July 2008 Commit Log

Number of Commits:
81
Number of Active Developers:
3
westram 2008-07-30 16:41 Rev.: 5495


* AWTC/AWTC_ClustalV.cxx: - replaced hardcoded 21's vs MAX_BASETYPES
- added two assertions failing in bugcase

86 lines of code changed in 1 file:

westram 2008-07-30 16:40 Rev.: 5494


fixed wrong deletes

4 lines of code changed in 2 files:

westram 2008-07-30 10:15 Rev.: 5493


Patch from Elmar:
make two identical error situations discenible

2 lines of code changed in 1 file:

westram 2008-07-30 10:13 Rev.: 5492


Patch from Elmar:
COMPIle time options to allow "fputs" et. al. to write files larger than 2GB

1 lines of code changed in 1 file:

westram 2008-07-30 09:58 Rev.: 5491


patches 010-030 from Elmar

8 lines of code changed in 3 files:

westram 2008-07-30 09:58 Rev.: 5490


remove ARB.c on 'clean'

1 lines of code changed in 1 file:

westram 2008-07-30 09:57 Rev.: 5489


private Noncopyable

5 lines of code changed in 2 files:

westram 2008-07-30 09:56 Rev.: 5488


Less rigid: Only fail on first try (i.e. after every change of a file containing tabs)

5 lines of code changed in 1 file:

westram 2008-07-27 13:09 Rev.: 5487


- score printed by turn-acknowledgement was wrong

8 lines of code changed in 1 file:

westram 2008-07-27 12:29 Rev.: 5486


* Summary: Mostly cosmetics:
- changed some types; use enums instead of hardcoded values
- fixed includes and include wrappers

235 lines of code changed in 3 files:

westram 2008-07-27 11:34 Rev.: 5485


* Summary: - moved common family find awars and their GUI elements to global functions
in awtc_next_neighbours
- Integrated Aligners:
. shortened several function interfaces by using structs
. use custom family find parameters
. store how many base positions of which relative have been used for
alignment (in field 'used_rels'). Do not store relatives of which
no base positions were used.
. respect sort order of relatives given by PT server (dont sort self, just test)
. documented field 'used_rels'
. linked family settings help with aligner help
. added 'Settings'-subdialog to aligner-settings (family_settings.fig)

459 lines of code changed in 9 files:

westram 2008-07-25 14:09 Rev.: 5483


- renamed the interactive version of aw_message() into aw_question()
- added some convenience functions (aw_ask_sure, aw_popup_ok, aw_popup_exit)

302 lines of code changed in 44 files:

westram 2008-07-25 10:16 Rev.: 5482


* WINDOW/AW_window.cxx: - disabled expose and resize callback for AW_MIDDLE_AREA when disable_callbacks is true
* WINDOW/AW_status.cxx: - added warning to unfinished function
* WINDOW/AW_device.cxx: - typo
* HELP_SOURCE/oldhelp/nt_keys.hlp: - keys -> hotkeys
* EDIT4/ED4_search.cxx: - increased search result warn-limit from 10000 -> 100000

28 lines of code changed in 5 files:

westram 2008-07-24 10:45 Rev.: 5481


* PROBE/PT_family.cxx: - number of hitten relatives reported by PT server was wrong
(it reported all species, not only hitten ones)

6 lines of code changed in 1 file:

westram 2008-07-24 08:58 Rev.: 5480


* SOURCE_TOOLS/build_info.pl: - first auto-upgrade, then update revision info.
otherwise version gets previous revision - not upgraded one.

17 lines of code changed in 1 file:

arb_build 2008-07-23 14:50 Rev.: 5479

Auto version upgrade by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2008-07-23 14:49 Rev.: 5478


- test automatic version upgrade

48 lines of code changed in 2 files:

westram 2008-07-23 14:10 Rev.: 5477


* Summary: - changed versioning:
. uses ~/.arb_build_info to set local build information (like 'mpi', 'org' ..)
. automatic version upgrading possible (allowVersionUpgrade=1).
- Todo: auto-commit to SVN
- changed several version/build related #defines
* util/arb_srclst.pl: - exclude *.bak
- support for packing generated files (needed for svn_revision.h)
* TEMPLATES/arb_version.h: - much simpler now: only includes headers generated by build_info.pl,
tests whether version is defined and concats final version string
* TEMPLATES/Makefile: - simply call build_info.pl
* TEMPLATES/svn_revision.h: - SVN ignored (file is generated in SVN checkouts,
but as well packed to source tarball)
* SOURCE_TOOLS/version_info: - real source for ARB version info
* SOURCE_TOOLS/generate_all_links.sh: - made svn_revision.h globally visible
* SOURCE_TOOLS/build_info.pl: - create/update arb_build.h and svn_revision.h
* Makefile: - new target 'stable'
- automatic version increment

229 lines of code changed in 9 files:

westram 2008-07-22 15:51 Rev.: 5476

- socket patch from Elmar

2 lines of code changed in 1 file:

westram 2008-07-22 15:46 Rev.: 5475

- ARB uses 'neighbour' (spelling fixes)

25 lines of code changed in 4 files:

westram 2008-07-22 13:51 Rev.: 5474

Write next neighbours to field of listed species:
- delete field, if no next neighbour found
- write multiple next neighbours to field (only 1 was written before)
- limit written next neighbours by minimum score
- score only written optional

Updated/created help files for next neighbour search

Changed complement parameter of next neighbour search:
- each search possibility (fwd,rev,compl,rev-compl) can be switched on/off
- declared enum for search possibilities

366 lines of code changed in 10 files:

westram 2008-07-22 09:15 Rev.: 5473

- additional parameters user-configurable for next-relatives-search:
oligo_len, mismatches, sort_type and complement
- send back number of results from PT-Server and display above result list
- added relative matches to AWTC_FIND_FAMILY_MEMBER and display
them. if sort_type is "relative matches"
- number items in result list
- added code for reverse and complement relative search into PT-Server
- renamed go() -> findFamily() and fixed all call
- track whether all results were displayed in next-relative-list or whether
the list is truncated and display it in the last line of the list.

490 lines of code changed in 10 files:

westram 2008-07-18 09:25 Rev.: 5470

* Makefile: - exclude .svn while cleaning
* SOURCE_TOOLS/find_newest_source.pl: - ignore .svn dirs
* SOURCE_TOOLS/fix_depends.pl: - comment
* SOURCE_TOOLS/grepx.pl: - updated from other location
* SOURCE_TOOLS/prep_old_arb_versions: - obsolete (was cvs specific)
* SOURCE_TOOLS/tabBrake.pl: - ignore .svn subdirs
* WINDOW/AW_status.cxx: - comment
* util/arb_compress: - excludes .svn
* util/arb_srclst: - obsolete (arb_srclst.pl is used)
* util/arb_srclst.pl: - added MAKEBIN and LIBLINK (empty directories no longer in repository)
- read .svn/entries if present

271 lines of code changed in 10 files:

westram 2008-07-17 19:00 Rev.: 5469

* PERL2ARB/Makefile.old: - ignore generated file

0 lines of code changed in 1 file:

westram 2008-07-17 16:03 Rev.: 5467

deleted test file

0 lines of code changed in 1 file:

westram 2008-07-17 15:25 Rev.: 5466

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2 lines of code changed in 1 file:

westram 2008-07-17 15:23 Rev.: 5465

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1 lines of code changed in 1 file:

westram 2008-07-17 15:20 Rev.: 5464

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1 lines of code changed in 1 file:

westram 2008-07-17 15:18 Rev.: 5463

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1 lines of code changed in 1 file:

westram 2008-07-17 15:13 Rev.: 5462

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1 lines of code changed in 1 file:

westram 2008-07-17 15:09 Rev.: 5461

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1 lines of code changed in 1 file:

westram 2008-07-17 15:08 Rev.: 5460

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1 lines of code changed in 1 file:

westram 2008-07-17 15:05 Rev.: 5459

blabla

0 lines of code changed in 1 file:

baderk 2008-07-16 16:24 Rev.: 5458

Removed .cvsignore files from repository. Hopefully this time all svn:ignore flags were set right.

8 lines of code changed in 57 files:

westram 2008-07-16 09:24 Rev.: 5454

- depends updated

0 lines of code changed in 1 file:

westram 2008-07-16 09:24 Rev.: 5453

- changed tree draw function to less misleading names

37 lines of code changed in 1 file:

westram 2008-07-16 09:24 Rev.: 5452

- changed tree draw function to less misleading names
- added definitions from awt_irstree.hxx

15 lines of code changed in 1 file:

westram 2008-07-16 09:24 Rev.: 5451

- moved to .cxx

0 lines of code changed in 1 file:

westram 2008-07-16 09:23 Rev.: 5450

- AWT_graphic_tree:
. made most protected things private
. changed tree draw function to less misleading names

43 lines of code changed in 1 file:

westram 2008-07-15 18:26 Rev.: 5449

- hotfix for link error

1 lines of code changed in 1 file:

westram 2008-07-15 17:47 Rev.: 5448

- removed duplicated command

0 lines of code changed in 1 file:

westram 2008-07-10 16:21 Rev.: 5447

- replaced overloaded functions of AW_device by pure virtual functions +
non-overloaded non-virtual functions
- added wrappers to derived classes where now pure functions were missing

48 lines of code changed in 6 files:

westram 2008-07-10 16:19 Rev.: 5446

- simplified

9 lines of code changed in 1 file:

westram 2008-07-10 14:32 Rev.: 5445

- IRS tree:
. removed strange ':0' behind groups
. hide upper-left-corner boxes if 'Show handles' is off
. draw bracket before handles

16 lines of code changed in 1 file:

westram 2008-07-10 12:15 Rev.: 5444

- depends updated

10 lines of code changed in 6 files:

westram 2008-07-10 12:14 Rev.: 5443

- fixed range check

5 lines of code changed in 1 file:

westram 2008-07-10 12:14 Rev.: 5442

- removed const modifier from value return type

1 lines of code changed in 1 file:

westram 2008-07-10 12:13 Rev.: 5441

- removed useless typedefs

5 lines of code changed in 3 files:

westram 2008-07-10 12:13 Rev.: 5440

- fix operator precedence warnings

4 lines of code changed in 3 files:

westram 2008-07-10 12:12 Rev.: 5439

- spaces @ empty loops
- braces

64 lines of code changed in 8 files:

westram 2008-07-10 12:10 Rev.: 5438

- char array indices
- ambiguous elses

16 lines of code changed in 1 file:

westram 2008-07-10 12:07 Rev.: 5437

- added safeCharIndex()

3 lines of code changed in 1 file:

westram 2008-07-10 12:07 Rev.: 5436

- fixed signed chars used as array index

117 lines of code changed in 14 files:

westram 2008-07-09 13:49 Rev.: 5435

- cleanup useless comments

78 lines of code changed in 9 files:

westram 2008-07-09 13:34 Rev.: 5434

- minor info

2 lines of code changed in 1 file:

westram 2008-07-09 13:33 Rev.: 5433

- get/set -> Get/Set
- removed useless comments
- fixed ambiguous-& warnings

9 lines of code changed in 1 file:

westram 2008-07-09 13:33 Rev.: 5432

- get/set -> Get/Set
- removed useless comments

11 lines of code changed in 1 file:

westram 2008-07-09 13:32 Rev.: 5431

- grant rights for debian distributions

14 lines of code changed in 1 file:

westram 2008-07-09 12:51 Rev.: 5430

- allowed gcc 4.3.1

2 lines of code changed in 1 file:

westram 2008-07-09 12:50 Rev.: 5429

- removed const qualifier from value return type

2 lines of code changed in 1 file:

westram 2008-07-09 12:50 Rev.: 5428

- fixed includes for gcc 4.3.1

136 lines of code changed in 20 files:

westram 2008-07-09 12:43 Rev.: 5427

- use labs() instead of abs()

2 lines of code changed in 1 file:

westram 2008-07-09 12:43 Rev.: 5426

- simplyfied code

13 lines of code changed in 1 file:

westram 2008-07-09 12:43 Rev.: 5425

- compile dump_dtree conditionally

8 lines of code changed in 1 file:

westram 2008-07-09 12:38 Rev.: 5424

- fixed dummy params

9 lines of code changed in 3 files:

westram 2008-07-09 12:37 Rev.: 5423

- added missing increment for dummy counter

1 lines of code changed in 1 file:

westram 2008-07-04 13:04 Rev.: 5422

- added di_assert

2 lines of code changed in 1 file:

westram 2008-07-04 13:04 Rev.: 5421

- added include wrapper
- added DI_dmatrix::handle_move

44 lines of code changed in 1 file:

westram 2008-07-04 13:04 Rev.: 5420

- define distance awars globally
- cosmetics & cleanup
- changed parameters of DI_MATRIX::load to load species list

24 lines of code changed in 1 file:

westram 2008-07-04 13:04 Rev.: 5419

- depends updated

2 lines of code changed in 1 file:

westram 2008-07-04 13:04 Rev.: 5418

- added input_cb and motion_cb, handling scroll with middle mouse
button, click on name to select species and left/right click on
displayed distance to define distance range
- DI_dmatrix::display
. may clear display before drawing
. highlights selected species
. adds client data to drawn elements (used by input_cb)
- scroll callbacks:
. now do fast scroll (w/o complete repaint) when scrolling more
than one cell-step (before only worked with single cell steps)
. avoid display if scroll is less than one cell-step
. tofix: some relicts of selection remain at upper+left border
- if di_view_set_distances is called with cl_setmax==2, then
init both borders. Used at startup to initialize distance range
saved into properties.
- focus callback does redisplay (not resize)
- distance awars are created globally and are only bound when creating
matrix viewer

298 lines of code changed in 1 file:

westram 2008-07-04 13:04 Rev.: 5417

- several changes to AWAR names, some made temp.
- default distance function is similarity
- name of generated tree defaults to 'tree_nj' (was 'tree_temp')
- autoselect tree used in NTREE and use as default sort tree
- matrix function now can work on a list of species (used to calculate
distance between selected species and rest)
- added di_mark_by_distance. marks alls species that have a defined
distance to selected species
- added GUI elems for 'Mark by distance to selected'
- added timer callback (to react on changes to global AWARs)
- redisplay if selected species changes
- use di_...fig (instead of ph_...fig). relicts from old code-copy

293 lines of code changed in 1 file:

westram 2008-07-04 13:04 Rev.: 5416

- added GUI positions for 'Mark by distance to selected'
- moved tree selection above matrix calculation GUI to
reflect workflow

57 lines of code changed in 1 file:

westram 2008-07-03 13:23 Rev.: 5415

- speeded up mark_gene_species_of_marked_genes
- disabled GEN_find_pseudo

18 lines of code changed in 1 file:

westram 2008-07-03 11:19 Rev.: 5414

- unused soon

0 lines of code changed in 2 files:

westram 2008-07-03 10:30 Rev.: 5413

- exclude bin directory

3 lines of code changed in 1 file:

westram 2008-07-03 10:29 Rev.: 5412

- minor rename

3 lines of code changed in 2 files:

westram 2008-07-03 10:29 Rev.: 5411

- depends updated

4 lines of code changed in 1 file:

westram 2008-07-02 09:23 Rev.: 5410

- indentation fixed

60 lines of code changed in 1 file:

westram 2008-07-02 09:16 Rev.: 5409

- indentation fixed

60 lines of code changed in 1 file:

westram 2008-07-02 09:12 Rev.: 5408

- renamed some functions to make them unique

25 lines of code changed in 8 files:

June 2008 »

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