-
westram
2017-11-30 19:07
#15
Rev.: 16773
-
13 lines of code changed in 1 file:
-
WINDOW:
AW_inotify.cxx (+13 -1)
-
westram
2017-11-30 16:12
#14
Rev.: 16772
-
5 lines of code changed in 1 file:
-
westram
2017-11-30 15:57
#13
Rev.: 16771
-
61 lines of code changed in 1 file:
-
WINDOW:
AW_root.cxx (+61 -4)
-
westram
2017-11-30 15:47
#12
Rev.: 16770
-
1 lines of code changed in 1 file:
-
ARBDB:
ad_load.cxx (+1 -1)
-
westram
2017-11-28 18:22
#11
Rev.: 16766
-
2376 lines of code changed in 237 files:
-
AISC:
aisc.c (+1 -4)
-
AISC_COM/C:
client.c (+16 -23),
server.c (+32 -42),
struct_man.c (+4 -7)
-
AISC_MKPTPS:
mkptypes.cxx (+1 -2)
-
ARBDB:
adRevCompl.cxx (+2 -4),
ad_core.cxx (+7 -14),
ad_load.cxx (+16 -28),
ad_save_load.cxx (+3 -6),
adali.cxx (+4 -5),
adcompr.cxx (+3 -4),
adindex.cxx (+4 -5),
aditem.cxx (+1 -2),
adlang1.cxx (+159 -161),
admalloc.cxx (+18 -36),
admap.cxx (+24 -43),
admatch.cxx (+11 -12),
adname.cxx (+1 -2),
adoptimize.cxx (+39 -52),
adseqcompr.cxx (+1 -1),
adsocket.cxx (+2 -4),
adstring.cxx (+5 -9),
arbdb.cxx (+27 -41),
gb_aci.h (+2 -1),
gb_map.h (+1 -2)
-
ARB_GDE:
GDE_FileIO.cxx (+30 -47),
GDE_Genbank.cxx (+62 -95),
GDE_HGLfile.cxx (+50 -108),
GDE_arbdb_io.cxx (+1 -2),
GDE_event.cxx (+8 -13)
-
AWT:
AWT_asciiprint.cxx (+2 -1),
AWT_canio.cxx (+1 -1),
AWT_db_browser.cxx (+1 -1),
AWT_input_mask.cxx (+37 -54),
awt_config_manager.hxx (+2 -2)
-
AWTC:
AWTC_next_neighbours.cxx (+2 -3),
AWTC_submission.cxx (+3 -6)
-
AWTI:
AWTI_import.cxx (+2 -4)
-
CONSENSUS_TREE:
CT_ctree.hxx (+1 -2),
CT_ntree.cxx (+2 -3)
-
CONVERTALN:
date.cxx (+2 -2),
embl.cxx (+8 -9),
genbank.cxx (+1 -1),
global.h (+1 -3),
mg.cxx (+5 -5),
rdp_info.h (+7 -6),
seq.h (+1 -2),
util.cxx (+1 -1)
-
CORE:
BufferedFileReader.cxx (+2 -4),
arb_assert.h (+7),
arb_file.cxx (+2 -2),
arb_match.cxx (+1 -1),
arb_mem.cxx (+3 -3)
-
DIST:
DI_clusters.cxx (+1 -1),
DI_matr.cxx (+1 -1),
DI_protdist.cxx (+18 -27),
DI_save_matr.cxx (+93 -95)
-
EDIT4:
ED4_ProteinViewer.cxx (+40 -45),
ED4_base.cxx (+25 -50),
ED4_container.cxx (+11 -13),
ED4_cursor.cxx (+10 -18),
ED4_edit_string.cxx (+8 -16),
ED4_main.cxx (+1 -2),
ED4_manager.cxx (+17 -22),
ED4_naligner.cxx (+3 -3),
ED4_nds.cxx (+2 -3),
ED4_no_class.cxx (+3 -4),
ED4_protein_2nd_structure.cxx (+1 -1),
ED4_root.cxx (+15 -23),
ED4_search.cxx (+33 -63),
ED4_terminal.cxx (+16 -29),
ED4_text_terminals.cxx (+4 -5),
ED4_visualizeSAI.cxx (+1 -1),
ED4_window.cxx (+13 -16),
EDB_root_bact.cxx (+2 -4),
ed4_defs.hxx (+5 -10),
ed4_search.hxx (+2 -4)
-
GENOM:
EXP_interface.cxx (+1 -1),
GEN_interface.cxx (+2 -2),
GEN_map.cxx (+1 -3)
-
GENOM_IMPORT:
DBwriter.cxx (+4 -8),
Feature.cxx (+3 -6),
MetaInfo.cxx (+8 -16)
-
MULTI_PROBE:
MP_Generation.cxx (+47 -87),
MP_GenerationDuplicates.cxx (+7 -14),
MP_Window.cxx (+1 -2),
MP_main.cxx (+5 -10),
MP_mo_liste.cxx (+22 -46),
MP_noclass.cxx (+33 -65),
MP_permute.cxx (+15 -27),
MP_probe.cxx (+26 -41),
MP_probe_combi_statistic.cxx (+63 -108),
MP_probe_tabs.cxx (+5 -10),
MP_sonde.cxx (+41 -69),
MP_sondentopf.cxx (+46 -108),
MultiProbe.hxx (+13 -13),
SoTl.hxx (+129 -214),
mpdefs.h (+1 -2)
-
NALIGNER:
ali_aligner.cxx (+22 -31),
ali_aligner.hxx (+8 -9),
ali_arbdb.cxx (+6 -14),
ali_global.cxx (+1 -2),
ali_main.cxx (+1 -2),
ali_misc.hxx (+54 -82),
ali_pathmap.cxx (+11 -22),
ali_pathmap.hxx (+2 -4),
ali_prealigner.cxx (+7 -10),
ali_prealigner.hxx (+4 -5),
ali_profile.cxx (+10 -18),
ali_profile.hxx (+2 -3),
ali_pt.cxx (+19 -35),
ali_sequence.cxx (+8 -18),
ali_sequence.hxx (+2 -2),
ali_solution.cxx (+29 -50),
ali_tarray.hxx (+4 -6),
ali_tlist.hxx (+13 -21)
-
NAMES:
names.cxx (+7 -6)
-
NTREE:
AP_pos_var_pars.cxx (+1 -1),
NT_extern.cxx (+4 -6),
NT_validNameParser.cxx (+4 -7),
ScrollSynchronizer.cxx (+1 -2),
ad_trees.cxx (+3 -6)
-
PARSIMONY:
AP_tree_edge.cxx (+1 -2),
AP_tree_nlen.cxx (+4 -8),
PARS_klprops.cxx (+1 -1),
PARS_main.cxx (+20 -29),
test_env.h (+1 -2)
-
PERLTOOLS:
arb_proto_2_xsub.cxx (+1 -2)
-
PHYLO:
PH_display.cxx (+12 -24),
PH_display.hxx (+1 -1),
PH_filt.cxx (+3 -6),
PH_main.cxx (+1 -2)
-
PRIMER_DESIGN:
PRD_Design.cxx (+27 -50),
PRD_Globals.hxx (+3 -6),
PRD_Item.cxx (+5 -10),
PRD_Node.cxx (+6 -12),
PRD_Node.hxx (+3 -3),
PRD_Pair.cxx (+5 -10),
PRD_Range.cxx (+4 -8),
PRD_SearchFIFO.cxx (+12 -22),
PRD_SequenceIterator.cxx (+4 -8),
primer_design.cxx (-1)
-
PROBE:
PT_etc.cxx (+2 -4),
PT_io.cxx (+1 -2),
PT_match.cxx (+2 -4),
PT_new_design.cxx (+3 -6),
PT_tools.h (+2 -2)
-
PROBE_DESIGN:
SaiProbeVisualization.cxx (+3 -4),
probe_collection.cxx (+27 -29),
probe_collection.hxx (+1 -1),
probe_design.cxx (+1 -1)
-
PROBE_SET:
ps_bitset.hxx (+2 -2),
ps_candidate.hxx (+3 -5),
ps_database.hxx (+1 -1),
ps_eval_candidates.cxx (+1 -1),
ps_filebuffer.cxx (+1 -2),
ps_filebuffer.hxx (+2 -2),
ps_node.hxx (+8 -10)
-
RNA3D:
RNA3D_Interface.cxx (+5 -13),
RNA3D_OpenGLEngine.cxx (+1 -2),
RNA3D_OpenGLGraphics.cxx (+5 -10),
RNA3D_Renderer.cxx (+5 -6),
RNA3D_StructureData.cxx (+189 -224)
-
RNACMA:
Cma.cxx (+1 -1)
-
SECEDIT:
SEC_abspos.cxx (+4 -8),
SEC_bonddef.cxx (+4 -8),
SEC_db.cxx (+1 -2),
SEC_helix.cxx (+1 -2)
-
SEQ_QUALITY:
SQ_GroupData.h (+3 -3),
SQ_helix.h (+1 -2)
-
SERVERCNTRL:
servercntrl.cxx (+2 -3)
-
SH:
dszmconnect.pl (+4 -3)
-
SL/ALILINK:
TranslateRealign.cxx (+14 -19)
-
SL/AP_TREE:
AP_Tree.cxx (+2 -4)
-
SL/AW_NAME:
AW_rename.cxx (+2 -2)
-
SL/CONSENSUS:
chartable.cxx (+23 -46)
-
SL/DB_QUERY:
db_query.cxx (+1 -2)
-
SL/FAST_ALIGNER:
fast_aligner.cxx (+7 -7)
-
SL/FILTER:
AP_filter.hxx (+2 -2)
-
SL/GUI_ALIVIEW:
AWT_filter.cxx (+1 -2),
ColumnStat.cxx (+1 -1)
-
SL/HELIX:
BI_helix.cxx (+10 -13)
-
SL/INSDEL:
insdel.cxx (+1 -2)
-
SL/ITEM_SHADER:
item_shader.cxx (+1 -1)
-
SL/NDS:
nds.cxx (+2 -2)
-
SL/NEIGHBOURJOIN:
NJ.cxx (+7 -14)
-
SL/PRONUC:
AP_codon_table.cxx (+1 -2),
iupac.cxx (+2 -4)
-
SL/SEQUENCE:
AP_seq_dna.cxx (+2 -4),
AP_seq_protein.cxx (+1 -2),
AP_seq_simple_pro.cxx (+2 -2),
AP_sequence.cxx (+1 -2)
-
SL/TREE_WRITE:
TreeWrite.cxx (+1 -2)
-
SOURCE_TOOLS:
svn_undo_depends.pl (+1 -1)
-
SOURCE_TOOLS/COMPILE_COMPAT:
Makefile (+10 -3)
-
STAT:
ST_ml.cxx (+1 -2)
-
TEMPLATES:
cache.h (+2 -4)
-
TOOLS:
arb_a2ps.c (+6 -8),
arb_dnarates.cxx (+14 -14),
arb_export_sequences.cxx (+1 -2),
arb_gene_probe.cxx (+3 -6),
arb_perf_test.cxx (+1 -2),
arb_primer.cxx (+4 -8),
arb_probe.cxx (+1 -2),
arb_read_tree.cxx (+1 -2),
arb_write_tree_comment.cxx (+1 -2)
-
TREEGEN:
base.c (+6 -12),
defines.c (+6 -12),
frand.c (+6 -12),
frand.h (+1 -2),
readcfg.c (+22 -44),
readcfg.h (+1 -2),
rns.c (+53 -106),
rns.h (+1 -2),
simcfg.c (+10 -20),
spreadin.c (+9 -18),
spreadin.h (+1 -2)
-
UNIT_TESTER:
test_unit.h (+12 -23)
-
WINDOW:
AW_at.cxx (+1 -1),
AW_button.cxx (+1 -2),
AW_global_awars.cxx (+1 -1),
AW_preset.cxx (+1 -2),
AW_question.cxx (+1 -2),
AW_status.cxx (+10 -20),
AW_window.cxx (+2 -2),
AW_xfig.cxx (+2 -4),
AW_xfont.cxx (+12 -17),
aw_device.hxx (+1 -1),
aw_position.hxx (+1 -1)
-
XML_IMPORT/IMP_TREE:
MySAXHandler.cxx (+12 -27),
MySAXHandler.hxx (+1 -2),
sax2Handler.cxx (+13 -32),
sax2Handler.hxx (+1 -2),
testParser.cxx (+2 -4),
testParser.hxx (+2 -4),
xmlParser.cxx (+2 -4),
xmlParser.hxx (+2 -4)
-
westram
2017-11-28 18:13
#10
Rev.: 16765
-
68 lines of code changed in 8 files:
-
RNA3D:
Makefile (+3),
RNA3D_Global.hxx (-1),
RNA3D_Interface.cxx (+12 -27),
RNA3D_OpenGLEngine.cxx (+29 -42),
RNA3D_OpenGLEngine.hxx (+1 -1),
RNA3D_Renderer.hxx (+9),
RNA3D_StructureData.cxx (+3 -1),
RNA3D_StructureData.hxx (+11)
-
westram
2017-11-28 17:09
#9
Rev.: 16763
-
7801 lines of code changed in 578 files:
-
Makefile (+1 -1)
-
AISC:
aisc.c (+9 -9),
aisc_commands.c (+24 -21),
aisc_def.h (+1 -1),
aisc_eval.c (+3 -3),
aisc_eval.h (+3 -3),
aisc_inline.h (+4 -2),
aisc_interpreter.h (+17 -17),
aisc_location.h (+3 -3),
aisc_mix.c (+15 -15),
aisc_parser.c (+17 -17),
aisc_parser.h (+1 -1),
aisc_token.h (+20 -20),
aisc_var_ref.c (+13 -13)
-
AISC_COM/AISC:
aisc_global.pa (+17 -11),
aisc_server.pa (+40 -30)
-
AISC_COM/C:
aisc_extern.c (+5 -5),
aisc_global.h (+1 -1),
client.c (+11 -11),
server.c (+32 -32),
struct_man.c (+13 -13)
-
AISC_MKPTPS:
mkptypes.cxx (+45 -47)
-
ARBDB:
TreeNode.cxx (+8 -8),
TreeNode.h (+25 -25),
adChangeKey.cxx (+10 -10),
adGene.cxx (+31 -31),
adGene.h (+1 -1),
adRevCompl.cxx (+1 -1),
adTest.cxx (+12 -12),
ad_cb.cxx (+27 -27),
ad_colorset.cxx (+5 -5),
ad_config.cxx (+9 -9),
ad_config.h (+3 -3),
ad_core.cxx (+43 -45),
ad_load.cxx (+54 -53),
ad_save_load.cxx (+58 -58),
ad_t_prot.h (+1 -1),
adali.cxx (+41 -41),
adcache.cxx (+4 -4),
adcomm.cxx (+70 -70),
adcompr.cxx (+18 -18),
adfile.cxx (+20 -20),
adhash.cxx (+14 -14),
adindex.cxx (+33 -32),
aditem.cxx (+16 -17),
adlang1.cxx (+114 -115),
admalloc.cxx (+21 -21),
admap.cxx (+20 -20),
admatch.cxx (+17 -17),
admath.cxx (+2 -2),
adname.cxx (+9 -10),
adoptimize.cxx (+62 -62),
adperl.cxx (+7 -7),
adquery.cxx (+40 -40),
adseqcompr.cxx (+14 -14),
adsocket.cxx (+69 -69),
adstring.cxx (+74 -71),
adsystem.cxx (+17 -17),
adtcp.cxx (+23 -23),
adtools.cxx (+47 -47),
adtree.cxx (+55 -55),
arbdb.cxx (+150 -164),
arbdbpp.cxx (+4 -4),
gb_aci.cxx (+54 -53),
gb_aci.h (+4 -4),
gb_aci_impl.h (+8 -8),
gb_cb.h (+1 -1),
gb_data.h (+8 -8),
gb_header.h (+1 -1),
gb_index.h (+1 -1),
gb_localdata.h (+1 -1),
gb_main.h (+4 -4),
gb_memory.h (+1 -1),
gb_ts.h (+1 -1)
-
ARB_GDE:
GDE.cxx (+11 -11),
GDE_FileIO.cxx (+18 -18),
GDE_Genbank.cxx (+19 -15),
GDE_HGLfile.cxx (+3 -3),
GDE_ParseMenu.cxx (+24 -24),
GDE_arbdb_io.cxx (+8 -8),
GDE_event.cxx (+22 -22)
-
AWT:
AWT_TreeAwars.cxx (+5 -5),
AWT_asciiprint.cxx (+9 -9),
AWT_canio.cxx (+17 -17),
AWT_canvas.cxx (+5 -5),
AWT_config_manager.cxx (+27 -27),
AWT_db_browser.cxx (+32 -32),
AWT_input_mask.cxx (+68 -68),
AWT_misc.cxx (+3 -3),
AWT_modules.cxx (+8 -8),
AWT_prompt.cxx (+8 -8),
AWT_sel_boxes.cxx (+11 -11),
AWT_www.cxx (+9 -9),
awt.hxx (+1 -1),
awt_canvas.hxx (+1 -1),
awt_config_manager.hxx (+3 -3),
awt_input_mask_internal.hxx (+51 -51),
awt_misc.hxx (+3 -3),
awt_prompt.hxx (+1 -1),
awt_sel_boxes.hxx (+3 -3)
-
AWTC:
AWTC_next_neighbours.cxx (+29 -29),
AWTC_submission.cxx (+3 -3)
-
AWTI:
AWTI_edit.cxx (+14 -14),
AWTI_export.cxx (+8 -8),
AWTI_import.cxx (+71 -71),
awti_imp_local.hxx (+7 -7)
-
BUGEX:
bugex.h (+2 -2)
-
CONSENSUS_TREE:
CT_ctree.cxx (+9 -9),
CT_ctree.hxx (+2 -2),
CT_dtree.cxx (+2 -2),
CT_hash.cxx (+3 -3),
CT_ntree.cxx (+12 -12),
CT_part.cxx (+3 -3),
CT_rbtree.cxx (+4 -4)
-
CONVERTALN:
convert.cxx (+1 -1),
date.cxx (+1 -1),
embl.cxx (+2 -2),
fconv.cxx (+6 -6),
fun.h (+1 -1),
gcg.cxx (+1 -1),
genbank.cxx (+4 -4),
global.h (+3 -3),
input_format.h (+1 -1),
macke.cxx (+6 -6),
macke.h (+1 -1),
main.cxx (+2 -2),
mg.cxx (+1 -1),
rdp_info.h (+1 -1),
reader.cxx (+6 -6),
reader.h (+4 -4),
refs.h (+1 -1),
seq.h (+1 -1),
util.cxx (+3 -3),
wrap.cxx (+1 -1),
wrap.h (+1 -1)
-
CORE:
BufferedFileReader.h (+5 -5),
FileContent.h (+1 -1),
MultiFileReader.cxx (+9 -9),
MultiFileReader.h (+1 -1),
arb_assert.h (+5 -5),
arb_cs.cxx (+12 -12),
arb_diff.cxx (+10 -10),
arb_file.cxx (+16 -16),
arb_handlers.cxx (+3 -3),
arb_match.cxx (+16 -16),
arb_mem.cxx (+4 -4),
arb_misc.cxx (+7 -7),
arb_msg.cxx (+15 -15),
arb_msg.h (+3 -3),
arb_pattern.cxx (+2 -2),
arb_progress.cxx (+7 -7),
arb_progress.h (+5 -5),
arb_signal.cxx (+1 -1),
arb_sort.cxx (+1 -1),
arb_strarray.cxx (+5 -5),
arb_strarray.h (+7 -7),
arb_strbuf.h (+9 -9),
arb_string.cxx (+7 -7),
arb_string.h (+3 -3),
arb_zfile.cxx (+11 -11),
pos_range.cxx (+3 -3)
-
DBSERVER:
db_server.cxx (+11 -11)
-
DIST:
DI_clusters.cxx (+17 -17),
DI_clustertree.cxx (+10 -10),
DI_compress_matrix.cxx (+7 -7),
DI_foundclusters.cxx (+14 -14),
DI_main.cxx (+1 -1),
DI_matr.cxx (+65 -65),
DI_protdist.cxx (+11 -11),
DI_save_matr.cxx (+2 -2),
DI_view_matrix.cxx (+17 -17),
di_clustertree.hxx (+17 -17),
di_foundclusters.hxx (+2 -2),
di_matr.hxx (+4 -4),
di_view_matrix.hxx (+2 -2)
-
EDIT4:
ED4_ProteinViewer.cxx (+12 -12),
ED4_base.cxx (+33 -33),
ED4_block.cxx (+35 -35),
ED4_colStat.cxx (+4 -4),
ED4_consensus.cxx (+3 -3),
ED4_container.cxx (+6 -6),
ED4_cursor.cxx (+28 -28),
ED4_dots.cxx (+7 -7),
ED4_dump.cxx (+2 -2),
ED4_edit_string.cxx (+35 -36),
ED4_flags.cxx (+12 -12),
ED4_main.cxx (+13 -13),
ED4_manager.cxx (+30 -30),
ED4_nds.cxx (+4 -4),
ED4_no_class.cxx (+55 -55),
ED4_objspec.cxx (+1 -1),
ED4_plugins.cxx (+8 -8),
ED4_protein_2nd_structure.cxx (+17 -17),
ED4_root.cxx (+89 -89),
ED4_search.cxx (+51 -51),
ED4_seq_colors.cxx (+11 -11),
ED4_terminal.cxx (+30 -30),
ED4_text_terminals.cxx (+8 -8),
ED4_visualizeSAI.cxx (+14 -14),
ED4_window.cxx (+3 -3),
EDB_root_bact.cxx (+7 -7),
ed4_block.hxx (+1 -1),
ed4_class.hxx (+38 -38),
ed4_flags.hxx (+1 -1),
ed4_list.hxx (+6 -6),
ed4_protein_2nd_structure.hxx (+1 -1),
graph_aligner_gui.cxx (+20 -20)
-
GENOM:
EXP_interface.cxx (+20 -20),
EXP_main.cxx (+1 -1),
GEN_gene.cxx (+13 -13),
GEN_graphic.cxx (+4 -4),
GEN_interface.cxx (+43 -43),
GEN_map.cxx (+60 -61),
GEN_nds.cxx (+13 -13),
GEN_translations.cxx (+8 -8)
-
GENOM_IMPORT:
DBwriter.cxx (+5 -5),
DBwriter.h (+5 -7),
Feature.cxx (+3 -3),
GenomeImport.cxx (+1 -1),
Importer.cxx (+5 -5),
MetaInfo.cxx (+3 -3),
MetaInfo.h (+4 -1),
MetaTag.h (+1 -1),
SequenceBuffer.h (+3 -2),
tools.h (+2 -2)
-
GL/glAW:
AW_window_ogl.cxx (+17 -17)
-
HELP_SOURCE:
arb_help2xml.cxx (+32 -32)
-
ISLAND_HOPPING:
Makefile (+3),
align.cxx (+14 -12),
i-hopper.cxx (+3 -3),
island_hopping.cxx (+2 -2),
island_hopping.h (+6 -7),
mem.cxx (+5 -4)
-
MERGE:
MG_adapt_ali.cxx (+24 -24),
MG_alignment.cxx (+2 -2),
MG_checkfield.cxx (+10 -10),
MG_configs.cxx (+1 -1),
MG_extendeds.cxx (+2 -2),
MG_gene_species.cxx (+18 -18),
MG_main.cxx (+11 -11),
MG_names.cxx (+6 -6),
MG_species.cxx (+38 -38),
MG_trees.cxx (+6 -6)
-
MULTI_PROBE:
MP_Generation.cxx (+10 -10),
MP_Window.cxx (+9 -9),
MP_main.cxx (+4 -4),
MP_mo_liste.cxx (+19 -19),
MP_noclass.cxx (+23 -23),
MP_probe.cxx (+2 -2),
MP_probe.hxx (+5 -5),
MP_probe_combi_statistic.cxx (+3 -3),
MP_sonde.cxx (+21 -21),
MP_sondentopf.cxx (+2 -2),
MultiProbe.hxx (+1 -1),
SoTl.hxx (+33 -33)
-
NALIGNER:
ali_aligner.cxx (+6 -6),
ali_aligner.hxx (+3 -3),
ali_arbdb.cxx (+7 -7),
ali_arbdb.hxx (+3 -3),
ali_global.cxx (+3 -3),
ali_main.cxx (+4 -4),
ali_pathmap.cxx (+11 -11),
ali_pathmap.hxx (+1 -1),
ali_prealigner.cxx (+6 -6),
ali_prealigner.hxx (+6 -6),
ali_profile.cxx (+7 -7),
ali_profile.hxx (+1 -1),
ali_pt.cxx (+27 -27),
ali_sequence.cxx (+3 -3),
ali_sequence.hxx (+2 -2),
ali_solution.cxx (+7 -7),
ali_tarray.hxx (+1 -1),
ali_tlist.hxx (+22 -22)
-
NAMES:
names.cxx (+19 -18)
-
NTREE:
AP_consensus.cxx (+5 -5),
AP_pos_var_pars.cxx (+7 -7),
AP_pos_var_pars.h (+1 -1),
ColumnStat_2_gnuplot.cxx (+21 -21),
NT_branchAnalysis.cxx (+4 -4),
NT_cb.cxx (+3 -3),
NT_concatenate.cxx (+30 -28),
NT_dbrepair.cxx (+31 -30),
NT_edconf.cxx (+26 -26),
NT_extern.cxx (+61 -61),
NT_group_search.cxx (+21 -21),
NT_import.cxx (+3 -3),
NT_ins_col.cxx (+16 -16),
NT_join.cxx (+4 -4),
NT_local.h (+4 -4),
NT_main.cxx (+27 -27),
NT_shadeTree.cxx (+2 -2),
NT_sort.cxx (+4 -4),
NT_taxonomy.cxx (+5 -5),
NT_trackAliChanges.cxx (+4 -4),
NT_tree_cmp.cxx (+17 -17),
NT_validManual.cxx (+3 -3),
NT_validNameParser.h (+9 -9),
NT_validNames.cxx (+5 -5),
ScrollSynchronizer.cxx (+3 -3),
ScrollSynchronizer.h (+3 -3),
ad_ext.cxx (+12 -12),
ad_spec.cxx (+11 -10),
ad_transpro.cxx (+2 -2),
ad_trees.cxx (+28 -28)
-
PARSIMONY:
AP_buffer.cxx (+4 -4),
AP_buffer.hxx (+3 -3),
AP_main.cxx (+3 -3),
AP_tree_edge.cxx (+25 -25),
AP_tree_nlen.cxx (+32 -32),
PARS_dtree.cxx (+15 -15),
PARS_main.cxx (+69 -64),
ap_main.hxx (+6 -6),
ap_main_type.hxx (+4 -4),
ap_tree_nlen.hxx (+6 -6),
pars_main.hxx (+1 -1),
test_env.h (+5 -5)
-
PERL2ARB:
Makefile.main (+9 -1),
perlmain_source.c (+1 -1)
-
PERLTOOLS:
arb_proto_2_xsub.cxx (+22 -22)
-
PHYLO:
PH_data.cxx (+6 -6),
PH_display.cxx (+1 -1),
PH_filt.cxx (+6 -6),
PH_main.cxx (+12 -12),
PH_root.cxx (+2 -2),
phylo.hxx (+21 -21)
-
PRIMER_DESIGN:
PRD_Design.cxx (+42 -42),
PRD_Item.cxx (+1 -1),
PRD_Node.cxx (+5 -5),
PRD_Pair.cxx (+8 -8),
PRD_SearchFIFO.cxx (+43 -43),
primer_design.cxx (+20 -21)
-
PROBE:
PT_buildtree.cxx (+3 -3),
PT_etc.cxx (+11 -11),
PT_findEx.cxx (+1 -1),
PT_io.cxx (+6 -6),
PT_main.cxx (+25 -25),
PT_match.cxx (+9 -9),
PT_mem.h (+8 -8),
PT_new_design.cxx (+10 -10),
PT_partition.h (+6 -6),
PT_prefixtree.cxx (+11 -11),
PT_rangeCheck.h (+2 -2),
probe.h (+5 -5),
probe_tree.h (+3 -3)
-
PROBE_COM:
PT_extern.c (+1 -1)
-
PROBE_DESIGN:
SaiProbeVisualization.cxx (+20 -19),
probe_collection.cxx (+70 -82),
probe_collection.hxx (+4 -4),
probe_design.cxx (+100 -99),
probe_match_parser.cxx (+15 -12)
-
PROBE_SET:
Makefile (+2),
ps_arb2asciipaths.cxx (+1 -1),
ps_bitmap.hxx (+13 -13),
ps_bitset.hxx (+6 -6),
ps_candidate.hxx (+22 -22),
ps_convert_db.cxx (+4 -6),
ps_database.hxx (+1 -1),
ps_detect_weak_differences.cxx (+2 -2),
ps_find_probes.cxx (+5 -6),
ps_get_probes.cxx (+5 -5),
ps_node.cxx (+3 -3),
ps_node.hxx (+7 -5),
ps_pg_specmap.hxx (+1 -1),
ps_tools.hxx (+5 -1)
-
RNA3D:
RNA3D_Graphics.cxx (+1 -1),
RNA3D_Interface.cxx (+26 -26),
RNA3D_OpenGLEngine.cxx (+4 -4),
RNA3D_OpenGLGraphics.cxx (+6 -6),
RNA3D_StructureData.cxx (+100 -100),
RNA3D_Textures.cxx (+1 -1)
-
RNACMA:
Analyser.cxx (+1 -1),
Makefile (+3 -2)
-
SECEDIT:
SEC_abspos.cxx (+7 -7),
SEC_bonddef.cxx (+1 -1),
SEC_db.cxx (+35 -35),
SEC_drawn_pos.hxx (+2 -2),
SEC_graphic.cxx (+34 -35),
SEC_helix.cxx (+8 -8),
SEC_io.cxx (+4 -4),
SEC_iter.hxx (+5 -5),
SEC_layout.cxx (+4 -4),
SEC_main.cxx (+23 -23),
SEC_paint.cxx (+7 -7),
SEC_read.cxx (+34 -34),
SEC_root.hxx (+6 -6),
SEC_split.cxx (+16 -16),
SEC_structure.cxx (+40 -40),
SEC_toggle.cxx (+13 -13)
-
SEQ_QUALITY:
SQ_GroupData.h (+1 -1),
SQ_ambiguities.h (+4 -4),
SQ_functions.cxx (+15 -15),
SQ_helix.h (+7 -7),
SQ_main.cxx (+6 -6)
-
SERVERCNTRL:
servercntrl.cxx (+13 -13)
-
SL/ALILINK:
AdminGui.cxx (+4 -4),
AliAdmin.h (+6 -6),
TranslateRealign.cxx (+69 -69)
-
SL/ALIVIEW:
AliView.cxx (+15 -9),
AliView.hxx (+1 -1)
-
SL/AP_TREE:
AP_Tree.cxx (+36 -36)
-
SL/ARB_TREE:
ARB_Tree.cxx (+13 -13),
ARB_Tree.hxx (+7 -7)
-
SL/AW_HELIX:
AW_helix.cxx (+3 -3)
-
SL/AW_NAME:
AW_names_admin.cxx (+2 -2),
AW_rename.cxx (+35 -35),
AW_rename.hxx (+1 -1)
-
SL/CB:
cbtypes.h (+1 -1)
-
SL/CONSENSUS:
chartable.cxx (+7 -7)
-
SL/DB_QUERY:
db_query.cxx (+64 -64)
-
SL/DB_SCANNER:
db_scanner.cxx (+7 -7),
db_scanner.hxx (+20 -20)
-
SL/DB_UI:
info_window.cxx (+2 -2),
info_window.h (+5 -5),
ui_species.cxx (+42 -39)
-
SL/FAST_ALIGNER:
ClustalV.cxx (+4 -4),
fast_aligner.cxx (+112 -114),
seq_search.cxx (+1 -1),
seq_search.hxx (+11 -11)
-
SL/FILTER:
AP_filter.cxx (+8 -8),
AP_filter.hxx (+2 -2)
-
SL/FILTSEQEXP:
FilteredExport.cxx (+12 -12),
FilteredExport.h (+1 -1)
-
SL/GROUP_SEARCH:
group_search.cxx (+26 -26),
group_search.h (+1 -1)
-
SL/GUI_ALIVIEW:
AWT_filter.cxx (+18 -15),
ColumnStat.cxx (+22 -21),
ColumnStat.hxx (+1 -1),
GUI_aliview.cxx (+7 -7)
-
SL/HELIX:
BI_basepos.cxx (+1 -1),
BI_basepos.hxx (+3 -3),
BI_helix.cxx (+14 -14),
BI_helix.hxx (+1 -1)
-
SL/INSDEL:
insdel.cxx (+33 -33)
-
SL/ITEMS:
changekey.cxx (+3 -3),
item_sel_list.cxx (+23 -23),
items.cxx (+3 -3),
items.h (+2 -2),
itemtools.cxx (+1 -1),
species.cxx (+8 -8)
-
SL/ITEM_SHADER:
field_shader.cxx (+25 -25),
item_shader.cxx (+13 -13),
item_shader.h (+2 -2)
-
SL/LOCATION:
Location.cxx (+2 -2)
-
SL/MACROS:
dbserver.cxx (+5 -5),
macro_gui.cxx (+4 -4),
recmac.cxx (+16 -16),
trackers.cxx (+19 -19),
trackers.hxx (+3 -3)
-
SL/MATRIX:
AP_matrix.cxx (+3 -3),
AP_matrix.hxx (+2 -2)
-
SL/NDS:
nds.cxx (+26 -26)
-
SL/NEIGHBOURJOIN:
NJ.cxx (+1 -1),
NJ.hxx (+1 -1)
-
SL/PRONUC:
AP_codon_table.cxx (+23 -23),
AP_codon_table.hxx (+1 -1),
AP_pro_a_nucs.cxx (+8 -8),
AP_pro_a_nucs.hxx (+4 -4),
iupac.cxx (+2 -2),
iupac.h (+1 -1)
-
SL/PTCLEAN:
ptclean.cxx (+3 -3)
-
SL/QUERY:
query_expr.cxx (+15 -15),
query_expr.h (+4 -4)
-
SL/REFENTRIES:
refentries.cxx (+10 -10)
-
SL/REGEXPR:
RegExpr.cxx (+12 -12),
RegExpr.hxx (+7 -7)
-
SL/SEQIO:
seq_export.cxx (+43 -43),
seqio.cxx (+4 -4)
-
SL/SEQUENCE:
AP_seq_dna.cxx (+6 -6),
AP_seq_protein.cxx (+9 -9),
AP_seq_protein.hxx (+1 -1),
AP_seq_simple_pro.cxx (+2 -2),
AP_seq_simple_pro.hxx (+1 -1),
AP_sequence.cxx (+8 -8),
AP_sequence.hxx (+6 -6)
-
SL/TRANSLATE:
Translate.cxx (+2 -2)
-
SL/TREEDISP:
Group.cxx (+2 -2),
Group.hxx (+6 -6),
TreeCallbacks.cxx (+27 -27),
TreeDisplay.cxx (+78 -78),
TreeDisplay.hxx (+14 -14)
-
SL/TREE_ADMIN:
TreeAdmin.cxx (+5 -5)
-
SL/TREE_READ:
TreeRead.cxx (+45 -45)
-
SL/TREE_WRITE:
TreeWrite.cxx (+15 -15),
TreeWrite.h (+3 -3)
-
SOURCE_TOOLS:
check_dirs_equal.sh (+1 -1),
diff2grep.pl (+35 -8),
remake_after_change.pl (+19 -5)
-
STAT:
MostLikelySeq.hxx (+1 -1),
ST_ml.cxx (+30 -30),
ST_quality.cxx (+9 -9),
ST_window.cxx (+7 -7),
st_ml.hxx (+1 -1)
-
TEMPLATES:
ChecksumCollector.h (+1 -1),
SuppressOutput.h (+4 -4),
arb_error.h (+8 -8),
arb_simple_assert.h (+4),
arb_sleep.h (+2 -2),
arb_str.h (+2 -2),
attributes.h (+1 -1),
cache.h (+5 -5),
command_output.h (+11 -8),
config_parser.h (+6 -6),
cxxforward.h (+8 -2),
downcast.h (+1 -1),
dupstr.h (+7 -7),
output.h (+7 -7),
perf_timer.h (+4 -4),
smartptr.h (+12 -12)
-
TOOLS:
arb_2_ascii.cxx (+3 -3),
arb_2_bin.cxx (+4 -4),
arb_a2ps.c (+25 -25),
arb_consensus_tree.cxx (+19 -19),
arb_dnarates.cxx (+28 -28),
arb_export_rates.cxx (+6 -6),
arb_export_seq_filtered.cxx (+7 -7),
arb_export_sequences.cxx (+16 -15),
arb_export_tree.cxx (+3 -3),
arb_gene_probe.cxx (+11 -11),
arb_message.cxx (+2 -2),
arb_perf_test.cxx (+7 -7),
arb_primer.cxx (+12 -12),
arb_probe.cxx (+61 -61),
arb_probe_match.cxx (+21 -17),
arb_read_tree.cxx (+12 -12),
arb_test.cxx (+11 -11),
arb_write_tree_comment.cxx (+6 -6)
-
UNIT_TESTER:
Makefile.test (+1 -1),
TestEnvironment.cxx (+6 -6),
UnitTester.cxx (+9 -9),
sym2testcode.pl (+3 -2),
test_global.h (+10 -7),
test_runtool.h (+1 -1),
test_unit.h (+11 -11)
-
WETC:
WETC_main.cxx (+2 -2)
-
WINDOW:
AW_Xm.cxx (+1 -1),
AW_advice.cxx (+6 -6),
AW_at.cxx (+4 -4),
AW_awar.cxx (+22 -22),
AW_button.cxx (+65 -65),
AW_cb_struct.cxx (+4 -4),
AW_clipable.cxx (+1 -1),
AW_device_click.cxx (+2 -2),
AW_edit.cxx (+1 -1),
AW_file.cxx (+19 -19),
AW_global_awars.cxx (+3 -3),
AW_help.cxx (+15 -15),
AW_inotify.cxx (+10 -10),
AW_modal.cxx (+11 -11),
AW_option_toggle.cxx (+38 -38),
AW_preset.cxx (+43 -43),
AW_print.cxx (+2 -2),
AW_question.cxx (+11 -11),
AW_root.cxx (+38 -38),
AW_root_debug.cxx (+5 -5),
AW_select.cxx (+35 -35),
AW_status.cxx (+46 -47),
AW_window.cxx (+196 -194),
AW_xfig.cxx (+11 -11),
AW_xfont.cxx (+93 -93),
AW_xkey.cxx (+36 -36),
aw_advice.hxx (+2 -2),
aw_awar.hxx (+1 -1),
aw_base.hxx (+4),
aw_common.hxx (+3 -3),
aw_device.hxx (+11 -11),
aw_device_click.hxx (+7 -7),
aw_font_group.hxx (+1 -1),
aw_nawar.hxx (+3 -3),
aw_question.hxx (+4 -4),
aw_rgb.hxx (+1 -1),
aw_root.hxx (+4 -4),
aw_scalar.cxx (+1 -1),
aw_select.hxx (+3 -3),
aw_varupdate.hxx (+1 -1),
aw_window.hxx (+14 -14),
aw_window_Xm.hxx (+3 -3),
aw_xfig.hxx (+2 -2)
-
XML:
xml.cxx (+17 -17)
-
westram
2017-11-28 11:32
#8
Rev.: 16761
-
2 lines of code changed in 1 file:
-
DIST:
DI_matr.cxx (+2 -2)
-
westram
2017-11-28 10:55
#7
Rev.: 16760
-
15 lines of code changed in 1 file:
-
HELP_SOURCE/oldhelp:
dist.hlp (+15 -6)
-
westram
2017-11-19 15:19
#6
Rev.: 16683
-
97 lines of code changed in 12 files:
-
Makefile (+37 -18)
-
CONVERTALN:
embl.cxx (+1 -1)
-
DIST:
DI_view_matrix.cxx (+2 -1)
-
EDIT4:
ED4_main.cxx (+16 -14),
ED4_manager.cxx (+1 -1)
-
NTREE:
ColumnStat_2_gnuplot.cxx (+2 -1),
NT_main.cxx (+1 -1)
-
PHYLO:
PH_main.cxx (+2 -1)
-
SL/ALILINK:
TranslateRealign.cxx (+1 -1)
-
SL/FILTSEQEXP:
FilteredExport.cxx (+3 -2)
-
SOURCE_TOOLS:
postcompile.pl (+30 -11)
-
WINDOW:
AW_root_debug.cxx (+1)
-
westram
2017-11-17 12:54
#5
Rev.: 16668
-
106 lines of code changed in 24 files:
-
Makefile (-4)
-
AISC_COM/C:
client.c (+16 -3)
-
ARBDB:
TreeNode.cxx (+6 -6),
adindex.cxx (+3 -3),
adquery.cxx (+3 -2),
adsocket.cxx (+2 -2)
-
CORE:
arb_mem.cxx (+11 -5)
-
EDIT4:
ED4_edit_string.cxx (+13 -13)
-
MERGE:
MG_species.cxx (+1),
MG_trees.cxx (+1 -1)
-
NTREE:
NT_edconf.cxx (+8),
ad_trees.cxx (+2 -2)
-
PARSIMONY:
PARS_dtree.cxx (+1 -1)
-
RNACMA:
Makefile (+4 -3)
-
SL/AP_TREE:
AP_Tree.hxx (+1)
-
SL/FAST_ALIGNER:
ClustalV.cxx (+1)
-
SL/FILTSEQEXP:
FilteredExport.cxx (+2)
-
SL/PTCLEAN:
ptclean.cxx (+1)
-
SL/TREEDISP:
TreeDisplay.cxx (+1 -1)
-
SOURCE_TOOLS:
export2sub (+1 -1),
postcompile.pl (+4)
-
TEMPLATES:
cxxforward.h (+10)
-
TOOLS:
Makefile (+7 -1)
-
WINDOW:
AW_inotify.cxx (+7 -2)
-
westram
2017-11-16 13:36
#4
Rev.: 16658
-
76 lines of code changed in 1 file:
-
HELP_SOURCE/oldhelp:
pos_var_pars.hlp (+76 -11)
-
westram
2017-11-14 14:36
#3
Rev.: 16653
-
80 lines of code changed in 10 files:
-
Makefile (+4 -3)
-
ARBDB:
adseqcompr.cxx (+1 -1)
-
MERGE:
MG_preserves.cxx (+1 -1)
-
PARSIMONY:
PARS_main.cxx (+14 -4),
test_env.h (+4 -1)
-
PROBE:
PT_match.cxx (+2 -2)
-
SL/CONSENSUS:
chartable.cxx (+10 -10)
-
SL/INSDEL:
insdel.cxx (+1 -1)
-
SOURCE_TOOLS:
postcompile.pl (+40 -17),
vectorize.README (+3)
-
westram
2017-11-12 14:53
#2
Rev.: 16649
-
57 lines of code changed in 15 files:
-
arbsrc_README_gcc.txt (+3 -10)
-
ARBDB:
ad_cb.cxx (+1 -1),
adquery.cxx (+1 -1),
adstring.cxx (+2 -2),
gb_aci.cxx (+3 -3)
-
CONVERTALN:
date.cxx (+1 -1)
-
CORE:
arb_misc.cxx (+1 -1)
-
NTREE:
ad_trees.cxx (+1 -1)
-
PROBE:
PT_buildtree.cxx (+1 -1)
-
SL/FAST_ALIGNER:
seq_search.cxx (+1 -1)
-
SL/INSDEL:
insdel.cxx (+3 -3)
-
SL/LOCATION:
Location.cxx (+1 -1)
-
TEMPLATES:
attributes.h (+3 -1)
-
TOOLS:
arb_probe.cxx (+1 -1)
-
UNIT_TESTER:
test_unit.h (+34)
-
westram
2017-11-06 13:54
#1
Rev.: 16628
-
413 lines of code changed in 53 files:
-
Makefile (+11 -23)
-
AISC_MKPTPS:
mkptypes.cxx (+4 -1)
-
ARBDB:
adGene.cxx (+1 -1),
adcompr.cxx (+7 -7),
adlang1.cxx (+2 -2),
adoptimize.cxx (+5 -5),
adseqcompr.cxx (+4 -4),
adstring.cxx (+1 -1),
gb_aci.cxx (+1 -1)
-
CONSENSUS_TREE:
CT_part.cxx (+4 -4),
CT_part.hxx (+1 -1)
-
MERGE:
MG_adapt_ali.cxx (+3 -3),
MG_checkfield.cxx (+1 -1),
MG_preserves.cxx (+1 -1)
-
MULTI_PROBE:
MP_Generation.cxx (+1 -1),
MP_noclass.cxx (+1 -1),
MP_probe.cxx (+2 -1),
MP_probe_tabs.cxx (+2 -2),
MP_sonde.cxx (+2 -3),
MP_sondentopf.cxx (+2 -3)
-
NTREE:
AP_pos_var_pars.cxx (+1 -1),
NT_concatenate.cxx (+1 -1),
NT_tree_cmp.cxx (+1 -1),
ad_spec.cxx (+1 -1)
-
PERL2ARB:
Makefile.main (+1)
-
PHYLO:
PH_filt.cxx (+2 -2)
-
PROBE:
Makefile (+1 -1),
PT_family.cxx (+1 -1),
PT_match.cxx (+1 -1),
PT_prefixIter.h (+1 -1),
PT_prefixtree.cxx (+11 -1),
pt_split.h (+1 -1)
-
SEQ_QUALITY:
SQ_GroupData.h (+2 -2)
-
SL/ALILINK:
TranslateRealign.cxx (+1 -1)
-
SL/CONSENSUS:
chartable.cxx (+11 -11)
-
SL/FAST_ALIGNER:
ClustalV.cxx (+6 -6)
-
SL/GROUP_SEARCH:
group_search.cxx (+2 -2)
-
SL/GUI_ALIVIEW:
ColumnStat.cxx (+2 -2)
-
SL/HELIX:
BI_basepos.cxx (+1 -1),
BI_basepos.hxx (+1 -1)
-
SL/INSDEL:
insdel.cxx (+5 -5)
-
SL/LOCATION:
Location.cxx (+1 -1)
-
SL/MATRIX:
AP_matrix.cxx (+1 -1)
-
SL/SEQIO:
seq_export.cxx (+1 -1)
-
SOURCE_TOOLS:
Makefile (+2 -1),
clean_checked_vectorizations.sh (new 23),
export2sub (+3),
postcompile.pl (+140 -9),
vectorize.README (new 90),
vectorized.source (+32)
-
STAT:
ST_ml.cxx (+3 -3)
-
TEMPLATES:
attributes.h (+5),
gccver.h (+2 -2)