November 2007 Commit Log

Number of Commits:

50

Number of Active Developers:

2

westram 2007-11-30 19:13 #50 Rev.: 4962

- some changes by WL

75 lines of code changed in 1 file:

• lib/import/nonformats: longebi.ift (+75 -65)

westram 2007-11-30 19:13 #49 Rev.: 4961

- basic embl import filter

152 lines of code changed in 1 file:

• lib/import: ebi_silva.ift (new 152)

westram 2007-11-30 19:13 #48 Rev.: 4960

- added set_clipall() - clips everything

6 lines of code changed in 1 file:

• WINDOW: aw_device.hxx (+6 -1)

westram 2007-11-30 19:13 #47 Rev.: 4959

- compiler switches for top-area size-limit

6 lines of code changed in 1 file:

• EDIT4: ed4_class.hxx (+6 -1)

westram 2007-11-30 19:12 #46 Rev.: 4958

- part of ED4_expose_cb moved to ED4_expose_recalculations()
- explicitely set sequence-pos after compression change.
call ED4_expose_recalculations instead of ED4_expose_cb

48 lines of code changed in 1 file:

• EDIT4: ED4_no_class.cxx (+48 -36)

westram 2007-11-30 19:12 #45 Rev.: 4957

- removed top-area-limit (optional)

19 lines of code changed in 2 files:

• EDIT4: ED4_base.cxx (+15 -18), ED4_manager.cxx (+4 -2)

westram 2007-11-30 19:12 #44 Rev.: 4956

- clean

0 lines of code changed in 1 file:

• EDIT4: ED4_cursor.cxx (-4)

westram 2007-11-21 17:40 #43 Rev.: 4955

- during aligning keep base-relative position.
Used wrong position when aligning blocks.
Always jumped to next base after position.

26 lines of code changed in 1 file:

• EDIT4: ED4_edit_string.cxx (+26 -6)

westram 2007-11-21 16:17 #42 Rev.: 4954

- moved from ../genbank.ift
- feature table parsing identical with longebi.ift

397 lines of code changed in 1 file:

• lib/import/nonformats: longgenbank.ift (new 397)

westram 2007-11-21 16:17 #41 Rev.: 4953

- modified embl import-filter (WL)
- feature table parsing identical with longgenbank.ift

170 lines of code changed in 1 file:

• lib/import/nonformats: longebi.ift (+170 -126)

westram 2007-11-21 16:17 #40 Rev.: 4952

- calls converter + nonformats/longgenbank.ift (like ebi.ift)

4 lines of code changed in 2 files:

• lib/import: genbank.ift (+2 -363), genbank_multi.ift (+2 -363)

westram 2007-11-21 16:17 #39 Rev.: 4951

- unwrap long qualifiers
- prefix with FT and FTx. Makes feature table
compatible with EMBL format

77 lines of code changed in 2 files:

• PERL_SCRIPTS/ARBTOOLS/IFTHELP: genbank_gen_long_features.pl (new 76)
• PERL_SCRIPTS/IFTHELP: genbank_gen_long_features.pl (new 1)

baderk 2007-11-21 16:05 #38 Rev.: 4950

Fixing ticket #91: Flickering (multiple refreshes)
All but one resize events are removed from the X11 event queue.
Please consider this patch as not fully tested: side effects may occur.

28 lines of code changed in 1 file:

• WINDOW: AW_window.cxx (+28 -1)

westram 2007-11-20 12:58 #37 Rev.: 4949

- fixed wrong param to GI_importGenomeFile()

1 lines of code changed in 1 file:

• AWTI: AWTI_import.cxx (+1 -1)

westram 2007-11-15 13:00 #36 Rev.: 4948

- type
- removed obsolete NUMLOCK warning
- doc for Ctrl-Up/Down/Home/End

11 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: e4.hlp (+11 -5)

westram 2007-11-15 13:00 #35 Rev.: 4947

- typo

1 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: arb_edit.hlp (+1 -1)

westram 2007-11-15 13:00 #34 Rev.: 4946

- new fun-type ED4_TerminalTest, use in get_upper_lower_pos()

6 lines of code changed in 1 file:

• EDIT4: ed4_class.hxx (+6 -4)

westram 2007-11-15 12:59 #33 Rev.: 4945

- don't set cursor in ED4_expose_cb()
- catch Ctrl-Home/End and derive to move_cursor()
- removed unused variables

4 lines of code changed in 1 file:

• EDIT4: ED4_no_class.cxx (+4 -7)

westram 2007-11-15 12:59 #32 Rev.: 4944

- backspace and delete do different things now

43 lines of code changed in 1 file:

• EDIT4: ED4_edit_string.cxx (+43 -43)

westram 2007-11-15 12:59 #31 Rev.: 4943

- removed global (current_position), fixing a bug (when using Up/Down,
cursor jumped back to column where Ctrl-Up/Down was used last)
- implemented Ctrl-Home/End (jump to first/last sequence)
rewrote move_cursor() (less duplicated code)
- new param for get_upper_lower_pos(), indicating used coordinate-type (screen or world)
- don't scroll terminal into view if in top-area. top-area is always visible.
caused scroll-to-top of bottom-area, when changing to top-area via mouse-click.
- use return-value instead of result-param for terget-terminal in get_upper_lower_pos()

118 lines of code changed in 1 file:

• EDIT4: ED4_cursor.cxx (+118 -105)

westram 2007-11-15 12:59 #30 Rev.: 4942

- changed typename

1 lines of code changed in 1 file:

• WINDOW: AW_window.cxx (+1 -1)

westram 2007-11-15 12:59 #29 Rev.: 4941

- added new keymap defining all MOD-flavors of contained keys
- DELETE and BACKSPACE return different codes now
- hashes contain pointers instead of indices into array - no longer
possible because there are 2 arrays now

141 lines of code changed in 1 file:

• WINDOW: AW_xkey.cxx (+141 -98)

westram 2007-11-15 12:59 #28 Rev.: 4940

- added new keymap defining all MOD-flavors of contained keys
- changed typename

8 lines of code changed in 1 file:

• WINDOW: aw_xkey.hxx (+8 -2)

westram 2007-11-14 19:06 #27 Rev.: 4939

- fixed tabs and indentation

39 lines of code changed in 2 files:

• WINDOW: AW_xkey.cxx (+32 -52), aw_xkey.hxx (+7 -7)

westram 2007-11-12 12:49 #26 Rev.: 4938

- cflags O2 -> O0 in DEBUG mode

2 lines of code changed in 1 file:

• Makefile (+2 -1)

westram 2007-11-12 12:49 #25 Rev.: 4937

- finer transaction granularity, to avoid late callback of rename reason

21 lines of code changed in 1 file:

• MERGE: MG_main.cxx (+21 -10)

westram 2007-11-12 11:17 #24 Rev.: 4936

- renamed 'update' into 'built' (ptserver)
- typo

6 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: probeadmin.hlp (+6 -4)

westram 2007-11-12 11:17 #23 Rev.: 4935

- renamed 'update' into 'built' (ptserver)

12 lines of code changed in 3 files:

• HELP_SOURCE/oldhelp: probedesign.hlp (+6 -9)
• PROBE_DESIGN: probe_design.cxx (+3 -3)
• SERVERCNTRL: servercntrl.c (+3 -3)

westram 2007-11-12 11:17 #22 Rev.: 4934

- renamed 'update' into 'built' (ptserver)
- fixed PT-admin menu-location

11 lines of code changed in 3 files:

• arb_README.txt (+2 -2), arb_install.sh (+3 -3)
• HELP_SOURCE/oldhelp: pt_server.hlp (+6 -6)

westram 2007-11-09 12:07 #21 Rev.: 4933

- " -> '

1 lines of code changed in 1 file:

• PERL2ARB: Makefile.main (+1 -1)

baderk 2007-11-08 19:14 #20 Rev.: 4932

Fixed various typos...

62 lines of code changed in 27 files:

• AISC_COM/C: server.c (+6 -6)
• ARBDB: adTest.c (+1 -1), ad_load.c (+1 -1), adcomm.c (+18 -18), adseqcompr.c (+2 -2), adsocket.c (+3 -3)
• ARBDBPP: admain.cxx (+2 -2)
• CONVERTALN: genbank.c (+1 -1)
• EDIT: edit.cxx (+1 -1)
• GDE/TREEPUZZLE/src: ppuzzle.c (+2 -2), puzzle1.c (+2 -2), puzzle2.c (+4 -4)
• GDEHELP/MENUS: align.menu (+4 -4)
• NALIGNER: ali_main.cxx (+2 -2)
• NTREE: NT_concatenate.cxx (+1 -1), ad_transpro.cxx (+1 -1)
• PARSIMONY: PARS_main.cxx (+1 -1)
• PROBE: PT_io.cxx (+1 -1)
• PROBE_DESIGN: SaiProbeVisualization.cxx (+1 -1)
• RNA3D: RNA3D_Interface.cxx (+1 -1)
• SECEDIT: SEC_graphic.cxx (+1 -1)
• SEER: SEER_interface.cxx (+1 -1), seer_interface.hxx (+1 -1)
• SL/DB_SCANNER: db_scanner.cxx (+1 -1)
• TOOLS: arb_primer.cxx (+1 -1), arb_proto_2_xsub.cxx (+1 -1)
• lib/pictures: arb_intro.fig (+1 -1)

westram 2007-11-08 15:22 #19 Rev.: 4931

- removed old code

0 lines of code changed in 1 file:

• ARBDB: adtools.c (-19)

westram 2007-11-08 15:15 #18 Rev.: 4930

- prototypes updated

1 lines of code changed in 1 file:

• ARBDB: ad_t_prot.h (+1 -2)

westram 2007-11-08 15:15 #17 Rev.: 4929

- show scaleWarning from GBT_load_tree()

15 lines of code changed in 1 file:

• TOOLS: arb_read_tree.cxx (+15 -5)

westram 2007-11-08 15:15 #16 Rev.: 4928

- fix call to GBT_load_tree()

1 lines of code changed in 1 file:

• TOOLS: arb_newick_2_otb.cxx (+1 -1)

westram 2007-11-08 15:15 #15 Rev.: 4927

- show scaleWarning from GBT_load_tree()
- use unlink() instead of 'rm ..'-system-call

37 lines of code changed in 1 file:

• NTREE: ad_trees.cxx (+37 -26)

westram 2007-11-08 15:15 #14 Rev.: 4926

- rewrote GBT_read_tree_and_size()
- changed DEFAULT_LENGTH_MARKER from -1 to -1000. Since there may be negative
branchlens, -1 is a dangerous marker
- use DEFAULT_LENGTH_MARKER instead of -0.01 in GBT_scale_tree()
- new result-parameter 'warningPtr' for GBT_load_tree().
returns warning about automatic branchlength scaling

71 lines of code changed in 1 file:

• ARBDB: adtools.c (+71 -45)

westram 2007-11-06 15:43 #13 Rev.: 4925

- use $ARBHOME (or /usr/arb if empty)

3 lines of code changed in 1 file:

• util: arb_export (+3 -3)

westram 2007-11-06 15:43 #12 Rev.: 4924

- fixed perl path

2 lines of code changed in 2 files:

• PERL_SCRIPTS/ARBTOOLS/IFTHELP: embl_gen_long_features.pl (+1 -1)
• PERL_SCRIPTS/IFTHELP: embl_gen_long_features.pl (+1 -1)

westram 2007-11-06 15:43 #11 Rev.: 4923

- added gcc 4.2.3
- target 'clean' creates 'links'

6 lines of code changed in 1 file:

• Makefile (+6 -2)

westram 2007-11-06 11:57 #10 Rev.: 4922

- pass species/SAI count to DB-fix functions (used for status)
- added NT_del_mark_move_REF. Removes useless 'mark' entries from species and SAIs.
Rename 'REF' into '_REF'; entries starting with '_' are not displayed in editor.

129 lines of code changed in 1 file:

• NTREE: NT_main.cxx (+129 -24)

westram 2007-11-06 11:57 #9 Rev.: 4921

- renamed variable 'string' -> 'String'
- removed '0' info params to put..-functions

21 lines of code changed in 1 file:

• NALIGNER: ali_main.cxx (+21 -22)

westram 2007-11-06 11:57 #8 Rev.: 4920

- remove param 'info' from put..-functions. Param was always default.
Functions always created an empty 'mark' entry, which is used nowhere.

3 lines of code changed in 1 file:

• NALIGNER: ali_arbdb.hxx (+3 -3)

westram 2007-11-06 11:57 #7 Rev.: 4919

- removed 'info'-param and 'mark'-creating code from put..-functions

19 lines of code changed in 1 file:

• NALIGNER: ali_arbdb.cxx (+19 -53)

westram 2007-11-06 11:56 #6 Rev.: 4918

- removed unused default-param 'info' from put_sequence_string()

1 lines of code changed in 1 file:

• ALIV3: a3_arbdb.hxx (+1 -2)

westram 2007-11-06 11:56 #5 Rev.: 4917

- removed code creating unused 'mark' entries

7 lines of code changed in 1 file:

• ALIV3: a3_arbdb.cxx (+7 -30)

westram 2007-11-06 11:56 #4 Rev.: 4916

- changed name of secondary structure information ('REF' -> '_REF') to
avoid display in ARB_EDIT4

2 lines of code changed in 1 file:

• SECEDIT: SEC_graphic.hxx (+2 -2)

westram 2007-11-06 11:55 #3 Rev.: 4915

- new ctor for BI_helix

18 lines of code changed in 2 files:

• SL/HELIX: BI_helix.cxx (+15 -8), BI_helix.hxx (+3 -1)

westram 2007-11-06 11:54 #2 Rev.: 4914

- GBT_count_species -> GBT_get_species_count

7 lines of code changed in 6 files:

• DIST: DI_matr.cxx (+1 -1)
• NTREE: AP_consensus.cxx (+1 -1), NT_trackAliChanges.cxx (+2 -2), ad_transpro.cxx (+1 -1)
• SL/AW_NAME: AW_rename.cxx (+1 -1)
• STAT: ST_quality.cxx (+1 -1)

westram 2007-11-06 11:53 #1 Rev.: 4913

- remove GBT_count_species(), GBT_get_species_count() does the same

2 lines of code changed in 1 file:

• ARBDB: adtools.c (+2 -14)

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