_root.cxx (+1)

(9012 more)