June 2026 Commit Log

Number of Commits:

1

Number of Active Developers:

1

westram 2026-06-26 15:01 #1 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)

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