April 2004 Commit Log

Number of Commits:
43
Number of Active Developers:
2
westram 2004-04-29 11:11 Rev.: 2690

*** empty log message ***

758 lines of code changed in 2 files:

westram 2004-04-29 11:08 Rev.: 2689

ale was removed -> useless script

0 lines of code changed in 1 file:

westram 2004-04-29 11:07 Rev.: 2688

- spell fix

6 lines of code changed in 4 files:

westram 2004-04-29 11:07 Rev.: 2687

- changed tag name
- removed 'Functions'

37 lines of code changed in 1 file:

westram 2004-04-29 11:06 Rev.: 2686

- added version
- changed some author names
- mentioned Prof. Schleifer

35 lines of code changed in 1 file:

westram 2004-04-29 11:04 Rev.: 2685

- added parameter 'interactive'
- changed parameter for threshold parsimony

11 lines of code changed in 1 file:

westram 2004-04-29 11:03 Rev.: 2684

- added parameter 'interactive'
- added parameter 'rate_variation'

15 lines of code changed in 1 file:

westram 2004-04-29 11:03 Rev.: 2683

- added parameter 'interactive'
- changed parameters for transversion/threshold parsimony

13 lines of code changed in 1 file:

westram 2004-04-29 11:02 Rev.: 2682

- removed broken chars

1 lines of code changed in 1 file:

westram 2004-04-29 11:01 Rev.: 2681

*** empty log message ***

4 lines of code changed in 1 file:

westram 2004-04-29 11:01 Rev.: 2680

deps updated

1 lines of code changed in 1 file:

westram 2004-04-29 11:00 Rev.: 2679

- 'tmp' field written to and deleted from species _and genes_
- probe design sends 'species/gene' instead of 'gene' only. *students suck*
- touches AWAR_TARGET_STRING after probe match selection (for better editor interaction ('auto jump'))
- improved error handling
- gene probe match displays 2 flags (1 for spec. 1 for gene)
- checks alignment type before updating pt-server
- uses toggle to select gene pt server creation (instead of button)
- simplified mismatch selection
- changed filename for temporary database (gene pt server)
- handle error if 'gene to mark' is not found
- stuffed too many memory leaks
- in case of error a transaction was left open in pd_get_the_names
- error handling for missing db entries in pd_get_the_names + pd_get_the_gene_names

345 lines of code changed in 1 file:

westram 2004-04-29 10:54 Rev.: 2678

minor change

1 lines of code changed in 1 file:

westram 2004-04-29 10:54 Rev.: 2677

cosmetics

2 lines of code changed in 1 file:

westram 2004-04-29 10:54 Rev.: 2676

updated

6 lines of code changed in 1 file:

westram 2004-04-29 10:53 Rev.: 2675

- reduced size of gene_struct
- made gene_struct a class
- removed map_ptr_idp
- added list for memory management of gene_struct's
- added two sets for fast access to arb<->internal name translation
- added copy ctor, op= and access functions for class gene_struct

78 lines of code changed in 1 file:

westram 2004-04-29 10:52 Rev.: 2674

- made map_ptr_idp local in PT_init_map
- build sets instead of stupid list for ARB<->internal name translation

69 lines of code changed in 1 file:

westram 2004-04-29 10:49 Rev.: 2673

- added get_gene_struct_by_arb_species_gene_name()
- added arb2internal_name()
- rewrote ptpd_read_names() (old function still present)
- get_gene_struct_by_...() functions use index set
- rewrote virt_name/virt_fullname
- added get_list_part() to ease parsing of names lists send from ARB

218 lines of code changed in 1 file:

westram 2004-04-29 10:46 Rev.: 2672

- homology -> similarity

2 lines of code changed in 1 file:

westram 2004-04-29 10:46 Rev.: 2671

- fixed lib path
- uses strict and warnings

4 lines of code changed in 1 file:

westram 2004-04-29 10:45 Rev.: 2670

- spell fix

3 lines of code changed in 2 files:

westram 2004-04-29 10:44 Rev.: 2669

- added version and copyright to intro window
- spell fix

8 lines of code changed in 1 file:

westram 2004-04-29 10:44 Rev.: 2668

- removed ALE editor

1 lines of code changed in 1 file:

westram 2004-04-29 10:44 Rev.: 2667

- version '_' -> '.' (for macro DATE)

1 lines of code changed in 1 file:

westram 2004-04-29 10:43 Rev.: 2666

- bugfix for alignment selection

6 lines of code changed in 1 file:

westram 2004-04-29 10:43 Rev.: 2665

- updated help

2 lines of code changed in 1 file:

westram 2004-04-29 10:41 Rev.: 2664

- added 'Interactive' toggle
- changed transversion/threshold parsimony parameters

22 lines of code changed in 1 file:

westram 2004-04-29 10:41 Rev.: 2663

- added 'Interactive' toggle
- added 'Rate variation among sites'

14 lines of code changed in 1 file:

westram 2004-04-29 10:41 Rev.: 2662

- phylip.help -> phylip_distance.help

2 lines of code changed in 1 file:

westram 2004-04-29 10:41 Rev.: 2661

- phylip.help -> DNAml_rates.help

1 lines of code changed in 1 file:

westram 2004-04-29 10:40 Rev.: 2660

*** empty log message ***

50 lines of code changed in 2 files:

westram 2004-04-29 10:39 Rev.: 2659

removed (was from old phylip version)

0 lines of code changed in 42 files:

westram 2004-04-29 10:38 Rev.: 2658

moved to $ARBHOME/GDEHELP/HELP_PLAIN

0 lines of code changed in 1 file:

westram 2004-04-29 10:36 Rev.: 2657

- moved from $ARBHOME/TOOLS

81 lines of code changed in 1 file:

westram 2004-04-29 10:35 Rev.: 2656

- greps for missing helpfile links
- create protml+readseq help tree
- accidently used $? instead of $^
- generate treepuzzle help

27 lines of code changed in 1 file:

westram 2004-04-29 10:35 Rev.: 2655

- removed german umlauts (xml is not prepared to handle them)

8 lines of code changed in 1 file:

westram 2004-04-29 10:33 Rev.: 2654

- merged alignment types GB_AT_AMI+GB_AT_PRO into GB_AT_AA

11 lines of code changed in 7 files:

westram 2004-04-29 10:32 Rev.: 2653

- spell fix

8 lines of code changed in 6 files:

westram 2004-04-29 10:31 Rev.: 2652

- if no directory awar is defined in awt_get_selected_fullname
auto-define one with GB_getcwd as content

7 lines of code changed in 1 file:

westram 2004-04-29 10:27 Rev.: 2651

changed comments

14 lines of code changed in 1 file:

westram 2004-04-29 10:26 Rev.: 2650

- removed Oli as ARB supervisor
- note that ARB will most likely never become commercial
- other minor changes

10 lines of code changed in 1 file:

westram 2004-04-29 10:26 Rev.: 2649

- removed ALEIO and target 'tarale'

9 lines of code changed in 1 file:

baderk 2004-04-07 14:55 Rev.: 2648

CHIP/CA_PROBE (needed for the chipanalyser) was modified to support weighted
mismatches. (Kai Bader)

22 lines of code changed in 2 files:

March 2004 »

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