August 2003 Commit Log

Number of Commits:

232

Number of Active Developers:

5

huberj 2003-08-27 17:59 #232 Rev.: 1798

*** empty log message ***

17 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_functions.cxx (+11 -7), SQ_main.cxx (+6 -9)

huberj 2003-08-26 17:19 #231 Rev.: 1797

added tree traversal
does not work right now

25 lines of code changed in 3 files:

• SEQ_QUALITY: SQ_functions.cxx (+23 -2), SQ_functions.h (+1 -3), SQ_main.cxx (+1 -1)

richter 2003-08-26 14:54 #230 Rev.: 1796

simple cgi URL to determine version of current tree on server
to be completed

8 lines of code changed in 1 file:

• PROBE_WEB/SERVER: getTreeVersion.cgi (new 8)

huberj 2003-08-25 17:37 #229 Rev.: 1795

*** empty log message ***

80 lines of code changed in 3 files:

• SEQ_QUALITY: SQ_functions.cxx (+77 -190), SQ_functions.h (+1 -1), SQ_main.cxx (+2 -5)

richter 2003-08-25 15:49 #228 Rev.: 1794

simple cgi script to decode node path information an send back any wanted information

49 lines of code changed in 1 file:

• PROBE_WEB/SERVER: getProbes.cgi (new 49)

richter 2003-08-25 15:46 #227 Rev.: 1793

invocation of cgi scripts, decoding of path information through cgi-script
retrieval of tree from web server
acces of jar file components not yet add

99 lines of code changed in 3 files:

• PROBE_WEB/CLIENT: Client.java (+12), HttpSubsystem.java (new 86), TreeDisplay.java (+1)

westram 2003-08-22 23:10 #226

*** empty log message ***

7 lines of code changed in 3 files:

• arb_CHANGES.txt (+4 -2)
• util: arb_export (+3 -2)

westram 2003-08-22 23:02 #225

*** empty log message ***

24 lines of code changed in 2 files:

• util: arb_export (+13 -9)

westram 2003-08-22 22:58 #224 Rev.: 1788

- fixed export paths
- fixed source export (exported all)

9 lines of code changed in 1 file:

• util: arb_export (+9 -7)

westram 2003-08-22 22:36 #223 Rev.: 1787

*** empty log message ***

1 lines of code changed in 1 file:

• Makefile (+1 -1)

westram 2003-08-22 22:19 #222 Rev.: 1786

- fixed to do export w/o questions

14 lines of code changed in 1 file:

• util: arb_export (+14 -14)

westram 2003-08-22 22:19 #221 Rev.: 1785

- new target 'export_beta'

5 lines of code changed in 1 file:

• Makefile (+5 -2)

westram 2003-08-22 22:14 #220 Rev.: 1784

*** empty log message ***

3 lines of code changed in 1 file:

• arb_CHANGES.txt (+3)

westram 2003-08-22 21:57 #219 Rev.: 1783

updated dependencies

12 lines of code changed in 3 files:

• EDIT4: Makefile (+2)
• NTREE: Makefile (+3 -2)
• SEQ_QUALITY: Makefile (+7 -1)

westram 2003-08-22 21:55 #218 Rev.: 1782

- added AW_copy_GCs()

45 lines of code changed in 2 files:

• WINDOW: AW_preset.cxx (+31), aw_preset.hxx (+14 -15)

westram 2003-08-22 21:54 #217 Rev.: 1781

- menu entries to sync colors with EDIT4
- removed trailing blanks from menu entries

39 lines of code changed in 1 file:

• SECEDIT: SEC_main.cxx (+39 -7)

westram 2003-08-22 21:53 #216 Rev.: 1780

- changed color names for search results to match those in EDIT4

4 lines of code changed in 1 file:

• SECEDIT: SEC_graphic.cxx (+4 -3)

westram 2003-08-22 21:52 #215 Rev.: 1779

- shows reason why SECEDIT could not be started

4 lines of code changed in 1 file:

• EDIT4: ED4_secedit.cxx (+4 -2)

westram 2003-08-22 21:52 #214 Rev.: 1778

- added "Save loaded Properties"

21 lines of code changed in 1 file:

• EDIT4: ED4_root.cxx (+21 -8)

westram 2003-08-22 14:16 #213 Rev.: 1777

minor changes

6 lines of code changed in 3 files:

• AWTC: AWTC_fast_aligner.cxx (+1 -1)
• MERGE: MG_species.cxx (+3 -2)
• NTREE: NT_extern.cxx (+2 -2)

westram 2003-08-22 14:15 #212 Rev.: 1776

- aw_create_shell allows to create uncloseable windows
- AW_window_message 'X' button does not minimize the window

20 lines of code changed in 1 file:

• WINDOW: AW_window.cxx (+20 -16)

westram 2003-08-22 14:14 #211 Rev.: 1775

recreated

32 lines of code changed in 1 file:

• NTREE: nt_internal.h (+32 -4)

westram 2003-08-22 14:14 #210 Rev.: 1774

- added prototype for NT_detach_information_window

2 lines of code changed in 1 file:

• NTREE: ad_spec.hxx (+2)

westram 2003-08-22 14:14 #209 Rev.: 1773

- Alignment auto formatter ignores security
- calls nt_check_database_consistency() in main3 (=create db from foreign format)

5 lines of code changed in 1 file:

• NTREE: NT_main.cxx (+5 -2)

westram 2003-08-22 14:13 #208 Rev.: 1772

- runs auto format after 'import sequences and fields'

7 lines of code changed in 1 file:

• NTREE: NT_import.cxx (+7 -6)

westram 2003-08-22 14:12 #207 Rev.: 1771

- removed NT_format_all_alignments from AWTC_import_go_cb
(there it only formats a temporary database)

0 lines of code changed in 1 file:

• AWTI: AWTI_import.cxx (-5)

westram 2003-08-22 14:08 #206 Rev.: 1770

- checks comment buffer for overflow
- increased size of comment buffer from 500 to 10000

10 lines of code changed in 1 file:

• AISC_MKPTPS: mkptypes.c (+10 -5)

westram 2003-08-21 15:33 #205 Rev.: 1769

- mark functions for species with data in current alignment

101 lines of code changed in 1 file:

• AWT: AWT_tree_cb.cxx (+101 -51)

westram 2003-08-21 15:32 #204 Rev.: 1768

- crashed if no tree in database

65 lines of code changed in 1 file:

• AWT: AWT_dtree.cxx (+65 -64)

westram 2003-08-21 15:32 #203 Rev.: 1767

- commented out GB_save_as

11 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.cxx (+11 -2)

westram 2003-08-21 15:30 #202 Rev.: 1766

- reads and links the tree
- basic error handling
- basic config window

136 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_main.cxx (+136 -41)

westram 2003-08-21 15:30 #201 Rev.: 1765

- only exports window interface

3 lines of code changed in 1 file:

• SEQ_QUALITY: seq_quality.h (+3 -1)

westram 2003-08-21 15:29 #200 Rev.: 1764

- removed obsolete file

0 lines of code changed in 1 file:

• SEQ_QUALITY: seq_quality.cxx (del)

westram 2003-08-21 15:29 #199 Rev.: 1763

*** empty log message ***

181 lines of code changed in 1 file:

• lib/pictures: seq_quality.fig (+181 -169)

westram 2003-08-21 15:28 #198 Rev.: 1762

- template for sequence quality help

23 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: seq_quality.hlp (new 23)

westram 2003-08-21 15:28 #197 Rev.: 1761

- changed SEQ_QUALITY interface

2 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+2 -11)

westram 2003-08-20 17:08 #196 Rev.: 1760

just prototype

197 lines of code changed in 1 file:

• lib/pictures: seq_quality.fig (new 197)

huberj 2003-08-19 13:23 #195 Rev.: 1759

code cleanup

164 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_functions.cxx (+164 -241), SQ_functions.h (-2)

huberj 2003-08-18 16:09 #194 Rev.: 1758

*** empty log message ***

12 lines of code changed in 3 files:

• SEQ_QUALITY: SQ_functions.cxx (+8 -4), SQ_functions.h (+2), SQ_main.cxx (+2)

huberj 2003-08-18 13:30 #193 Rev.: 1757

*** empty log message ***

120 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_functions.cxx (+115 -8), SQ_main.cxx (+5 -2)

westram 2003-08-16 14:31 #192 Rev.: 1756

cosmetics

6 lines of code changed in 1 file:

• ARB_GDE: GDE_ParseMenu.cxx (+6 -6)

westram 2003-08-16 14:30 #191 Rev.: 1755

- fixed for ClustalW v 1.83

18 lines of code changed in 1 file:

• GDE/CLUSTALW: Makefile (+18 -20)

westram 2003-08-16 14:30 #190 Rev.: 1754

updated to version 1.83

2795 lines of code changed in 14 files:

• GDE/CLUSTALW: README (+20 -1), amenu.c (+22 -1), calctree.c (+5 -9), clustalw.c (+4 -1), clustalw.h (+12 -7), clustalw_help (+35 -4), interface.c (+1697 -1129), makefile.org (+5 -9), pairalign.c (+303 -303), param.h (+21), prfalign.c (+10 -9), readmat.c (-1), sequence.c (+8 -2), trees.c (+653 -1)

westram 2003-08-16 14:29 #189 Rev.: 1753

not in version 1.83

0 lines of code changed in 4 files:

• GDE/CLUSTALW: coldna.par (del), colprint.par (del), colprot.par (del), phcolor.par (del)

westram 2003-08-16 14:24 #188 Rev.: 1752

*** empty log message ***

40 lines of code changed in 3 files:

• arb_CHANGES.txt (+3 -2)
• GDE/CORE: functions.h (+7)
• GDEHELP: protml.help (new 30)

westram 2003-08-16 14:24 #187 Rev.: 1751

- split long lines

134 lines of code changed in 15 files:

• GDEHELP/MENUS: blast.menu (+15 -3), blastp.menu (+18 -4), desoete.menu (+5 -1), dna_rna.menu (+12 -2), dnamlrates.menu (+9 -2), fastdnaml.menu (+7 -1), inc_fastdnaml.menu (+7 -1), molphy.menu (+6 -1), phylip_dist.menu (+12 -2), phylip_dist_org.menu (+6 -1), phylip_pars.menu (+6 -2), pretty_print.menu (+15 -13), protein.menu (+5 -1), puzzle.menu (+4 -1), seq_management.menu (+7 -2)

westram 2003-08-16 14:23 #186 Rev.: 1750

- added seperators for overview
- split long lines

29 lines of code changed in 1 file:

• GDEHELP/MENUS: align.menu (+29 -11)

westram 2003-08-16 14:22 #185 Rev.: 1749

- added *.genmenu

1 lines of code changed in 1 file:

• GDEHELP/MENUS: .cvsignore (+1)

westram 2003-08-16 14:22 #184 Rev.: 1748

- .menu files are first translated into .genmenu files
to get rid of leading spaces in multilines

7 lines of code changed in 1 file:

• GDEHELP: Makefile (+7 -2)

westram 2003-08-16 14:21 #183 Rev.: 1747

- now includes .genmenu (instead of .menu)

20 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+20 -20)

westram 2003-08-16 14:21 #182 Rev.: 1746

- beautified

420 lines of code changed in 1 file:

• GDE/CORE: ParseMenu.c (+420 -486)

westram 2003-08-16 14:21 #181 Rev.: 1745

- added fig2dev

1 lines of code changed in 1 file:

• arb_INSTALL.txt (+1 -1)

westram 2003-08-15 22:18 #180 Rev.: 1744

- wrapper for protml

28 lines of code changed in 1 file:

• SH: arb_protml (+28 -1)

westram 2003-08-15 22:18 #179 Rev.: 1743

- remove echos
- added error handling
- echoes to stdin of treeprog now optional (bad for protml)
- check for empty output of treeprog

1 lines of code changed in 1 file:

• SH: arb_bootstrap (+1)

westram 2003-08-15 22:17 #178 Rev.: 1742

- fixed protml bootstrapping

22 lines of code changed in 1 file:

• GDEHELP/MENUS: molphy.menu (+22 -20)

westram 2003-08-15 19:09 #177 Rev.: 1741

dependencies updated

3 lines of code changed in 2 files:

• SEQ_QUALITY: Makefile (+1)
• TREEGEN: Makefile (+2)

westram 2003-08-15 19:08 #176 Rev.: 1740

deps updated

2 lines of code changed in 1 file:

• EDIT4: Makefile (+2 -1)

westram 2003-08-15 19:06 #175 Rev.: 1739

hmpf

1 lines of code changed in 1 file:

• TOOLS: Makefile (+1 -1)

westram 2003-08-15 19:05 #174 Rev.: 1738

- fixed call to GBT_load_tree()

1 lines of code changed in 1 file:

• TOOLS: arb_newick_2_otb.cxx (+1 -1)

westram 2003-08-15 19:05 #173 Rev.: 1737

- dependencies were completely wrong (have no .o files here)

89 lines of code changed in 1 file:

• TOOLS: Makefile (+89 -83)

westram 2003-08-15 18:38 #172 Rev.: 1736

- again fixed reading of bootstrap trees
- fixed call to GBT_load_tree

31 lines of code changed in 1 file:

• TOOLS: arb_read_tree.cxx (+31 -30)

westram 2003-08-15 18:37 #171 Rev.: 1735

- warning fix

5 lines of code changed in 2 files:

• SECEDIT: SEC_main.cxx (+2)
• SEQ_QUALITY: SQ_main.cxx (+3 -4)

westram 2003-08-15 18:37 #170 Rev.: 1734

- changed parameter option to 'const char *'

26 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_functions.cxx (+24 -24), SQ_functions.h (+2 -2)

westram 2003-08-15 18:29 #169 Rev.: 1733

- fixed call to GBT_load_tree

1 lines of code changed in 1 file:

• NTREE: ad_trees.cxx (+1 -1)

westram 2003-08-15 18:28 #168 Rev.: 1732

- fixed dnapars/protpars bootstrapping

9 lines of code changed in 1 file:

• GDEHELP/MENUS: phylip_pars.menu (+9 -9)

westram 2003-08-15 18:28 #167 Rev.: 1731

- does not clear display

53 lines of code changed in 4 files:

• GDE/PHYLIP: consense.c (+9 -8), dnapars.c (+15 -14), protpars.c (+15 -14), seqboot.c (+14 -13)

westram 2003-08-15 18:27 #166 Rev.: 1730

show another error

1 lines of code changed in 1 file:

• EDIT4: ED4_root.cxx (+1)

westram 2003-08-15 18:27 #165 Rev.: 1729

- get_symbol again invisible if _USE_AW_WINDOW undefined

88 lines of code changed in 2 files:

• AWT: BI_helix.cxx (+17 -18), BI_helix.hxx (+71 -70)

westram 2003-08-15 18:26 #164 Rev.: 1728

updated

2 lines of code changed in 2 files:

• arb_CHANGES.txt (+1 -1)
• ARBDB: ad_t_prot.h (+1 -1)

westram 2003-08-15 18:26 #163 Rev.: 1727

- added flag to GBT_load_tree() specifying whether scaling of lengths is allowed or not

4 lines of code changed in 1 file:

• ARBDB: adtools.c (+4 -2)

westram 2003-08-15 18:26 #162 Rev.: 1726

- mentions version 0.82 of sablotron
- mentions bash

3 lines of code changed in 1 file:

• arb_INSTALL.txt (+3 -2)

westram 2003-08-15 18:25 #161 Rev.: 1725

- target 'menus' depends on 'binlink'

2 lines of code changed in 1 file:

• Makefile (+2 -2)

westram 2003-08-15 18:18 #160 Rev.: 1724

* arb_protml: - wrapper for protml
* arb_bootstrap: - remove echos
- added error handling
- echoes to stdin of treeprog now optional (bad for protml)
- check for empty output of treeprog

66 lines of code changed in 2 files:

• SH: arb_bootstrap (+45 -18), arb_protml (new 21)

huberj 2003-08-15 12:56 #159 Rev.: 1723

*** empty log message ***

210 lines of code changed in 3 files:

• SEQ_QUALITY: SQ_functions.cxx (+146 -3), SQ_functions.h (+29 -1), SQ_main.cxx (+35 -2)

westram 2003-08-15 02:21 #158 Rev.: 1722

fix for NDEBUG version

2 lines of code changed in 1 file:

• SECEDIT: SEC_main.cxx (+2)

westram 2003-08-15 02:01 #157 Rev.: 1721

- removed echos

0 lines of code changed in 1 file:

• SH: arb_bootstrap (-3)

westram 2003-08-15 01:58 #156 Rev.: 1720

- fixed calls to init()

3 lines of code changed in 1 file:

• MULTI_PROBE: MP_Window.cxx (+3 -3)

westram 2003-08-15 01:55 #155 Rev.: 1719

updated (to ensure correct window sizes)

153 lines of code changed in 4 files:

• lib/pictures: ad_delof.fig (+9 -9), di_ge_ma.fig (+68 -81), message.fig (+8 -6), ph_ge_ma.fig (+68 -81)

westram 2003-08-15 01:54 #154 Rev.: 1718

- uses AWAR_FOOTER

105 lines of code changed in 3 files:

• SECEDIT: SEC_graphic.cxx (+5 -5)
• TESTAWT: TB_main.cxx (+50 -47)
• TESTVECTORFONT: TB_main.cxx (+50 -47)

westram 2003-08-15 01:53 #153 Rev.: 1717

- uses AWAR_FOOTER
- test mode help for max allowed length (=AWAR_FOOTER_MAX_LEN)

73 lines of code changed in 1 file:

• TEST: D_main.cxx (+73 -67)

westram 2003-08-15 01:52 #152 Rev.: 1716

- fixed calls to init()
- beautified

108 lines of code changed in 1 file:

• STAT: ST_window.cxx (+108 -108)

westram 2003-08-15 01:52 #151 Rev.: 1715

- fixed calls to init()
- test mode help for max allowed length (=AWAR_FOOTER_MAX_LEN)
- size of AWAR_FOOTER does not affect overall window size
- resized main window
- changed title (please note: Everytime you change a window title you have
to correct ALL help files that refer to that window title by name)
- replaced save properties by help

47 lines of code changed in 1 file:

• SECEDIT: SEC_main.cxx (+47 -32)

westram 2003-08-15 01:49 #150 Rev.: 1714

- fixed calls to init()

699 lines of code changed in 57 files:

• ARB_GDE: GDE.cxx (+3 -3)
• AWT: AWT_advice.cxx (+2 -2), AWT_asciiprint.cxx (+1 -1), AWT_canio.cxx (+3 -3), AWT_csp.cxx (+1 -1), AWT_filter.cxx (+1 -1), AWT_nds.cxx (+3 -3), AWT_sel_boxes.cxx (+5 -5), AWT_seq_colors.cxx (+37 -37), AWT_species_sel_box.cxx (+2 -2), AWT_tables.cxx (+150 -150), AWT_www.cxx (+1 -1), BI_helix.cxx (+1 -1)
• AWTC: AWTC_fast_aligner.cxx (+2 -2), AWTC_names_admin.cxx (+39 -39), AWTC_rename.cxx (+1 -1), AWTC_submission.cxx (+2 -2)
• AWTI: AWTI_import.cxx (+1 -1)
• DIST: DI_matr.cxx (+4 -4), DI_view_matrix.cxx (+18 -18)
• EDIT: edit.cxx (+5 -5), edit_naligner.cxx (+3 -3), edit_tools.cxx (+58 -58)
• EDIT4: ED4_block.cxx (+1 -1), ED4_nds.cxx (+1 -1), ED4_no_class.cxx (+9 -9), ED4_root.cxx (+2 -2), ED4_tools.cxx (+3 -3), ED4_visualizeSAI.cxx (+5 -5)
• MERGE: MG_alignment.cxx (+5 -5), MG_configs.cxx (+4 -4), MG_gene_species.cxx (+2 -2), MG_main.cxx (+5 -5), MG_preserves.cxx (+2 -2), MG_species.cxx (+4 -4), MG_trees.cxx (+3 -3)
• NTREE: AP_consensus.cxx (+4 -4), AP_conservProfile2Gnuplot.cxx (+5 -5), AP_cprofile.cxx (+7 -7), AP_csp_2_gnuplot.cxx (+1 -1), AP_pos_var_pars.cxx (+1 -1), NT_cb.cxx (+2 -2), NT_concatenate.cxx (+2 -2), NT_edconf.cxx (+2 -2), NT_ins_col.cxx (+65 -65), NT_join.cxx (+1 -1), NT_main.cxx (+1 -1), NT_sort.cxx (+183 -183), NT_validManual.cxx (+1 -1), ad_ali.cxx (+4 -4), ad_ext.cxx (+3 -3), ad_spec.cxx (+16 -16), ad_transpro.cxx (+2 -2)
• PHYLO: PH_filt.cxx (+1 -1), PH_main.cxx (+4 -4), PH_matr.cxx (+3 -3)
• PRIMER_DESIGN: primer_design.cxx (+2 -2)

westram 2003-08-15 01:48 #149 Rev.: 1713

new help

26 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: sec_props.hlp (new 26)

westram 2003-08-15 01:47 #148 Rev.: 1712

- link to EDIT4 help

7 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: arb_secedit.hlp (+7 -6)

westram 2003-08-15 01:47 #147 Rev.: 1711

- note about fast aligner

1 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: align.hlp (+1)

westram 2003-08-15 01:45 #146 Rev.: 1710

- fixed calls to init()
- added default bond values

16 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+16 -8)

westram 2003-08-15 01:45 #145 Rev.: 1709

- fixed calls to init()
- ignore size of AWAR_FOOTER

16 lines of code changed in 1 file:

• PARSIMONY: PARS_main.cxx (+16 -6)

westram 2003-08-15 01:44 #144 Rev.: 1708

- beautified
- fixed calls to init()

511 lines of code changed in 3 files:

• MERGE: MG_checkfield.cxx (+281 -281)
• NTREE: ETC_check_gcg.cxx (+184 -184)
• PARSIMONY: PARS_klprops.cxx (+46 -46)

westram 2003-08-15 01:44 #143 Rev.: 1707

- beautified

22 lines of code changed in 1 file:

• PARSIMONY: parsimony.hxx (+22 -23)

westram 2003-08-15 01:43 #142 Rev.: 1706

- changed calls to init()

39 lines of code changed in 2 files:

• WINDOW: AW_preset.cxx (+6 -6), AW_status.cxx (+33 -15)

westram 2003-08-15 01:43 #141 Rev.: 1705

- added AWAR_FOOTER, AWAR_FOOTER_MAX_LEN

3 lines of code changed in 1 file:

• WINDOW: aw_awars.hxx (+3 -1)

westram 2003-08-15 01:43 #140 Rev.: 1704

- added at_set_min_size()
- removed xpos/ypos from all and width/height from most window init functions
- added class AW_at_maxsize

24 lines of code changed in 1 file:

• WINDOW: aw_window.hxx (+24 -20)

westram 2003-08-15 01:42 #139 Rev.: 1703

- changed init() functions
- use initial size of window (provided by call to init) as minimum size
- mode buttons affect window size
- load_xfig does only _increase_ max size

67 lines of code changed in 1 file:

• WINDOW: AW_window.cxx (+67 -35)

westram 2003-08-15 01:42 #138 Rev.: 1702

- added at_set_min_size()
- at_set_to() allows to set unattached position
- implemented AW_at_maxsize

28 lines of code changed in 1 file:

• WINDOW: AW_at.cxx (+28 -10)

westram 2003-08-15 01:40 #137 Rev.: 1701

- create_tree_last_window() crashed when no tree selected
- fixed calls to init()

27 lines of code changed in 1 file:

• NTREE: ad_trees.cxx (+27 -16)

westram 2003-08-15 01:40 #136 Rev.: 1700

- uses NT_popup_species_window instead of NT_create_species_window
- fixed calls to init()
- uses AWAR_FOOTER and AWAR_FOOTER_MAX_LEN

27 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+27 -16)

westram 2003-08-15 01:38 #135 Rev.: 1699

- fixed calls to init()
- beautified

414 lines of code changed in 3 files:

• GENOM: GEN_nds.cxx (+232 -232)
• MERGE: MG_extendeds.cxx (+159 -159), MG_names.cxx (+23 -23)

westram 2003-08-15 01:37 #134 Rev.: 1698

- uses GEN_popup_organism_window instead of NT_create_organism_window
- uses AWAR_FOOTER
- test mode help for max allowed length (=AWAR_FOOTER_MAX_LEN)
- fixed calls to init()

19 lines of code changed in 1 file:

• GENOM: GEN_map.cxx (+19 -10)

westram 2003-08-15 01:37 #133 Rev.: 1697

- added GEN_popup_gene_window
- fixed calls to init()

10 lines of code changed in 1 file:

• GENOM: GEN_interface.cxx (+10 -5)

westram 2003-08-15 01:37 #132 Rev.: 1696

- added GEN_popup_gene_window

1 lines of code changed in 1 file:

• GENOM: GEN.hxx (+1)

westram 2003-08-15 01:36 #131 Rev.: 1695

- uses EXP_popup_experiment_window

3 lines of code changed in 1 file:

• GENOM: EXP_main.cxx (+3 -2)

westram 2003-08-15 01:36 #130 Rev.: 1694

- added EXP_popup_experiment_window

2 lines of code changed in 1 file:

• GENOM: EXP_local.hxx (+2 -1)

westram 2003-08-15 01:36 #129 Rev.: 1693

- added EXP_popup_experiment_window
- fixed calls to init()

11 lines of code changed in 1 file:

• GENOM: EXP_interface.cxx (+11 -6)

westram 2003-08-15 01:34 #128 Rev.: 1692

updated

3 lines of code changed in 2 files:

• ARBDB: ad_prot.h (+2 -2), ad_t_prot.h (+1 -1)

westram 2003-08-15 01:34 #127 Rev.: 1691

- GBS_find_lib_file() may or may not warn when file is missing

8 lines of code changed in 1 file:

• ARBDB: adstring.c (+8 -7)

westram 2003-08-15 01:34 #126 Rev.: 1690

- changed messages

10 lines of code changed in 1 file:

• ARBDB: ad_load.c (+10 -4)

westram 2003-08-15 01:33 #125 Rev.: 1689

- beautified
- fixed calls to init()

358 lines of code changed in 1 file:

• EDIT: ed_conf.cxx (+358 -358)

westram 2003-08-15 01:31 #124 Rev.: 1688

- fixed calls to init()
- beautified

172 lines of code changed in 2 files:

• AWT: AWT_map_key.cxx (+63 -63)
• AWTI: AWTI_export.cxx (+109 -109)

westram 2003-08-15 01:29 #123 Rev.: 1687

- uses AWAR_FOOTER
- test mode help for max allowed length (=AWAR_FOOTER_MAX_LEN)

3 lines of code changed in 1 file:

• AWT: AWT_tree_cb.cxx (+3 -1)

westram 2003-08-15 01:29 #122 Rev.: 1686

- ignores user size for user masks
- fixed calls to init()

6 lines of code changed in 1 file:

• AWT: AWT_input_mask.cxx (+6 -4)

westram 2003-08-15 01:28 #121 Rev.: 1685

- search windows use query_box_popup_view_window() to open info window
- fixed calls to init()

15 lines of code changed in 1 file:

• AWT: AWT_query_and_functions.cxx (+15 -5)

westram 2003-08-14 18:44 #120 Rev.: 1684

Script for bootstrapping

27 lines of code changed in 1 file:

• SH: arb_bootstrap (new 27)

huberj 2003-08-14 16:00 #119 Rev.: 1683

*** empty log message ***

98 lines of code changed in 3 files:

• SEQ_QUALITY: SQ_functions.cxx (+93 -55), SQ_functions.h (+2 -1), SQ_main.cxx (+3 -3)

westram 2003-08-14 10:14 #118 Rev.: 1682

- some words about 'Fit on page'

5 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: tree2prt.hlp (+5 -2)

westram 2003-08-14 09:50 #117 Rev.: 1681

- options help: spell checked and reformatted

8 lines of code changed in 1 file:

• PARSIMONY: PARS_main.cxx (+8 -6)

westram 2003-08-14 09:50 #116 Rev.: 1680

- sequence not shown during load in parsimony

1 lines of code changed in 1 file:

• AWT: AWT_seq_dna.cxx (+1 -1)

westram 2003-08-14 09:22 #115 Rev.: 1679

- changed AWUSE

2 lines of code changed in 1 file:

• WINDOW: aw_root.hxx (+2 -1)

westram 2003-08-14 09:21 #114 Rev.: 1678

- if window size has been increase to 4000x3000 recalc_size_at_show always gets set

2 lines of code changed in 1 file:

• WINDOW: AW_window.cxx (+2)

westram 2003-08-14 09:21 #113 Rev.: 1677

- main window is exposed by startup_sequence_cb
(before too many things are uninitialized)

16 lines of code changed in 1 file:

• PHYLO: PH_main.cxx (+16 -7)

westram 2003-08-14 09:21 #112 Rev.: 1676

- beautified
- fixed AP_display::resized, display
- display_status does nothing when windowList is zero
(especially it does even not initialize static variables!!)

199 lines of code changed in 1 file:

• PHYLO: PH_display.cxx (+199 -191)

westram 2003-08-14 09:20 #111 Rev.: 1675

- command line was too long; put into arb_bootstrap (not finished)
- added "broken" info

10 lines of code changed in 1 file:

• GDEHELP/MENUS: molphy.menu (+10 -7)

westram 2003-08-14 09:20 #110 Rev.: 1674

- command line was too long; put into arb_bootstrap

6 lines of code changed in 1 file:

• GDEHELP/MENUS: phylip_pars.menu (+6 -6)

richter 2003-08-13 16:04 #109 Rev.: 1673

path information and coding add to TreeNode

109 lines of code changed in 3 files:

• PROBE_WEB/CLIENT: Client.java (+18 -2), TreeDisplay.java (+10), TreeNode.java (+81 -1)

westram 2003-08-13 13:57 #108 Rev.: 1672

removes arb.tgz and arbsrc.tgz to make them unavailable
during rebuild

3 lines of code changed in 1 file:

• Makefile (+3 -1)

westram 2003-08-13 13:50 #107 Rev.: 1671

updated export targets

6 lines of code changed in 1 file:

• Makefile (+6 -3)

westram 2003-08-13 13:25 #106 Rev.: 1670

*** empty log message ***

84 lines of code changed in 3 files:

• lib/pictures: ad_align.fig (+25 -25), ad_ext.fig (+35 -28)
• lib/pictures/awt: import_db.fig (+24 -21)

westram 2003-08-13 13:24 #105 Rev.: 1669

- comment

5 lines of code changed in 1 file:

• WINDOW: aw_window.hxx (+5 -1)

westram 2003-08-13 13:24 #104 Rev.: 1668

- Text elements may be X/Y attached

39 lines of code changed in 1 file:

• WINDOW: AW_xfig.cxx (+39 -23)

westram 2003-08-13 13:24 #103 Rev.: 1667

- awar name generation by functions
- ajust window size (if user size is too small)
- windows are initially created with size 4000x3000 (if user size has been found)
(this fixes the crippled widgets occurring when widgets were drawn in invisible areas)
- cleanup

73 lines of code changed in 1 file:

• WINDOW: AW_window.cxx (+73 -63)

westram 2003-08-13 13:16 #102 Rev.: 1666

- aw_attach_widget() increases max. size of window
(this does not finally fix auto-size problems but makes them occur more rarely)
- aw_attach_widget respects value of correct_for_at_center
- aw_attach_widget corrects x-position for right and center justified widgets

48 lines of code changed in 1 file:

• WINDOW: AW_button.cxx (+48 -20)

westram 2003-08-13 13:16 #101 Rev.: 1665

- fixed at_set_to() (did wrong justification)

4 lines of code changed in 1 file:

• WINDOW: AW_at.cxx (+4 -8)

westram 2003-08-13 13:15 #100 Rev.: 1664

cosmetics

1 lines of code changed in 1 file:

• GDEHELP: ARB_GDEmenus.source (+1 -1)

westram 2003-08-13 13:15 #99 Rev.: 1663

- cleanup

0 lines of code changed in 1 file:

• EDIT4: ED4_visualizeSAI.cxx (-44)

westram 2003-08-13 13:15 #98 Rev.: 1662

- changed color defaults for ranges (RANGE 0 .. RANGE 9)

12 lines of code changed in 1 file:

• EDIT4: ED4_root.cxx (+12 -11)

westram 2003-08-13 13:14 #97 Rev.: 1661

- changed radio button text

2 lines of code changed in 1 file:

• AWTI: AWTI_import.cxx (+2 -3)

yadhu 2003-08-13 12:20 #96 Rev.: 1660

Help file for visualisation of SAIs updated.

8 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: visualizeSAI.hlp (+8 -4)

huberj 2003-08-12 16:56 #95 Rev.: 1659

by Ralf

61 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_functions.cxx (+57 -23), seq_quality.cxx (+4 -4)

huberj 2003-08-12 16:55 #94 Rev.: 1658

get_symbol always visible

4 lines of code changed in 2 files:

• AWT: BI_helix.cxx (+2 -2), BI_helix.hxx (+2 -1)

westram 2003-08-12 10:42 #93 Rev.: 1657

- valgrinds

4 lines of code changed in 1 file:

• NTREE: ad_trees.cxx (+4 -4)

westram 2003-08-12 10:42 #92 Rev.: 1656

- AWAR_EX_DEST,AWAR_EX_NAME -> AWAR_SAI_DEST,AWAR_SAI_NAME

16 lines of code changed in 2 files:

• NTREE: ad_ext.cxx (+15 -15), ad_ext.hxx (+1 -2)

westram 2003-08-12 10:42 #91 Rev.: 1655

- create AWAR_SAI_NAME

1 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+1)

westram 2003-08-12 10:41 #90 Rev.: 1654

new toggle

187 lines of code changed in 1 file:

• lib/pictures: visualizeSAI.fig (+187 -183)

westram 2003-08-12 10:41 #89 Rev.: 1653

- added global awar AWAR_SAI_NAME

1 lines of code changed in 1 file:

• WINDOW: aw_awars.hxx (+1)

westram 2003-08-12 10:40 #88 Rev.: 1652

- branchlength and bootstrap correction now done in GBT_load_tree
- rewrote tree comment generation

46 lines of code changed in 1 file:

• TOOLS: arb_read_tree.cxx (+46 -56)

westram 2003-08-12 10:39 #87 Rev.: 1651

- fixed call to getSaiColorString

6 lines of code changed in 1 file:

• SECEDIT: SEC_paint.cxx (+6 -4)

westram 2003-08-12 10:39 #86 Rev.: 1650

- fixed molphy entries (used protml.tre, treefile and outfile for same thing)

5 lines of code changed in 1 file:

• GDEHELP/MENUS: molphy.menu (+5 -5)

westram 2003-08-12 10:38 #85 Rev.: 1649

- branchlength scaling is done here
- const correctness

59 lines of code changed in 1 file:

• ARBDB: adtools.c (+59 -15)

westram 2003-08-12 10:38 #84 Rev.: 1648

- cosmetics

1 lines of code changed in 1 file:

• ARBDB: adstring.c (+1 -1)

westram 2003-08-12 10:38 #83 Rev.: 1647

- updated

1 lines of code changed in 1 file:

• ARBDB: ad_t_prot.h (+1 -1)

westram 2003-08-12 10:37 #82 Rev.: 1646

- uses existing flag 'is_SAI' instead of calling checkSai()

22 lines of code changed in 1 file:

• EDIT4: ED4_text_terminals.cxx (+22 -20)

westram 2003-08-12 10:37 #81 Rev.: 1645

- always create SAI visualize awars
- create AWAR_SAI_NAME

4 lines of code changed in 1 file:

• EDIT4: ED4_main.cxx (+4)

westram 2003-08-12 10:37 #80 Rev.: 1644

- valgrinded

1 lines of code changed in 1 file:

• EDIT4: ED4_edit_string.cxx (+1 -1)

westram 2003-08-12 10:36 #79 Rev.: 1643

- when selecting SAI then AWAR_SAI_NAME is updated (instead of AWAR_SPECIES_NAME)
- added ED4_select_named_sequence_terminal and ED4_selected_SAI_changed_cb
- avoids to write same species/SAI name to global awars multiple times
(this fixes the bug where EDIT4 always sets the selected species back to one
of the loaded species)

97 lines of code changed in 1 file:

• EDIT4: ED4_cursor.cxx (+97 -34)

westram 2003-08-12 10:36 #78 Rev.: 1642

- added ED4_selected_SAI_changed_cb

7 lines of code changed in 1 file:

• EDIT4: ed4_class.hxx (+7 -6)

westram 2003-08-12 10:36 #77 Rev.: 1641

- "dat2" and "bits" entries get compressed as well

11 lines of code changed in 1 file:

• EDIT4: EDB_root_bact.cxx (+11 -1)

westram 2003-08-12 10:35 #76 Rev.: 1640

- moved all AWAR definitions from header
- once creates some default translation tables
- added colorTransTable_exists()
- cleaned code in createCopyClrTransTable()
- bugfix: it was possible to create multiple translation tables with the same name
- selects new table (after create/copy)
- made many functions static (if they are not used outside the module, there's no need to make
them global)
- ED4_createVisualizeSAI_Awars initializes related variables in ED4_ROOT
- AWARS logic seperated from windows (config windows do not have to exist for rest of code to work)
- removed global variables (AW_window and AW_selection_list)
- AW_root passed to getSaiColorString()
- removed unneeded function checkSai()
- fixed memory bug (GBS_strclose returns a copy)
- initialize awars for current table
- saiChanged_callback gets AW_selection_list as parameter
- can handle binary SAIs (e.g. 'markerline')
- some static variables moved into getSaiColorString (only used there - so why allow change from elsewhere?)
- when something goes wrong it displays as if disabled
- moved SAI->transTab relation into sub container (to avoid possible name conflicts)
- added option "Autoselect SAI"
- when SAI data is changed -> display is updated

468 lines of code changed in 1 file:

• EDIT4: ED4_visualizeSAI.cxx (+468 -259)

westram 2003-08-12 10:35 #75 Rev.: 1639

- saves AWAR_SAI_ENABLE, AWAR_SAI_ALL_SPECIES and AWAR_SAI_CLR_TRANS_TABLE to props
- removed all AWAR definitions from header
- added ED4_createVisualizeSAI_Awars
- AW_root passed to getSaiColorString()
- removed unneeded function checkSai()

2 lines of code changed in 1 file:

• EDIT4: ed4_visualizeSAI.hxx (+2 -28)

westram 2003-08-12 10:34 #74 Rev.: 1638

- 'tools' depend on 'shared_libs'

1 lines of code changed in 1 file:

• Makefile (+1 -1)

westram 2003-08-09 19:41 #73 Rev.: 1637

new radio botton

24 lines of code changed in 1 file:

• lib/pictures: ad_align.fig (+24 -22)

westram 2003-08-09 19:40 #72 Rev.: 1636

- added is...callback() functions

6 lines of code changed in 1 file:

• WINDOW: aw_window_Xm.hxx (+6)

westram 2003-08-09 19:40 #71 Rev.: 1635

- added is...callback() functions
- added AW_cb_struct::contains()

23 lines of code changed in 1 file:

• WINDOW: aw_window.hxx (+23 -7)

westram 2003-08-09 19:40 #70 Rev.: 1634

- aw_message() supports a HELP button

25 lines of code changed in 2 files:

• WINDOW: AW_status.cxx (+24 -4), aw_root.hxx (+1 -1)

westram 2003-08-09 19:39 #69 Rev.: 1633

- added AW_repeated_question::add_help
- AW_repeated_question can no longer be copied

15 lines of code changed in 1 file:

• WINDOW: aw_question.hxx (+15 -4)

westram 2003-08-09 19:39 #68 Rev.: 1632

- allow AW_POPUP_HELP when disable_callbacks is true
- allow other callbacks occurring during expose and resize
- added is...callback() functions
- removed 'this->'

84 lines of code changed in 1 file:

• WINDOW: AW_window.cxx (+84 -48)

westram 2003-08-09 19:38 #67 Rev.: 1631

- added AW_repeated_question::add_help
- calls aw_message() with helpfile

15 lines of code changed in 1 file:

• WINDOW: AW_question.cxx (+15 -8)

westram 2003-08-09 19:38 #66 Rev.: 1630

- beautified

97 lines of code changed in 1 file:

• NTREE: ad_fields.cxx (+97 -100)

westram 2003-08-09 19:37 #65 Rev.: 1629

- added auto-format toggle to Alignment info
- 'format alignments' code moved to GBT_format_alignment

40 lines of code changed in 1 file:

• NTREE: ad_ali.cxx (+40 -21)

westram 2003-08-09 19:36 #64 Rev.: 1628

- added nt_check_database_consistency()
- added NT_format_all_alignments()

112 lines of code changed in 1 file:

• NTREE: NT_main.cxx (+112 -3)

westram 2003-08-09 19:36 #63 Rev.: 1627

- doc for auto format
- some words about "ali_genom"

9 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: ad_align.hlp (+9)

westram 2003-08-09 19:36 #62 Rev.: 1626

- doc for format alignment prompt

31 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp/prompt: format_alignments.hlp (new 31)

westram 2003-08-09 19:35 #61 Rev.: 1625

- added subdirectory prompt

9 lines of code changed in 1 file:

• HELP_SOURCE: Makefile (+9 -1)

westram 2003-08-09 19:35 #60 Rev.: 1624

- formats all alignments after importing
- cosmetics

8 lines of code changed in 1 file:

• AWTI: AWTI_import.cxx (+8 -7)

westram 2003-08-09 19:32 #59 Rev.: 1623

updated

2 lines of code changed in 1 file:

• ARBDB: ad_t_prot.h (+2 -1)

westram 2003-08-09 19:32 #58 Rev.: 1622

- renamed len and minlen to static_buffer_len and static_buffer_minlen
to avoid unwarned conflicts

5 lines of code changed in 1 file:

• ARBDB: adlmacros.h (+5 -5)

westram 2003-08-09 19:32 #57 Rev.: 1621

- cosmetics

2 lines of code changed in 1 file:

• ARBDB: adstring.c (+2 -2)

westram 2003-08-09 19:32 #56 Rev.: 1620

- assert nobody formats ali_genom
- added GBT_format_alignment()

21 lines of code changed in 1 file:

• ARBDB: adtools.c (+21 -6)

westram 2003-08-09 19:31 #55 Rev.: 1619

- there's no need for extensions of length 3 for backup files
(hoping this fixes problems with OSX)

4 lines of code changed in 1 file:

• ARBDB: ad_save_load.c (+4 -18)

westram 2003-08-09 14:00 #54 Rev.: 1617

- updated dependencies for all Makefiles
- rewrote dependency generation code. Only real changes
propagate into Makefiles - so it does no longer hurt to
call 'make depends' in ARB directory!

2590 lines of code changed in 66 files:

• Makefile (+28 -30)
• AISC: Makefile (+17 -7)
• AISC_MKPTPS: Makefile (+12 -5)
• ALEIO: Makefile (+20 -9)
• ALIV3: Makefile (+40 -27)
• ARBDB: Makefile (+89 -57)
• ARBDB2: Makefile (+96 -80)
• ARBDBPP: Makefile (+28 -9)
• ARBDBS: Makefile (+102 -63)
• ARBDB_COMPRESS: Makefile (+19 -5)
• ARB_GDE: Makefile (+38 -20)
• AWDEMO: Makefile (+16 -5)
• AWT: Makefile (+120 -90)
• AWTC: Makefile (+34 -16)
• AWTI: Makefile (+17 -7)
• CAT: Makefile (+13 -5)
• CONSENSUS_TREE: Makefile (+30 -16)
• CONVERTALN: Makefile (+42 -20)
• DBSERVER: Makefile (+14 -5)
• DIST: Makefile (+27 -9)
• EDIT: Makefile (+38 -20)
• EDIT4: Makefile (+50 -20)
• EISPACK: Makefile (+15 -4)
• GDE: Makefile (+12 -8)
• GDE/AxML: Makefile (+14 -7)
• GDE/CLUSTAL: Makefile (+24 -12)
• GDE/CLUSTALW: Makefile (+43 -25)
• GDE/CORE: Makefile (+41 -24)
• GDE/FASTDNAML: Makefile (+12 -4)
• GDE/HGL_SRC: Makefile (+34 -16)
• GDE/LOOPTOOL: Makefile (+22 -11)
• GDE/MOLPHY: Makefile (+93 -641)
• GDE/PHYLIP: Makefile (+69 -375)
• GDE/SUPPORT: Makefile (+20 -80)
• GDE/TREEPUZZLE: Makefile (+30 -131)
• GENOM: Makefile (+49 -29)
• HELP_SOURCE: Makefile (+16 -4)
• ISLAND_HOPPING: Makefile (+21 -18)
• MERGE: Makefile (+36 -11)
• MULTI_PROBE: Makefile (+78 -73)
• NALIGNER: Makefile (+51 -48)
• NAMES: Makefile (+17 -6)
• NAMES_COM: Makefile (+5 -2)
• NTREE: Makefile (+341 -3)
• ORS_CGI: Makefile (+45 -24)
• ORS_COM: Makefile (+5 -2)
• ORS_SERVER: Makefile (+35 -22)
• PARSIMONY: Makefile (+34 -20)
• PHYLO: Makefile (+36 -32)
• PRIMER_DESIGN: Makefile (+33 -21)
• PROBE: Makefile (+40 -24)
• PROBE_COM: Makefile (+4 -2)
• PROBE_DESIGN: Makefile (+16 -6)
• PROBE_SET: Makefile (+49 -37)
• READSEQ: Makefile (+15 -5)
• SECEDIT: Makefile (+25 -14)
• SEER: Makefile (+27 -13)
• SEQ_QUALITY: Makefile (+24 -3)
• SERVERCNTRL: Makefile (+21 -4)
• STAT: Makefile (+20 -10)
• TEST: Makefile (+19 -9)
• TOOLS: Makefile (+98 -340)
• TRS: Makefile (+15 -7)
• WETC: Makefile (+13 -5)
• WINDOW: Makefile (+71 -38)
• XML: Makefile (+12 -3)

westram 2003-08-09 13:56 #53 Rev.: 1616

- raises error if not included from C++

5 lines of code changed in 1 file:

• TEMPLATES: inline.h (+5 -1)

westram 2003-08-09 13:55 #52 Rev.: 1615

- added class Noncopyable

33 lines of code changed in 1 file:

• TEMPLATES: arbtools.h (new 33)

westram 2003-08-09 13:54 #51 Rev.: 1614

- added arbtools.h

1 lines of code changed in 1 file:

• SOURCE_TOOLS: generate_all_links.sh (+1)

westram 2003-08-09 13:54 #50 Rev.: 1613

nomen et omen

19 lines of code changed in 1 file:

• SOURCE_TOOLS: mv_if_diff (new 19)

westram 2003-08-09 13:53 #49 Rev.: 1612

translated to english

92 lines of code changed in 8 files:

• TREEGEN: Makefile (+21 -11), defines.c (+2 -2), defines.h (+2 -2), readcfg.c (+7 -7), rns.c (+22 -8), rns.h (+1 -1), sim.c (+14 -7), simcfg.c (+23 -24)

huberj 2003-08-07 18:54 #48 Rev.: 1611

*** empty log message ***

1 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+1 -1)

huberj 2003-08-07 14:45 #47 Rev.: 1610

*** empty log message ***

4 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.cxx (+4 -1)

huberj 2003-08-07 14:40 #46 Rev.: 1609

*** empty log message ***

64 lines of code changed in 3 files:

• SEQ_QUALITY: SQ_functions.cxx (+60 -82), SQ_functions.h (+1), SQ_main.cxx (+3 -2)

westram 2003-08-07 12:38 #45 Rev.: 1608

- closed memory leak

3 lines of code changed in 1 file:

• WINDOW: AW_button.cxx (+3 -2)

westram 2003-08-07 12:37 #44 Rev.: 1607

- pd_export_pt_server() made less obnoxious
- valgrinded

1 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+1 -1)

westram 2003-08-07 12:37 #43 Rev.: 1606

- fixed many memory leaks
(these coders were really, really bad hackers..)

1012 lines of code changed in 12 files:

• MULTI_PROBE: MP_Generation.cxx (+113 -113), MP_Window.cxx (+160 -162), MP_main.cxx (+32 -35), MP_mo_liste.cxx (+52 -50), MP_noclass.cxx (+128 -118), MP_permute.cxx (+1 -1), MP_probe.cxx (+50 -49), MP_probe.hxx (+99 -99), MP_probe_combi_statistic.cxx (+36 -36), MP_sonde.cxx (+94 -95), MP_sondentopf.cxx (+56 -55), MultiProbe.hxx (+191 -191)

westram 2003-08-07 12:36 #42 Rev.: 1605

- removed strange hint to delete property file

0 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: multiproberesults.hlp (-3)

westram 2003-08-07 12:36 #41 Rev.: 1604

- keyboard error on OSX fixed

185 lines of code changed in 1 file:

• EDIT4: ED4_no_class.cxx (+185 -180)

westram 2003-08-07 12:35 #40 Rev.: 1603

- valgrinded

2 lines of code changed in 1 file:

• AWT: AWT_sel_boxes.cxx (+2 -2)

westram 2003-08-07 12:35 #39 Rev.: 1602

- cosmetics

1 lines of code changed in 1 file:

• AISC_COM/C: client.c (+1 -2)

westram 2003-08-07 10:12 #38 Rev.: 1601

*** empty log message ***

1 lines of code changed in 1 file:

• ARBDB: ad_lpro.h (+1 -1)

westram 2003-08-07 10:12 #37 Rev.: 1600

- verbose flag for gb_is_valid_mapfile()

7 lines of code changed in 1 file:

• ARBDB: admap.c (+7 -3)

westram 2003-08-07 10:12 #36 Rev.: 1599

- do not show 'Opening FastLoad File' twice

1 lines of code changed in 1 file:

• ARBDB: ad_load.c (+1 -1)

westram 2003-08-07 09:57 #35 Rev.: 1598

- pd_export_pt_server() made less obnoxious

10 lines of code changed in 1 file:

• PROBE_DESIGN: probe_design.cxx (+10 -9)

westram 2003-08-07 09:57 #34 Rev.: 1597

- removed double warning

2 lines of code changed in 1 file:

• NAMES: names.cxx (+2 -3)

westram 2003-08-07 09:57 #33 Rev.: 1596

updated

2 lines of code changed in 2 files:

• ARBDB: ad_lpro.h (+1), ad_prot.h (+1)

westram 2003-08-07 09:57 #32 Rev.: 1595

- added GB_is_directory()

7 lines of code changed in 1 file:

• ARBDB: adsocket.c (+7)

westram 2003-08-07 09:56 #31 Rev.: 1594

- better error messages
- check whether directory exists in gb_check_saveable()

34 lines of code changed in 1 file:

• ARBDB: ad_save_load.c (+34 -14)

westram 2003-08-07 09:56 #30 Rev.: 1593

- warning fixed

1 lines of code changed in 1 file:

• ARBDB: ad_core.c (+1 -1)

westram 2003-08-06 17:39 #29 Rev.: 1592

*** empty log message ***

5 lines of code changed in 1 file:

• lib/pictures/awt: nds.fig (+5 -5)

westram 2003-08-06 17:39 #28 Rev.: 1591

- added at_(un)set_to()

4 lines of code changed in 1 file:

• WINDOW: aw_window.hxx (+4 -1)

westram 2003-08-06 17:38 #27 Rev.: 1590

- detect whether windows has been resized in previous session
(and never recalc size of user-resized windows)
- changed semantic of 'recalc_size_at_show'
- Allow resize for AW_window_simple and AW_window_simple_menu

42 lines of code changed in 1 file:

• WINDOW: AW_window.cxx (+42 -10)

westram 2003-08-06 17:37 #26 Rev.: 1589

- ARB crashed when pressing BROWSE after help search

14 lines of code changed in 1 file:

• WINDOW: AW_status.cxx (+14 -3)

westram 2003-08-06 17:37 #25 Rev.: 1588

- untabified/indented
- simplified at_ifdef
- added at_(un)set_to()

228 lines of code changed in 1 file:

• WINDOW: AW_at.cxx (+228 -186)

westram 2003-08-06 17:36 #24 Rev.: 1587

- fixed macro name

1 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+1 -1)

westram 2003-08-06 17:36 #23 Rev.: 1586

- added AWT_graphic_exports::init()

1 lines of code changed in 1 file:

• AWT: awt_canvas.hxx (+1)

westram 2003-08-06 17:36 #22 Rev.: 1585

- untabified/indented
- attached ACI/SRT input field to right border

338 lines of code changed in 1 file:

• AWT: AWT_nds.cxx (+338 -335)

westram 2003-08-06 17:35 #21 Rev.: 1584

- untabified/indented
- fixed miss-sized scrollbar

467 lines of code changed in 1 file:

• AWT: AWT_canvas.cxx (+467 -460)

westram 2003-08-06 17:35 #20 Rev.: 1583

- doc for 'eval'

24 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: commands.hlp (+24)

westram 2003-08-06 17:34 #19 Rev.: 1582

- added new ACI command 'eval'

41 lines of code changed in 1 file:

• ARBDB: adlang1.c (+41 -3)

westram 2003-08-06 17:34 #18 Rev.: 1581

updated

1 lines of code changed in 1 file:

• arb_CHANGES.txt (+1)

huberj 2003-08-06 17:03 #17 Rev.: 1580

*** empty log message ***

135 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.cxx (+135 -34)

huberj 2003-08-06 16:28 #16 Rev.: 1579

*** empty log message ***

3 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_functions.h (+1 -1), SQ_main.cxx (+2 -2)

westram 2003-08-05 12:55 #15 Rev.: 1578

annotated

9 lines of code changed in 1 file:

• SEQ_QUALITY: SQ_functions.cxx (+9 -3)

spanfeln 2003-08-05 12:37 #14 Rev.: 1577

Serveral changes to enable gene-search

108 lines of code changed in 4 files:

• AISC_COM/C: server.c (+2)
• PROBE: PT_etc.cxx (+17 -3), PT_main.cxx (+74), probe.h (+15)

huberj 2003-08-04 15:50 #13 Rev.: 1576

*** empty log message ***

74 lines of code changed in 4 files:

• SEQ_QUALITY: Makefile (+1 -1), SQ_functions.cxx (+68 -8), SQ_functions.h (+1 -1), SQ_main.cxx (+4 -3)

huberj 2003-08-03 17:23 #12 Rev.: 1575

*** empty log message ***

37 lines of code changed in 2 files:

• SEQ_QUALITY: SQ_functions.cxx (new 36), SQ_functions.h (new 1)

huberj 2003-08-03 17:21 #11 Rev.: 1574

First attempt to get the raw Sequence Data

11 lines of code changed in 3 files:

• SEQ_QUALITY: SQ_main.cxx (+9 -8), seq_quality.cxx (+2 -1), seq_quality.h (-1)

westram 2003-08-01 15:06 #10 Rev.: 1573

new/updated windows for alignment preservation

96 lines of code changed in 2 files:

• lib/pictures/merge: preserves.fig (new 33), species.fig (+63 -62)

westram 2003-08-01 15:05 #9 Rev.: 1572

- added MG_select_preserves_cb

8 lines of code changed in 1 file:

• MERGE: merge.hxx (+8 -7)

westram 2003-08-01 15:05 #8 Rev.: 1571

- added MG_preserves.o

12 lines of code changed in 1 file:

• MERGE: Makefile (+12 -1)

westram 2003-08-01 15:05 #7 Rev.: 1570

- added SELECT for alignment preserves
- default for 'Preserve' is OFF
- alignment preservation works with SAIs as well

73 lines of code changed in 1 file:

• MERGE: MG_species.cxx (+73 -41)

westram 2003-08-01 15:05 #6 Rev.: 1569

- find candidates for alignment preservation

452 lines of code changed in 1 file:

• MERGE: MG_preserves.cxx (new 452)

westram 2003-08-01 15:04 #5 Rev.: 1568

- untabified/indented

290 lines of code changed in 1 file:

• MERGE: MG_alignment.cxx (+290 -290)

westram 2003-08-01 15:04 #4 Rev.: 1567

- New/updated help files for alignment preservation

63 lines of code changed in 3 files:

• HELP_SOURCE/oldhelp: mg_alignment.hlp (+3 -6), mg_preserve.hlp (new 56), mg_species.hlp (+4 -4)

westram 2003-08-01 15:03 #3 Rev.: 1566

updated

2 lines of code changed in 2 files:

• ARBDB: ad_prot.h (+1), ad_t_prot.h (+1)

westram 2003-08-01 15:03 #2 Rev.: 1565

- added GBT_generate_SAI_hash

17 lines of code changed in 1 file:

• ARBDB: adtools.c (+17)

westram 2003-08-01 15:03 #1 Rev.: 1564

- added GBS_hash_count_elems

18 lines of code changed in 1 file:

• ARBDB: adhash.c (+18)

July 2003 »