June 2018 Commit Log

Number of Commits:

4

Number of Active Developers:

1

westram 2018-06-25 16:04 #4 Rev.: 17121

* reintegrates 'saiexport' into 'trunk'
- no longer expand dangerous ranges (e.g. {{{--pass allbut .-=012345}}})
* adds: log:branches/saiexport@17112:17120

119 lines of code changed in 6 files:

• SL/FILTSEQEXP: FilteredExport.cxx (+21 -5), FilteredExport.h (+22 -8)
• TOOLS: arb_export_seq_filtered.cxx (+3 -1), arb_test.cxx (+33 -18)
• UNIT_TESTER/run/tools: exflt_DNA_pvp_g05.fasta.expected (new 20), exflt_DNA_pvp_gaps.fasta.expected (new 20)

westram 2018-06-25 09:57 #3 Rev.: 17114

* only refer to {{{/etc/bash.bashrc}}} (for global alias)
* add howto-edit-global-bashrc for unintended sysadmins :)

7 lines of code changed in 1 file:

• arb_install.sh (+7 -3)

westram 2018-06-15 12:08 #2 Rev.: 17110

* reintegrates 'tree' into 'trunk'
- implements #735
* adds:
- log:branches/addtest@17040:17044
- log:branches/tree@16921:17109

1801 lines of code changed in 69 files:

• arb_CHANGES.txt (+2 -1)
• ARBDB: TreeNode.cxx (+62 -43), TreeNode.h (+141 -25), ad_t_prot.h (+2 -1), adlang1.cxx (+24 -6), adname.cxx (+1 -1), adseqcompr.cxx (+6 -6), adtree.cxx (+206 -54)
• CONSENSUS_TREE: CT_ctree.hxx (+1 -1), CT_dtree.cxx (+5 -5), CT_rbtree.cxx (+5 -5)
• DIST: DI_clusters.cxx (+10 -8), DI_clustertree.cxx (+8 -8), DI_compress_matrix.cxx (+1 -1), DI_foundclusters.cxx (+3 -3), DI_matr.cxx (+2 -2), di_matr.hxx (+1 -1)
• HELP_SOURCE/oldhelp: group_search.hlp (+3), keeled_groups.hlp (new 83), mode_group.hlp (+12 -3), mode_move.hlp (+23 -1), mode_setroot.hlp (+3 -1), tr_export.hlp (+7)
• NTREE: NT_edconf.cxx (+3 -3), NT_extern.cxx (+4), NT_group_search.cxx (+5 -5), NT_local_proto.h (+1), NT_sort.cxx (+1 -1), NT_species_set.h (+1 -1), NT_taxonomy.cxx (+7 -7), NT_tree_cmp.cxx (+31 -27), ScrollSynchronizer.cxx (+1 -1), ad_trees.cxx (+80 -3), tree_position.h (+1 -1)
• PARSIMONY: AP_buffer.cxx (+1 -1), AP_buffer.hxx (+2 -1), AP_main.cxx (+1 -1), AP_tree_edge.cxx (+13 -13), AP_tree_nlen.cxx (+36 -60), PARS_dtree.cxx (+2 -2), PARS_main.cxx (+10 -10), ap_tree_nlen.hxx (+3 -5)
• SEQ_QUALITY: SQ_functions.cxx (+3 -3), SQ_main.cxx (+1 -1)
• SL/AP_TREE: AP_Tree.cxx (+125 -77), AP_Tree.hxx (+21 -10), AP_TreeSet.cxx (+19 -8)
• SL/ARB_TREE: ARB_Tree.cxx (+7 -7)
• SL/GROUP_SEARCH: group_search.cxx (+335 -50), group_search.h (+31 -8)
• SL/NDS: nds.cxx (+72 -40), nds.h (+2 -1)
• SL/NEIGHBOURJOIN: NJ.cxx (+2 -2)
• SL/PVP: AP_pos_var.cxx (+1 -1)
• SL/TREEDISP: Group.cxx (+19 -9), Group.hxx (+19 -4), GroupIterator.hxx (+11 -5), TreeCallbacks.cxx (+3 -2), TreeDisplay.cxx (+251 -159), TreeDisplay.hxx (+13 -6), irstree_display.cxx (+9 -8)
• SL/TREE_READ: TreeRead.cxx (+7 -7)
• SL/TREE_WRITE: Makefile (+1), TreeWrite.cxx (+26 -10)
• STAT: ST_ml.cxx (+5 -5)
• TOOLS: arb_consensus_tree.cxx (+2 -2), arb_read_tree.cxx (+2 -2)
• UNIT_TESTER/run: TEST_trees.arb (changed)

westram 2018-06-14 09:41 #1 Rev.: 17100

* document valid characters for PVP

2 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: pos_var_pars.hlp (+2)

May 2018 »