July 2002 Commit Log

Number of Commits:
106
Number of Active Developers:
4
westram 2002-07-30 12:53 Rev.: 803

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38 lines of code changed in 6 files:

westram 2002-07-30 12:52 Rev.: 802

- new label 'toggle1'
- corrected label 'user2'

3 lines of code changed in 1 file:

westram 2002-07-30 12:51 Rev.: 801

tabbed NDS save

12 lines of code changed in 2 files:

westram 2002-07-30 12:50 Rev.: 800

added new type to save options

1 lines of code changed in 1 file:

westram 2002-07-30 12:50 Rev.: 799

* ph_matr.hxx: - new save type PH_SAVE_TABBED

3 lines of code changed in 1 file:

westram 2002-07-30 12:50 Rev.: 798

* PH_save_matr.cxx: - save tabbed matrix (for calc-sheet)
- '.'->',' in tabbed mode

134 lines of code changed in 1 file:

westram 2002-07-30 12:49 Rev.: 797

* AWT_nds.cxx: - make_node_text_nds() knows new mode (2 == MNTN_TABBED) for tabbed output
- '.'->',' in MNTN_TABBED mode

69 lines of code changed in 1 file:

westram 2002-07-30 09:01 Rev.: 796

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21 lines of code changed in 4 files:

westram 2002-07-26 17:13 Rev.: 795

menu rename

1 lines of code changed in 1 file:

westram 2002-07-26 17:13 Rev.: 794

some updates

21 lines of code changed in 3 files:

westram 2002-07-26 16:38 Rev.: 793

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1 lines of code changed in 1 file:

westram 2002-07-26 16:37 Rev.: 792

note about hierarchical fields

3 lines of code changed in 1 file:

westram 2002-07-26 16:36 Rev.: 791

* GDE_event.cxx: - error when wrong macro replacement happens

20 lines of code changed in 1 file:

westram 2002-07-26 16:32 Rev.: 790

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7 lines of code changed in 1 file:

westram 2002-07-26 16:30 Rev.: 789

- name and acc are not allowed as destination fields

48 lines of code changed in 1 file:

westram 2002-07-26 16:29 Rev.: 788

* AWT_seq_protein.cxx: - rewrote AP_sequence_protein::combine to be more obvious
- counts adjacent gaps as 1 mutation
* AWT_pro_a_nucs.cxx: - awt_pro_a_nucs->realmax_aa was zero (has to be number of 'real' codons)
[this was the reason why dots in sequences were handled like dashes]
* AWT_seq_dna.cxx: - rewrote AP_sequence_parsimony::combine
- counts adjacent gaps as 1 mutation

494 lines of code changed in 4 files:

westram 2002-07-24 12:10 Rev.: 787

beautified

475 lines of code changed in 1 file:

westram 2002-07-18 14:44 Rev.: 786

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41 lines of code changed in 1 file:

yadhu 2002-07-18 14:00 Rev.: 785

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1 lines of code changed in 1 file:

yadhu 2002-07-18 11:15 Rev.: 784

zoom bug fixed

54 lines of code changed in 2 files:

westram 2002-07-17 12:46 Rev.: 783

* xml.cxx: - encodes acute-forward as normal acute

2 lines of code changed in 1 file:

westram 2002-07-17 12:46 Rev.: 782

* arb_export_rates.cxx: - if no RATES should be used then '--none' or "" should be specified on command line
instead of SAI-name
- accepts empty arguments in [other_fastdnaml_args]*
- special ordering of new fastDNAml flags (i.e. 'Y')

28 lines of code changed in 1 file:

westram 2002-07-17 12:41 Rev.: 781

* inc_fastdnaml.menu: - call to arb_export_rates has been changed
- changed default tree to ''

6 lines of code changed in 1 file:

westram 2002-07-17 12:41 Rev.: 780

* fastdnaml.menu: - call to arb_export_rates has been changed

3 lines of code changed in 1 file:

westram 2002-07-17 12:40 Rev.: 779

* dnamlrates.menu: - added option F to arb_export_rates (else arb_dnarates complains about missing user frequencies)
- call to arb_export_rates has been changed

12 lines of code changed in 1 file:

westram 2002-07-17 12:39 Rev.: 778

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1 lines of code changed in 1 file:

westram 2002-07-17 12:39 Rev.: 777

fastdnaml 1.2.2

309 lines of code changed in 3 files:

westram 2002-07-17 12:38 Rev.: 776

deleted old versions

0 lines of code changed in 6 files:

westram 2002-07-17 12:36 Rev.: 775

original version 1.2.2

6091 lines of code changed in 3 files:

westram 2002-07-17 12:35 Rev.: 774

* arb_help_prefix.txt: - used to generate fastdnaml.hlp

4 lines of code changed in 1 file:

westram 2002-07-17 12:34 Rev.: 773

* ARB/GDE/Makefile: - removed ZUKER

0 lines of code changed in 1 file:

westram 2002-07-17 12:33 Rev.: 772

* GDE_menu.h: - added textwidth to GmenuItemArg

44 lines of code changed in 1 file:

westram 2002-07-17 12:33 Rev.: 771

* GDE_def.h: - define TEXTFIELDWIDTH globally

16 lines of code changed in 1 file:

westram 2002-07-17 12:33 Rev.: 770

* GDE_ParseMenu.cxx: - sets GmenuItemArg.textwidth to specified textwidth or to default TEXTFIELDWIDTH
- textwidth may be specified in GDE menus using 'text(width)'

18 lines of code changed in 1 file:

westram 2002-07-17 12:33 Rev.: 769

* GDE.cxx: - GmenuItemArg.textwidth is used to define width of textfield

10 lines of code changed in 1 file:

westram 2002-07-17 12:32 Rev.: 768

* ARB/arb_CHANGES.txt: - added headline (appears as title in .hlp file)

6 lines of code changed in 1 file:

westram 2002-07-17 12:30 Rev.: 767

License for ARB and other programs delivered with the release
This file is as well used in ./HELP_SOURCE/genhelp!

220 lines of code changed in 1 file:

westram 2002-07-17 12:28 Rev.: 766

* Makefile: - warns about duplicated helpfiles
- calls make in genhelp

40 lines of code changed in 1 file:

westram 2002-07-17 12:26 Rev.: 765

* arb_help2xml.cxx: - searches ./oldhelp and ./genhelp for missing links
- accepts multiple spaces after . and ,
- improved error handling

43 lines of code changed in 1 file:

westram 2002-07-17 12:23 Rev.: 764

link to changes

1 lines of code changed in 1 file:

westram 2002-07-17 12:23 Rev.: 763

generated (see ../genhelp)

0 lines of code changed in 1 file:

westram 2002-07-17 12:22 Rev.: 762

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46 lines of code changed in 3 files:

westram 2002-07-16 11:15 Rev.: 761

smaller

5 lines of code changed in 1 file:

westram 2002-07-16 11:15 Rev.: 760

* AW_status.cxx: - Message Box has OK button (Clear&Hide)

9 lines of code changed in 1 file:

westram 2002-07-16 11:11 Rev.: 759

now needs 'used program name' as parameter

1 lines of code changed in 1 file:

westram 2002-07-16 11:09 Rev.: 758

* GDE_event.cxx: - GDE arguments ($VAR) are replaced repeated until no change occurred.
(this allows usage of $VAR in values of arguments )

29 lines of code changed in 1 file:

westram 2002-07-16 11:09 Rev.: 757

gde help window resizeable

10 lines of code changed in 1 file:

westram 2002-07-16 11:08 Rev.: 756

wasn't used

0 lines of code changed in 1 file:

westram 2002-07-16 11:04 Rev.: 755

- new toggle to switch between AxML and fastdnaML
- the value is passed to arb_fastdnaml

16 lines of code changed in 2 files:

westram 2002-07-16 11:03 Rev.: 754

This file is now generated by $ARBHOME/GDE/FASTDNAML/Makefile

0 lines of code changed in 1 file:

westram 2002-07-16 11:02 Rev.: 753

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0 lines of code changed in 2 files:

westram 2002-07-16 11:02 Rev.: 752

* arb_help_prefix.txt: - used to generate fastdnaml.hlp

19 lines of code changed in 1 file:

westram 2002-07-16 11:00 Rev.: 751

builds $ARBHOME/GDEHELP/fastdnaml.help

13 lines of code changed in 2 files:

westram 2002-07-16 09:10 Rev.: 750

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3 lines of code changed in 1 file:

westram 2002-07-16 09:10 Rev.: 749

added new button label (hide+clear)

18 lines of code changed in 1 file:

westram 2002-07-15 14:09 Rev.: 748

added AxML

28 lines of code changed in 1 file:

westram 2002-07-15 14:08 Rev.: 747

made depends

20 lines of code changed in 4 files:

westram 2002-07-15 14:07 Rev.: 746

AxML 1.9

5957 lines of code changed in 3 files:

westram 2002-07-15 14:06 Rev.: 745

- added AxML
- reorganized ARCHS for different systems

28 lines of code changed in 1 file:

westram 2002-07-11 18:03 Rev.: 744

bugfix fuer arb_phylo bei char >= ASCII128 in sequenzen

46 lines of code changed in 1 file:

westram 2002-07-11 12:29 Rev.: 743

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503 lines of code changed in 14 files:

westram 2002-07-11 12:25 Rev.: 742

other changes needed for transfer fields of gene-species

489 lines of code changed in 4 files:

westram 2002-07-11 12:24 Rev.: 741

access flags

2 lines of code changed in 1 file:

westram 2002-07-11 12:23 Rev.: 740

fixed a bug (the wrong helpfile was edited)

24 lines of code changed in 1 file:

westram 2002-07-11 12:22 Rev.: 739

if names.dat is missing it is created from its template

21 lines of code changed in 1 file:

westram 2002-07-11 12:20 Rev.: 738

added 'Save properties' to ARB_MERGE

3 lines of code changed in 1 file:

westram 2002-07-11 12:20 Rev.: 737

- window for gene-species tranfer definitions
- function to transfer defined fields

639 lines of code changed in 1 file:

westram 2002-07-11 12:18 Rev.: 736

- many basic C functions moved to ARBDB/adGene

2 lines of code changed in 2 files:

westram 2002-07-11 12:17 Rev.: 735

error message about wrong tree name occurs _before_ calculating tree

73 lines of code changed in 1 file:

westram 2002-07-11 12:16 Rev.: 734

* AD_MOBJECTS.h: - added adGene.o

2 lines of code changed in 1 file:

westram 2002-07-11 12:16 Rev.: 733

* adlang1.c: - new ACI functions origin_organism() and origin_gene()

44 lines of code changed in 1 file:

westram 2002-07-11 12:16 Rev.: 732

- fixed error message for invalid keys

35 lines of code changed in 1 file:

foerster 2002-07-06 00:01 Rev.: 731

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0 lines of code changed in 1 file:

foerster 2002-07-05 23:59 Rev.: 730

(WF) Ueberarbeitung der ASCII Exportierung

252 lines of code changed in 10 files:

westram 2002-07-04 18:36 Rev.: 729

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1 lines of code changed in 1 file:

westram 2002-07-04 18:35 Rev.: 728

inserted debugging output

8 lines of code changed in 1 file:

westram 2002-07-04 18:16 Rev.: 727

debug removed

9 lines of code changed in 1 file:

westram 2002-07-04 18:06 Rev.: 726

inserted debugging output

39 lines of code changed in 1 file:

westram 2002-07-04 17:56 Rev.: 725

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1 lines of code changed in 1 file:

westram 2002-07-04 17:55 Rev.: 724

- added some error messages to stop users from doing it wrong
- bugfix when pressing DONE in select alignment window w/o selecting any alignment

359 lines of code changed in 2 files:

foerster 2002-07-04 00:01 Rev.: 723

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2 lines of code changed in 1 file:

foerster 2002-07-03 17:05 Rev.: 722

(WF) implemented compression of numbers in PS_FileBuffer
(WF) adjusted load/save/append routines in PS_Node to use compression
(WF) compression was 'stolen' from Ralf Westrams BinFile

227 lines of code changed in 4 files:

westram 2002-07-03 15:37 Rev.: 721

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75 lines of code changed in 4 files:

westram 2002-07-03 15:37 Rev.: 720

* AWTI_export.cxx: - error messages for 'reading export form errors' was not shown
- AWTI_XML_recursive always adds name as attribute
- Tags in uppercase

55 lines of code changed in 1 file:

westram 2002-07-03 15:36 Rev.: 719

add AWT_date_string

1 lines of code changed in 1 file:

westram 2002-07-03 15:35 Rev.: 718

* AWT_imp_exp.cxx: - cuts off \n from AWT_date_string

7 lines of code changed in 1 file:

westram 2002-07-03 15:34 Rev.: 717

- bug fix: comments where encoded ('&lt;!--' instead of '<!--')

189 lines of code changed in 2 files:

westram 2002-07-03 15:34 Rev.: 716

* inline.h: - added ARB_strupper etc.

4 lines of code changed in 1 file:

foerster 2002-07-03 15:30 Rev.: 715

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141 lines of code changed in 7 files:

lai 2002-07-03 13:06 Rev.: 714

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42 lines of code changed in 2 files:

westram 2002-07-03 10:26 Rev.: 713

minor fixes

360 lines of code changed in 15 files:

westram 2002-07-03 10:25 Rev.: 712

re-recorded

16 lines of code changed in 1 file:

westram 2002-07-03 10:24 Rev.: 711

changed default application color

1 lines of code changed in 1 file:

westram 2002-07-03 10:22 Rev.: 710

- default colors for different programs
- initialization for color group awars
- window to configure color group names
- toggle for color groups usage

3 lines of code changed in 1 file:

westram 2002-07-03 10:20 Rev.: 709

exits if an error occurres when loading tree

5 lines of code changed in 1 file:

westram 2002-07-03 10:20 Rev.: 708

- request for color group defaults 'arb_pars' (none defined yet)

2 lines of code changed in 1 file:

westram 2002-07-03 10:19 Rev.: 707

* AP_tree_nlen.cxx: - shows error if less than 2 valid species in tree

43 lines of code changed in 1 file:

westram 2002-07-03 10:18 Rev.: 706

fix for perl

4 lines of code changed in 1 file:

westram 2002-07-03 10:15 Rev.: 705

* AWTI_export.cxx: - bugfix for recursive export formats
- write new stringname to filename-input if suffix was auto-appended

2 lines of code changed in 1 file:

westram 2002-07-03 10:14 Rev.: 704

* awt.hxx: - added awt_get_selected_fullname() to get the full name of a file selected in
a file selection box

22 lines of code changed in 1 file:

westram 2002-07-03 10:14 Rev.: 703

added member previous_filename to adawcbstruct

1 lines of code changed in 1 file:

westram 2002-07-03 10:13 Rev.: 702

inputMaskDir uses statics to avoid multiple calls to AWT_unfold_path

18 lines of code changed in 1 file:

westram 2002-07-03 10:13 Rev.: 701

* AWT_file_selection.cxx: - rewrote awt_create_selection_box_changed_filename()
- last used file name stay selected when changing directories
- general search for * wildcards
- awt_get_selected_fullname
- awt_refresh_selection_box

270 lines of code changed in 1 file:

westram 2002-07-03 10:11 Rev.: 700

added GBT_remote_read_awar (allows perl to read value of awars)

56 lines of code changed in 1 file:

westram 2002-07-03 10:10 Rev.: 699

added GB_export_IO_error()

39 lines of code changed in 1 file:

foerster 2002-07-01 12:14 Rev.: 698

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2 lines of code changed in 1 file:

June 2002 »

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