July 2003 Commit Log

Number of Commits:

67

Number of Active Developers:

5

huberj 2003-07-31 17:43 #67 Rev.: 1563

*** empty log message ***

13 lines of code changed in 1 file:

• SEQ_QUALITY: seq_quality.cxx (+13)

huberj 2003-07-31 17:34 #66 Rev.: 1562

*** empty log message ***

16 lines of code changed in 4 files:

• NTREE: NT_extern.cxx (+6 -3)
• SEQ_QUALITY: SQ_main.cxx (+9 -4), seq_quality.cxx (new), seq_quality.h (+1 -1)

richter 2003-07-31 15:39 #65 Rev.: 1561

multi node history in tree navigation enabled now

19 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: TreeDisplay.java (+19 -10)

richter 2003-07-31 15:25 #64 Rev.: 1560

also missed before

25 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: ProbesGUIActionListener.java (new 25)

richter 2003-07-31 15:24 #63 Rev.: 1559

lost at check in before

75 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: ProbeMenu.java (new 75)

richter 2003-07-31 15:23 #62 Rev.: 1558

shorcuts for tree navigation add;
only one step back possible up to now

13 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: TreeDisplay.java (+13)

richter 2003-07-31 14:45 #61 Rev.: 1557

basic menu functions added, callbacks work now
no keybord shortcuts yet

100 lines of code changed in 5 files:

• PROBE_WEB/CLIENT: Client.java (+2), Makefile (new 17), ProbesGUI.java (+24 -3), TreeDisplay.java (+57), mymanifest (new)

westram 2003-07-31 13:20 #60 Rev.: 1556

new attribute 'folded'

3 lines of code changed in 1 file:

• lib/dtd: arb_tree.dtd (+3 -2)

westram 2003-07-31 13:19 #59 Rev.: 1555

XML-Tags of Species-XML-Export are case-sensitive now

1 lines of code changed in 1 file:

• AWTI: AWTI_export.cxx (+1 -6)

westram 2003-07-31 13:19 #58 Rev.: 1554

added attribute 'folded' to XML-Tree-Export

9 lines of code changed in 1 file:

• AWT: AWT_imp_exp.cxx (+9 -3)

spanfeln 2003-07-29 09:54 #57 Rev.: 1553

IDP: Modifying return names

8 lines of code changed in 1 file:

• PROBE: PT_etc.cxx (+8)

richter 2003-07-28 15:38 #56 Rev.: 1552

missong file added

6 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: TreeReader.java (new 6)

richter 2003-07-28 14:37 #55 Rev.: 1551

marking and unmarking of subtrees
reorganization of event handling code in separate class
left and right mouse button now distinguished

263 lines of code changed in 4 files:

• PROBE_WEB/CLIENT: DisplayMouseAdapter.java (new 53), ProbesGUI.java (new 87), TreeDisplay.java (+101 -55), TreeNode.java (+22)

richter 2003-07-25 12:39 #54 Rev.: 1550

wrong root node reference in TreeParser.java fixed

2 lines of code changed in 1 file:

• PROBE_WEB/CLIENT: TreeParser.java (+2)

westram 2003-07-24 11:42 #53 Rev.: 1549

*** empty log message ***

1 lines of code changed in 1 file:

• arb_README_gcc3.2.txt (+1 -1)

richter 2003-07-23 12:39 #52 Rev.: 1548

core classes for WEB-ARB / ALLPROBES for the local java client
contains: - TreeParser
- TreeLoader
- GUI frame
- TreeLayout and Display
- TreeNode definition
- supplementary helper and debug classes

514 lines of code changed in 9 files:

• PROBE_WEB/CLIENT: Client.java (new), LineArea.java (new 11), LineAreaFactory.java (new), NodeError.java (new 15), TreeDisplay.java (new 55), TreeNode.java (new 78), TreeParser.java (new 352), WindowClosingAdapter.java (new 2), demo.newick (new 1)

westram 2003-07-23 11:09 #51 Rev.: 1547

updated

7 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: mg_trees.hlp (+7 -14)

westram 2003-07-23 11:09 #50 Rev.: 1546

- Help file for config merging

9 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: mg_configs.hlp (new 9)

westram 2003-07-23 10:59 #49 Rev.: 1545

depends :|

9 lines of code changed in 1 file:

• MERGE: Makefile (+9)

westram 2003-07-23 10:57 #48 Rev.: 1544

layout changed (wider subwindows)

35 lines of code changed in 1 file:

• lib/pictures/merge: trees.fig (+35 -26)

westram 2003-07-23 10:56 #47 Rev.: 1543

config merge button

39 lines of code changed in 1 file:

• lib/pictures/merge: main.fig (+39 -29)

westram 2003-07-23 10:56 #46 Rev.: 1542

config merge window

35 lines of code changed in 1 file:

• lib/pictures/merge: configs.fig (new 35)

westram 2003-07-23 10:55 #45 Rev.: 1541

- added MG_merge_configs_cb, MG_create_config_awar

3 lines of code changed in 1 file:

• MERGE: merge.hxx (+3 -1)

westram 2003-07-23 10:55 #44 Rev.: 1540

- added MG_configs.o

8 lines of code changed in 1 file:

• MERGE: Makefile (+8 -9)

westram 2003-07-23 10:55 #43 Rev.: 1539

- untabified/indented
- minor changes

156 lines of code changed in 1 file:

• MERGE: MG_trees.cxx (+156 -156)

westram 2003-07-23 10:55 #42 Rev.: 1538

- added 'Transfer Configurations' button
- calls MG_create_config_awar

6 lines of code changed in 1 file:

• MERGE: MG_main.cxx (+6)

westram 2003-07-23 10:55 #41 Rev.: 1537

- windows and functions for config merging

233 lines of code changed in 1 file:

• MERGE: MG_configs.cxx (new 233)

thomasw 2003-07-17 16:29 #40 Rev.: 1536

statusmeldung verbessert - WT

8 lines of code changed in 1 file:

• CHIP: ca_probe.cxx (+8 -2)

westram 2003-07-16 16:14 #39 Rev.: 1535

*** empty log message ***

1 lines of code changed in 1 file:

• arb_INSTALL.txt (+1 -1)

westram 2003-07-16 16:14 #38 Rev.: 1534

new module for juergen

56 lines of code changed in 6 files:

• Makefile (+2)
• NTREE: NT_extern.cxx (+13)
• SEQ_QUALITY: Makefile (new 15), SQ_main.cxx (new 15), seq_quality.h (new 10)
• SOURCE_TOOLS: generate_all_links.sh (+1)

westram 2003-07-16 10:04 #37 Rev.: 1533

- allow tear-off for menus

1 lines of code changed in 1 file:

• WINDOW: AW_window.cxx (+1)

westram 2003-07-16 10:04 #36 Rev.: 1532

- added ST_sequence_ml::partial_match

57 lines of code changed in 2 files:

• STAT: ST_ml.cxx (+6), st_ml.hxx (+51 -50)

westram 2003-07-16 10:03 #35 Rev.: 1531

- fileIndex now indexes 'fname' and 'dir/fname'

16 lines of code changed in 1 file:

• SOURCE_TOOLS: valgrind2grep (+16 -5)

westram 2003-07-16 10:02 #34 Rev.: 1530

- define ap_assert

4 lines of code changed in 1 file:

• PARSIMONY: ap_tree_nlen.hxx (+4 -3)

westram 2003-07-16 10:01 #33 Rev.: 1529

- insert partial sequences into tree
- remove_species_in_tree_from_hash -> NT_remove_species_in_tree_from_hash

390 lines of code changed in 1 file:

• PARSIMONY: PARS_main.cxx (+390 -30)

westram 2003-07-16 10:01 #32 Rev.: 1528

- untabified
- uses dynamic cast

319 lines of code changed in 1 file:

• PARSIMONY: AP_tree_nlen.cxx (+319 -316)

westram 2003-07-16 10:01 #31 Rev.: 1527

- untabified; assert->ap_assert

110 lines of code changed in 1 file:

• PARSIMONY: AP_tree_edge.cxx (+110 -109)

westram 2003-07-16 10:00 #30 Rev.: 1526

- menu layout

91 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+91 -93)

westram 2003-07-16 10:00 #29 Rev.: 1525

*** empty log message ***

70 lines of code changed in 3 files:

• HELP_SOURCE/oldhelp: colorize.hlp (+1 -1), pa_partial.hlp (new 35), partial_sequences.hlp (new 34)

westram 2003-07-16 09:59 #28 Rev.: 1524

- new member partial_match()

10 lines of code changed in 1 file:

• AWT: awt_seq_dna.hxx (+10 -9)

westram 2003-07-16 09:58 #27 Rev.: 1523

- untabified
- removed result of swap_sons()
- added get_branchlength() and set_branchlength() to AP_tree

155 lines of code changed in 1 file:

• AWT: awt_tree.hxx (+155 -139)

westram 2003-07-16 09:58 #26 Rev.: 1522

- removed AP_sequence_protein_old
- added AP_sequence_protein::partial_match

5 lines of code changed in 1 file:

• AWT: awt_seq_protein.hxx (+5 -28)

westram 2003-07-16 09:58 #25 Rev.: 1521

- added functions to mark partial sequences
- remove_species_in_tree_from_hash -> NT_remove_species_in_tree_from_hash
- added function to mark/unmark species NOT in tree

173 lines of code changed in 1 file:

• AWT: AWT_tree_cb.cxx (+173 -51)

westram 2003-07-16 09:58 #24 Rev.: 1520

- removed AP_sequence_protein_old
- AP_sequence_protein::partial_match

87 lines of code changed in 1 file:

• AWT: AWT_seq_protein.cxx (+87 -237)

westram 2003-07-16 09:57 #23 Rev.: 1519

- AP_sequence_parsimony::partial_match

78 lines of code changed in 1 file:

• AWT: AWT_seq_dna.cxx (+78 -48)

westram 2003-07-16 09:57 #22 Rev.: 1518

updated prototypes

3 lines of code changed in 1 file:

• AWT: awt_tree_cb.hxx (+3 -1)

westram 2003-07-16 09:56 #21 Rev.: 1517

- added AP_sequence_simple_protein::partial_match

71 lines of code changed in 2 files:

• AWT: AWT_seq_simple_pro.cxx (+60 -54), awt_seq_simple_pro.hxx (+11 -10)

westram 2003-07-16 09:56 #20 Rev.: 1516

- removed result of swap_sons()

1 lines of code changed in 1 file:

• AWT: AWT_tree.cxx (+1 -2)

westram 2003-07-16 09:55 #19 Rev.: 1515

- untabified
- mark_tree splitted into mark_species_in_tree and mark_species_in_tree_that
- mark_rest_tree splitted into mark_species_in_rest_of_tree and mark_species_in_rest_of_tree_that

147 lines of code changed in 2 files:

• AWT: AWT_dtree.cxx (+66 -74), awt_dtree.hxx (+81 -77)

westram 2003-07-16 09:55 #18 Rev.: 1514

updated

2 lines of code changed in 1 file:

• ARBDB: ad_t_prot.h (+2)

westram 2003-07-16 09:54 #17 Rev.: 1513

- fixed GBS_hash_first_element()

15 lines of code changed in 1 file:

• ARBDB: adhash.c (+15 -15)

westram 2003-07-16 09:54 #16 Rev.: 1512

- added GBT_is_partial()
- added GBT_mark_all_that()

72 lines of code changed in 1 file:

• ARBDB: adtools.c (+72)

westram 2003-07-16 09:54 #15 Rev.: 1511

- warning fix

1 lines of code changed in 1 file:

• ARBDB: adperl.c (+1 -1)

westram 2003-07-16 09:53 #14 Rev.: 1510

*** empty log message ***

3 lines of code changed in 1 file:

• arb_CHANGES.txt (+3 -5)

thomasw 2003-07-15 15:45 #13 Rev.: 1509

ca_probe behandelt jetzt input von numMismatches -WT

26 lines of code changed in 2 files:

• CHIP: ca_probe.cxx (+25 -15), ca_probe.hxx (+1 -1)

westram 2003-07-08 15:48 #12 Rev.: 1508

prots updated

4 lines of code changed in 2 files:

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

westram 2003-07-08 15:48 #11 Rev.: 1507

- added gb_rename_entry()

19 lines of code changed in 1 file:

• ARBDB: ad_core.c (+19 -1)

westram 2003-07-08 15:47 #10 Rev.: 1506

- added gb_rename, GB_rename

43 lines of code changed in 1 file:

• ARBDB: arbdb.c (+43 -4)

westram 2003-07-08 15:47 #9 Rev.: 1505

minor change

4 lines of code changed in 1 file:

• ARBDB: adoptimize.c (+4 -2)

westram 2003-07-08 15:46 #8 Rev.: 1504

- GB_rename -> GB_rename_file

8 lines of code changed in 5 files:

• ARBDB: ad_save_load.c (+4 -4), adsocket.c (+1 -1)
• AWTC: AWTC_names_admin.cxx (+1 -1)
• NAMES: names.cxx (+1 -1)
• PROBE: PT_buildtree.cxx (+1 -1)

westram 2003-07-08 15:45 #7 Rev.: 1503

*** empty log message ***

12 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+12 -5)

westram 2003-07-08 15:01 #6 Rev.: 1502

test code

30 lines of code changed in 1 file:

• NTREE: NT_extern.cxx (+30 -1)

westram 2003-07-03 08:11 #5 Rev.: 1501

- untabified
- changed hotkeys

111 lines of code changed in 1 file:

• PARSIMONY: PARS_main.cxx (+111 -111)

westram 2003-07-03 07:39 #4 Rev.: 1500

- defines for parsimony behavior

46 lines of code changed in 1 file:

• AWT: awt_parsimony_defaults.hxx (new 46)

westram 2003-07-03 07:39 #3 Rev.: 1499

- AP_sequence_protein::combine()
+ gaps are forwarded upwards again
+ multiple gaps are multiple mutations again

14 lines of code changed in 1 file:

• AWT: AWT_seq_protein.cxx (+14 -6)

westram 2003-07-03 07:39 #2 Rev.: 1498

- AP_sequence_parsimony::combine()
+ gaps are forwarded upwards again
+ multiple gaps are multiple mutations again

12 lines of code changed in 1 file:

• AWT: AWT_seq_dna.cxx (+12 -8)

thomasw 2003-07-01 16:06 #1 Rev.: 1497

Einlesen des input-Files verbessert - WT

84 lines of code changed in 1 file:

• CHIP: ca_probe.cxx (+84 -37)

June 2003 »