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35 lines of code changed in 2 files:
* oldhelp/csp_2_gnuplot.hlp: - added some info about different calculations
21 lines of code changed in 1 file:
* awt_csp.hxx: - untabified and indented
35 lines of code changed in 1 file:
* AWT_csp.cxx: - untabified, indented and valgrinded
- if no helix is found -> ignored
28 lines of code changed in 1 file:
* AP_csp_2_gnuplot.cxx: - valgrinded, indented and untabified
- rewrote parts of AP_csp_2_gnuplot_cb
- plot shows type of data in gnuplot
202 lines of code changed in 1 file:
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0 lines of code changed in 1 file:
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32 lines of code changed in 2 files:
* GDE.cxx: - valgrinded
3 lines of code changed in 1 file:
- aw_status_timer_listen_event (initial gauge value set to 0)
5 lines of code changed in 1 file:
* ad_ext.cxx: - valgrinded, untabified and indented
50 lines of code changed in 1 file:
* AP_pos_var_pars.cxx: - valgrinded
1 lines of code changed in 1 file:
* AP_cprofile.cxx: - valgrinded, indented and untabified
1227 lines of code changed in 1 file:
* AP_consensus.cxx: - valgrinded
- rewrote CON_calculate_cb (was really weird)
572 lines of code changed in 1 file:
* oldhelp/ad_extended.hlp: - added info about 'ASSIGN GROUP'
8 lines of code changed in 1 file:
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205 lines of code changed in 4 files:
* AW_status.cxx: - untabified and indented
- logfile always written in users home
21 lines of code changed in 1 file:
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21 lines of code changed in 1 file:
added *.cc and *.hh
1 lines of code changed in 1 file:
* phylo.hxx: - untabified and indented
74 lines of code changed in 1 file:
* PH_matr.cxx: - untabified and indented
101 lines of code changed in 1 file:
* ad_transpro.cxx: - valgrinded
7 lines of code changed in 1 file:
* NT_extern.cxx: - menu resort
- moved some stuff into debugging menu (for internal use only)
15 lines of code changed in 1 file:
* NT_concatenate.cxx: - fixed a display error (close button)
11 lines of code changed in 1 file:
* CONSENSUS_TREE/CT_part.cxx: - untabified, indented and valgrinded
140 lines of code changed in 1 file:
* CONSENSUS_TREE/CT_mem.cxx: - getmem() returns 0 if memory couldn't be allocated
5 lines of code changed in 1 file:
* awt_pro_a_nucs.hxx: - ctors for arb_r2a_pro_2_nuc, arb_r2a_pro_2_nucs and arb_r2a_struct
- untabified and indented
33 lines of code changed in 1 file:
* AWT_tree.cxx: - bootstrapping had an serious error causing use of random positions from OUTSIDE
the sequence (i.e. random memory locations)
- valgrinded
* AWT_tree.cxx: - untabified, indented and valgrinded
73 lines of code changed in 1 file:
* AWT_seq_dna.cxx: - valgrinded
114 lines of code changed in 1 file:
* AWT_pro_a_nucs.cxx: - structs arb_r2a_pro_2_nuc and arb_r2a_pro_2_nucs were allocated by GB_calloc (using new now!)
- ctors for arb_r2a_pro_2_nuc, arb_r2a_pro_2_nucs and arb_r2a_struct
47 lines of code changed in 1 file:
* AWT_nei.cxx: - untabified, indented and valgrinded
211 lines of code changed in 1 file:
* AWT_dtree.cxx: - hotkeys 'm' and 'c' crashed when zombie in tree
2 lines of code changed in 1 file:
* di_matr.hxx: - untabified and indented
50 lines of code changed in 1 file:
* DI_matr.cxx: - untabified, indented and valgrinded
126 lines of code changed in 1 file:
* DI_compress_matrix.cxx: - valgrinded
70 lines of code changed in 1 file:
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17 lines of code changed in 1 file:
changed prefix of filename from 'PH_' to 'DI_'
becaused they clashed with files in PHYLO
4055 lines of code changed in 29 files:
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287 lines of code changed in 1 file:
reordered definitions and inserted some comments
12 lines of code changed in 1 file:
new function PS_Node::removeProbes()
5 lines of code changed in 1 file:
fixed bug with allocating memory when calling PS_BitMap_Counted(PS_FileBuffer *)
177 lines of code changed in 2 files:
exception handling; writing import messages and errors to file arb.log
39 lines of code changed in 2 files:
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0 lines of code changed in 1 file:
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33 lines of code changed in 2 files:
avoid compilation with other compiler than gcc 2.95.3 (Linux only)
33 lines of code changed in 1 file:
* NT_extern.cxx: - re-arranged menus according to fogs requests
80 lines of code changed in 1 file:
* ED4_root.cxx: - renamed NDS menu entry (according to arb_ntree)
1 lines of code changed in 1 file:
new function PS_apply_candidate_to_bitmap() -- currently produces a seg.fault at the deletion of __MAP when used
97 lines of code changed in 1 file:
moved unction flush() from private to public area
1 lines of code changed in 1 file:
new function PS_BitMap(_Counted)::printGNUplot(..)
86 lines of code changed in 1 file:
spell correction in comment
1 lines of code changed in 1 file:
bug fixed in getSpeciesCount()
1 lines of code changed in 1 file:
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126 lines of code changed in 2 files:
new functions:
PS_calc_next_speciesid_sets()
PS_find_probes(..)
PS_find_probe_for_sets(..)
PS_print_set_ranges(..)
260 lines of code changed in 1 file:
testing of new functions PS_Bit(Map|Set)::get(True|False)Indices(...)
35 lines of code changed in 1 file:
new function PS_Bit(Map|Set)::get(True|False)Indices(...)
fixed bug in functions setting a bit to false in PS_BitSet
166 lines of code changed in 2 files:
new function PS_Database::getSpeciesCount()
3 lines of code changed in 1 file:
fixed bug in lines for ps_find
3 lines of code changed in 1 file:
made more clear, that user has to do some config
70 lines of code changed in 1 file:
install script fixes
4 lines of code changed in 1 file:
introduction of 4th step : ps_find_probes.cxx
87 lines of code changed in 1 file:
introduction of 4th step : ps_find_probes.cxx
resorted Makefile a bit
73 lines of code changed in 1 file:
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3 lines of code changed in 2 files:
seleciton list for valid names continued
63 lines of code changed in 2 files:
changed name of member variable size to max_index/max_row to reflect its actual meaning
154 lines of code changed in 2 files:
introduction of db_min_id because not every database has the SpeciesID 0 (zero) assigned to a species
4 lines of code changed in 1 file:
fixed bug handling next_path_id in PS_print_and_evaluate()
21 lines of code changed in 1 file:
manual name selection file added
176 lines of code changed in 6 files:
modified output behavior due to introduction of ps_show_results
57 lines of code changed in 6 files:
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63 lines of code changed in 1 file:
minor changes in handling program parameters
minor changes in output behavior
84 lines of code changed in 3 files:
Color transalation table window
35 lines of code changed in 1 file:
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220 lines of code changed in 7 files:
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21 lines of code changed in 8 files:
fixes for arb_probe_group_design
12 lines of code changed in 1 file:
milestone 1 -- converting / merging / detecting works
1480 lines of code changed in 11 files:
interface to database files in my format
bundles mapping and tree
351 lines of code changed in 2 files:
renamed from ps_dumb_db.cxx
326 lines of code changed in 1 file:
renamed to ps_convert_db.cxx
0 lines of code changed in 1 file:
test programs
277 lines of code changed in 3 files:
moved logic to PS_Database
0 lines of code changed in 1 file: