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38 lines of code changed in 6 files:
- new label 'toggle1'
- corrected label 'user2'
3 lines of code changed in 1 file:
tabbed NDS save
12 lines of code changed in 2 files:
added new type to save options
1 lines of code changed in 1 file:
* ph_matr.hxx: - new save type PH_SAVE_TABBED
3 lines of code changed in 1 file:
* PH_save_matr.cxx: - save tabbed matrix (for calc-sheet)
- '.'->',' in tabbed mode
134 lines of code changed in 1 file:
* 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:
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21 lines of code changed in 4 files:
menu rename
1 lines of code changed in 1 file:
some updates
21 lines of code changed in 3 files:
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1 lines of code changed in 1 file:
note about hierarchical fields
3 lines of code changed in 1 file:
* GDE_event.cxx: - error when wrong macro replacement happens
20 lines of code changed in 1 file:
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7 lines of code changed in 1 file:
- name and acc are not allowed as destination fields
48 lines of code changed in 1 file:
* 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:
beautified
475 lines of code changed in 1 file:
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41 lines of code changed in 1 file:
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1 lines of code changed in 1 file:
zoom bug fixed
54 lines of code changed in 2 files:
* xml.cxx: - encodes acute-forward as normal acute
2 lines of code changed in 1 file:
* 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:
* inc_fastdnaml.menu: - call to arb_export_rates has been changed
- changed default tree to ''
6 lines of code changed in 1 file:
* fastdnaml.menu: - call to arb_export_rates has been changed
3 lines of code changed in 1 file:
* 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:
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1 lines of code changed in 1 file:
fastdnaml 1.2.2
309 lines of code changed in 3 files:
deleted old versions
0 lines of code changed in 6 files:
original version 1.2.2
6091 lines of code changed in 3 files:
* arb_help_prefix.txt: - used to generate fastdnaml.hlp
4 lines of code changed in 1 file:
* ARB/GDE/Makefile: - removed ZUKER
0 lines of code changed in 1 file:
* GDE_menu.h: - added textwidth to GmenuItemArg
44 lines of code changed in 1 file:
* GDE_def.h: - define TEXTFIELDWIDTH globally
16 lines of code changed in 1 file:
* 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:
* GDE.cxx: - GmenuItemArg.textwidth is used to define width of textfield
10 lines of code changed in 1 file:
* ARB/arb_CHANGES.txt: - added headline (appears as title in .hlp file)
6 lines of code changed in 1 file:
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:
* Makefile: - warns about duplicated helpfiles
- calls make in genhelp
40 lines of code changed in 1 file:
* 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:
link to changes
1 lines of code changed in 1 file:
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46 lines of code changed in 3 files:
smaller
5 lines of code changed in 1 file:
* AW_status.cxx: - Message Box has OK button (Clear&Hide)
9 lines of code changed in 1 file:
now needs 'used program name' as parameter
1 lines of code changed in 1 file:
* 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:
gde help window resizeable
10 lines of code changed in 1 file:
- new toggle to switch between AxML and fastdnaML
- the value is passed to arb_fastdnaml
16 lines of code changed in 2 files:
This file is now generated by $ARBHOME/GDE/FASTDNAML/Makefile
0 lines of code changed in 1 file:
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0 lines of code changed in 2 files:
* arb_help_prefix.txt: - used to generate fastdnaml.hlp
19 lines of code changed in 1 file:
builds $ARBHOME/GDEHELP/fastdnaml.help
13 lines of code changed in 2 files:
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3 lines of code changed in 1 file:
added new button label (hide+clear)
18 lines of code changed in 1 file:
added AxML
28 lines of code changed in 1 file:
made depends
20 lines of code changed in 4 files:
AxML 1.9
5957 lines of code changed in 3 files:
- added AxML
- reorganized ARCHS for different systems
28 lines of code changed in 1 file:
bugfix fuer arb_phylo bei char >= ASCII128 in sequenzen
46 lines of code changed in 1 file:
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505 lines of code changed in 14 files:
other changes needed for transfer fields of gene-species
489 lines of code changed in 4 files:
access flags
2 lines of code changed in 1 file:
fixed a bug (the wrong helpfile was edited)
24 lines of code changed in 1 file:
if names.dat is missing it is created from its template
21 lines of code changed in 1 file:
added 'Save properties' to ARB_MERGE
3 lines of code changed in 1 file:
- window for gene-species tranfer definitions
- function to transfer defined fields
639 lines of code changed in 1 file:
- many basic C functions moved to ARBDB/adGene
2 lines of code changed in 2 files:
error message about wrong tree name occurs _before_ calculating tree
73 lines of code changed in 1 file:
* AD_MOBJECTS.h: - added adGene.o
2 lines of code changed in 1 file:
* adlang1.c: - new ACI functions origin_organism() and origin_gene()
44 lines of code changed in 1 file:
- fixed error message for invalid keys
35 lines of code changed in 1 file:
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0 lines of code changed in 1 file:
(WF) Ueberarbeitung der ASCII Exportierung
252 lines of code changed in 10 files:
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1 lines of code changed in 1 file:
inserted debugging output
8 lines of code changed in 1 file:
debug removed
9 lines of code changed in 1 file:
inserted debugging output
39 lines of code changed in 1 file:
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1 lines of code changed in 1 file:
- 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:
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2 lines of code changed in 1 file:
(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:
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75 lines of code changed in 4 files:
* 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:
add AWT_date_string
1 lines of code changed in 1 file:
* AWT_imp_exp.cxx: - cuts off \n from AWT_date_string
7 lines of code changed in 1 file:
- bug fix: comments where encoded ('<!--' instead of '<!--')
189 lines of code changed in 2 files:
* inline.h: - added ARB_strupper etc.
4 lines of code changed in 1 file:
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141 lines of code changed in 7 files:
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42 lines of code changed in 2 files:
minor fixes
360 lines of code changed in 15 files:
re-recorded
16 lines of code changed in 1 file:
changed default application color
1 lines of code changed in 1 file:
- 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:
exits if an error occurres when loading tree
5 lines of code changed in 1 file:
- request for color group defaults 'arb_pars' (none defined yet)
2 lines of code changed in 1 file:
* AP_tree_nlen.cxx: - shows error if less than 2 valid species in tree
43 lines of code changed in 1 file:
fix for perl
4 lines of code changed in 1 file:
* 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:
* 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:
added member previous_filename to adawcbstruct
1 lines of code changed in 1 file:
inputMaskDir uses statics to avoid multiple calls to AWT_unfold_path
18 lines of code changed in 1 file:
* 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:
added GBT_remote_read_awar (allows perl to read value of awars)
56 lines of code changed in 1 file:
added GB_export_IO_error()
39 lines of code changed in 1 file:
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2 lines of code changed in 1 file: