October 2008 Commit Log

Number of Commits:

48

Number of Active Developers:

4

boehnel 2008-10-31 22:23 #48 Rev.: 5567

Added PTPan

1 lines of code changed in 1 file:

• config.makefile.template (+1 -1)

boehnel 2008-10-31 22:07 #47

Adding PTPan

1312 lines of code changed in 28 files:

• Makefile (+72), config.makefile.template (+2)
• ptpan: Makefile (new 131), Makefile.old (new), PT_buildtree.cxx (new 45), PT_cachehandler.cxx (new 4), PT_etc.cxx (new 2), PT_family.cxx (new), PT_findEx.cxx (new 9), PT_hashing.cxx (new 2), PT_huffman.cxx (new 1), PT_io.cxx (new 3), PT_lowlevel.cxx (new 1), PT_main.cxx (new 42), PT_match.cxx (new 51), PT_new_design.cxx (new 750), PT_treepack.cxx (new 1), dlist.cxx (new), dlist.h (new), globalprefs.h (new 2), hooks.cxx (new), hooks.h (new), pd.makefile (new), probe.h (new), probe_debug.cxx (new), pt_manualprotos.h (new), pt_prototypes.h (new 176), types.h (new 18)

westram 2008-10-31 18:21 #46 Rev.: 5564

* ARBDB/adtools.c: - tree reader uses struct TreeReader instead of static variables
- Unescape tree comment when reading newick tree
('\\', '\{' and '\}' are replaced by '\', '[' abd ']')
- now reads any length of comment (comment was restricted to 1024 characters)
* AWT/AWT_imp_exp.cxx: - Escape tree comment

326 lines of code changed in 7 files:

• ARBDB: Makefile (-1), ad_t_lpro.h (-2), ad_t_prot.h (+1), adtools.c (+312 -200)
• ARBDB2: Makefile (-1)
• ARBDBS: Makefile (-1)
• AWT: AWT_imp_exp.cxx (+13 -4)

arb_build 2008-10-30 14:53 #45 Rev.: 5563

Auto version upgrade to 4.16 by devel@arb-home.de

2 lines of code changed in 1 file:

• SOURCE_TOOLS: version_info (+2 -2)

westram 2008-10-30 14:49 #44 Rev.: 5562

- given 2 lists of species (or accs, ...) create difference lists and common list

99 lines of code changed in 1 file:

• PERL_SCRIPTS/GENERAL: listDiff.pl (new 99)

westram 2008-10-30 01:45 #43 Rev.: 5561

from elmar:
- reserve memory needed for nmap at startup
(raises chances memory is unfragmented when actual nmap happens)

7 lines of code changed in 1 file:

• PROBE: PT_main.cxx (+7)

westram 2008-10-29 13:41 #42 Rev.: 5560

libpng3 -> libpng12-0

1 lines of code changed in 1 file:

• arb_UBUNTU.txt (+1 -1)

arb_build 2008-10-29 13:19 #41 Rev.: 5559

Auto version upgrade to 4.15 by devel@arb-home.de

2 lines of code changed in 1 file:

• SOURCE_TOOLS: version_info (+2 -2)

westram 2008-10-29 13:09 #40 Rev.: 5558

* NTREE/NT_dbrepair.cxx: - less panic messages about dictionary compression bug
* ARBDB/ad_load.c: - ARB crashed with "ARB ERROR: keyword 'time' not found in reading GB_file"
followed by a SIGSEGV when a DB-key had maximum allowed length.
- added warning if a key exceeds allowed length (not occurred ITW yet)

23 lines of code changed in 2 files:

• ARBDB: ad_load.c (+18 -7)
• NTREE: NT_dbrepair.cxx (+5 -3)

westram 2008-10-24 15:23 #39 Rev.: 5557

- updated packet list for openGL compile

35 lines of code changed in 1 file:

• arb_UBUNTU.txt (+35 -13)

westram 2008-10-24 13:37 #38 Rev.: 5556

- compiles with gcc 4.2.4
- removed probe-library-client (obsolete, new client in PLEASE-repository)
-> arb compile no longer needs jdk

9 lines of code changed in 1 file:

• Makefile (+9 -6)

westram 2008-10-23 12:43 #37 Rev.: 5555

- switched back to old behavior (auto-upgrade version once per hour)

1 lines of code changed in 1 file:

• SOURCE_TOOLS: build_info.pl (+1 -2)

arb_build 2008-10-23 12:27 #36 Rev.: 5554

Auto version upgrade to 4.14 by devel@arb-home.de

2 lines of code changed in 1 file:

• SOURCE_TOOLS: version_info (+2 -2)

westram 2008-10-23 12:27 #35 Rev.: 5553

test (upgrade instantly)

2 lines of code changed in 1 file:

• SOURCE_TOOLS: build_info.pl (+2 -1)

westram 2008-10-23 12:22 #34 Rev.: 5552

syntax

2 lines of code changed in 1 file:

• Makefile (+2 -2)

westram 2008-10-23 12:20 #33 Rev.: 5551

- auto-upgrade version more early
- write new version into svn-comment
idea: have automatic version history at
http://bugs.arb-home.de/log/SOURCE_TOOLS/version_info

4 lines of code changed in 2 files:

• Makefile (+2 -1)
• SOURCE_TOOLS: build_info.pl (+2 -2)

arb_build 2008-10-23 11:49 #32 Rev.: 5550

Auto version upgrade by devel@arb-home.de

2 lines of code changed in 1 file:

• SOURCE_TOOLS: version_info (+2 -2)

westram 2008-10-23 11:29 #31 Rev.: 5549

- moved com-codes for familyfind from 50-59 to 70-89

36 lines of code changed in 1 file:

• PROBE_COM: PT.aisc (+36 -33)

westram 2008-10-22 15:53 #30 Rev.: 5548

from Elmar:
* replace deprecated XtAppInitialize with XtOpenApplication
* turn of "xmouse" effect for textinput fields

10 lines of code changed in 1 file:

• WINDOW: AW_window.cxx (+10 -9)

westram 2008-10-22 15:24 #29 Rev.: 5547

from Elmar:
allow partial sequences to achieve maximum score on the relative fam search

3 lines of code changed in 1 file:

• PROBE: PT_family.cxx (+3 -3)

baderk 2008-10-22 14:11 #28 Rev.: 5546

Fixed a bug in the sequence quality tool: the whole tree was evaluated although only parts of it were marked.

12 lines of code changed in 3 files:

• SEQ_QUALITY: SQ_functions.cxx (+8 -6), SQ_functions.h (+1 -1), SQ_main.cxx (+3 -2)

westram 2008-10-22 13:40 #27 Rev.: 5545

from elmar:

Add a parameter to the PT server that allows limiting the family search result
to a fraction of the sequences. We are not really interessted in a completely
sorted result, usually only the n best matching sequences are required.

ralf:
- use that feature from ARB

15 lines of code changed in 3 files:

• AWTC: AWTC_next_neighbours.cxx (+1)
• PROBE: PT_family.cxx (+13 -5)
• PROBE_COM: PT.aisc (+1 -1)

westram 2008-10-22 13:15 #26 Rev.: 5544

from elmar:

Make the aisc client side threadsafe. This allows e.g. running more
than one PT server from one process.

133 lines of code changed in 2 files:

• AISC_COM/C: client.c (+112 -117), client_privat.h (+21 -11)

westram 2008-10-22 12:42 #25 Rev.: 5543

from elmar:

use stl sort and templates / function objects instead of GB_mergesort
the reduction in function calls improves the speed of the family search
massively

18 lines of code changed in 1 file:

• PROBE: PT_family.cxx (+18 -29)

westram 2008-10-22 12:27 #24 Rev.: 5542

from elmar:

Improves performance by making PT_read_chain() a template.
Using a function object instead of a function pointer allows the
compiler to inline the code within func().

59 lines of code changed in 7 files:

• PROBE: PT_buildtree.cxx (+5 -4), PT_family.cxx (+11 -9), PT_match.cxx (+7 -3), PT_new_design.cxx (+24 -20), PT_prefixtree.cxx (+1 -8), probe_tree.hxx (+10 -2), pt_prototypes.h (+1 -4)

westram 2008-10-22 09:56 #23 Rev.: 5541

from elmar:

AMD64; use bswap in PROBE

The macros PT_READ_PTR and PT_WRITE_PTR need to be 64bit aware.
Also: Use bswap instead of changing byteorder manually

TODO: Why is byteorder _ALWAYS_ changed? Can't this be skipped altogether?

ralf:
I guess it could, seems to be a relict from that time where ARB was running on machines
with different byte orders.
When changing this, old PT-Server-databases need to be rejected by ARB

10 lines of code changed in 1 file:

• PROBE: probe_tree.hxx (+10 -30)

westram 2008-10-22 09:44 #22 Rev.: 5540

- prototypes and dependencies updated

40 lines of code changed in 6 files:

• AWTC: Makefile (+5)
• EDIT4: Makefile (+24)
• NTREE: Makefile (+7 -1), nt_cb.hxx (+1 -1), nt_internal.h (+2 -1)
• PROBE: pt_prototypes.h (+1)

westram 2008-10-22 09:38 #21 Rev.: 5539

- corrected indented defines

3 lines of code changed in 1 file:

• PROBE: probe_tree.hxx (+3 -3)

westram 2008-10-22 09:22 #20 Rev.: 5538

erm.. + help

0 lines of code changed in 1 file:

• HELP_SOURCE/oldhelp: galign_main.hlp (new)

westram 2008-10-22 09:21 #19 Rev.: 5537

from elmar:

add SILVA/SINA frontend to edit4

changed by ralf:
- rewrote filter_sai()
- const char *
- fixed calls to GB_find()
- added item filter AWM_DISABLED and use it in galign_mask()
- use GB_executable to find galign

467 lines of code changed in 5 files:

• EDIT4: ED4_main.cxx (+2), ED4_root.cxx (+2), Makefile (+1), graph_aligner_gui.cxx (new 459), graph_aligner_gui.hxx (new 3)

westram 2008-10-22 09:19 #18 Rev.: 5536

- added item mode AWM_DISABLED (used for dynamic items)

12 lines of code changed in 1 file:

• WINDOW: aw_window.hxx (+12 -11)

westram 2008-10-22 09:19 #17 Rev.: 5535

- renamed search_executable into GB_executable (to make it public)

4 lines of code changed in 2 files:

• ARBDB: ad_prot.h (+1), adsocket.c (+3 -3)

westram 2008-10-22 08:26 #16 Rev.: 5534

ignore subdir 'patches'

1 lines of code changed in 1 file:

• SOURCE_TOOLS: tabBrake.pl (+1)

westram 2008-10-22 08:10 #15

TAB

4 lines of code changed in 2 files:

• PROBE: PT_buildtree.cxx (+3 -3)

westram 2008-10-22 08:09 #14 Rev.: 5531

From Elmar:

add fflushes to pt server build sequence
(necessary on buffered output terminals, e.g. when capturing the log via "tee")

7 lines of code changed in 2 files:

• PROBE: PT_buildtree.cxx (+5 -1), PT_io.cxx (+2 -1)

westram 2008-10-16 11:44 #13 Rev.: 5530

* NTREE/ad_trees.cxx: - added new export format 'NEWICK TREE FORMAT (pretty, but big)'
- format 'NEWICK TREE FORMAT' now exports condensed tree
* AWT/AWT_imp_exp.cxx: - AWT_export_Newick_tree now exports pretty (old-style) or condensed

52 lines of code changed in 4 files:

• AWT: AWT_imp_exp.cxx (+29 -25), AWT_tree_cmp.cxx (+1 -1), awt_imp_exp.hxx (+1 -1)
• NTREE: ad_trees.cxx (+21 -18)

westram 2008-10-16 09:56 #12 Rev.: 5529

* arb_INSTALL.txt: - mentioned Ubuntu packets list
- no longer need to rename arb_noOPENGL.tgz
* arb_UBUNTU.txt: - list of packets needed for ARB on Ubuntu 8.04
* arb_install.sh: - fixed instruction for local install (into user dir)
- if arb.tgz is missing, try to use arb_noOPENGL.tgz automatically
- command to detect shell is 'echo $SHELL'

51 lines of code changed in 3 files:

• arb_INSTALL.txt (+5 -1), arb_UBUNTU.txt (new 34), arb_install.sh (+12 -3)

boehnel 2008-10-14 03:35 #11 Rev.: 5528

added some comments

added code for long diffs

31 lines of code changed in 1 file:

• PROBE: PT_prefixtree.cxx (+31 -11)

boehnel 2008-10-14 03:34 #10 Rev.: 5527

added a comment

2 lines of code changed in 1 file:

• PROBE: PT_buildtree.cxx (+2)

boehnel 2008-10-14 03:29 #9 Rev.: 5526

changed "estimated_kb" calculation (value by try and error)

added some code for long diffs

15 lines of code changed in 1 file:

• PROBE: PT_buildtree.cxx (+15)

boehnel 2008-10-14 00:28 #8 Rev.: 5525

0 -> NULL

89 lines of code changed in 4 files:

• ARBDB: adquery.c (+36 -36), adtables.c (+5 -5), adtools.c (+36 -36), arbdb.c (+12 -12)

boehnel 2008-10-10 17:58 #7 Rev.: 5524

added two assertions

2 lines of code changed in 1 file:

• TOOLS: arb_gene_probe.cxx (+2 -1)

westram 2008-10-08 09:33 #6 Rev.: 5523

5 lines of code changed in 1 file:

• arb_README_gcc.txt (+5)

boehnel 2008-10-07 05:28 #5 Rev.: 5522

added some comments

added code for long diffs

135 lines of code changed in 2 files:

• PROBE: PT_prefixtree.cxx (+73 -15), probe_tree.hxx (+62 -7)

boehnel 2008-10-06 22:26 #4 Rev.: 5521

added stats for long diffs

15 lines of code changed in 1 file:

• PROBE: probe.h (+15)

boehnel 2008-10-05 20:13 #3 Rev.: 5520

added some comments

added code to handle long diffs

46 lines of code changed in 1 file:

• PROBE: PT_prefixtree.cxx (+46 -14)

boehnel 2008-10-05 18:51 #2 Rev.: 5519

added some comments

7 lines of code changed in 1 file:

• PROBE: probe_tree.hxx (+7 -7)

boehnel 2008-10-01 23:35 #1 Rev.: 5518

added some comments...

9 lines of code changed in 2 files:

• PROBE: PT_prefixtree.cxx (+7 -7), probe_tree.hxx (+2 -2)

September 2008 »