October 2008 Commit Log

Number of Commits:
48
Number of Active Developers:
4
boehnel 2008-10-31 23:23 Rev.: 5567

Added PTPan


1 lines of code changed in 1 file:

boehnel 2008-10-31 23:07

Adding PTPan

12654 lines of code changed in 28 files:

westram 2008-10-31 19:21 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:

arb_build 2008-10-30 15:53 Rev.: 5563

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

2 lines of code changed in 1 file:

westram 2008-10-30 15:49 Rev.: 5562


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

99 lines of code changed in 1 file:

westram 2008-10-30 02:45 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:

westram 2008-10-29 14:41 Rev.: 5560


libpng3 -> libpng12-0

1 lines of code changed in 1 file:

arb_build 2008-10-29 14:19 Rev.: 5559

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

2 lines of code changed in 1 file:

westram 2008-10-29 14:09 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:

westram 2008-10-24 16:23 Rev.: 5557


- updated packet list for openGL compile

35 lines of code changed in 1 file:

westram 2008-10-24 14:37 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:

westram 2008-10-23 13:43 Rev.: 5555

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

1 lines of code changed in 1 file:

arb_build 2008-10-23 13:27 Rev.: 5554

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

2 lines of code changed in 1 file:

westram 2008-10-23 13:27 Rev.: 5553

test (upgrade instantly)

2 lines of code changed in 1 file:

westram 2008-10-23 13:22 Rev.: 5552


syntax

2 lines of code changed in 1 file:

westram 2008-10-23 13:20 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:

arb_build 2008-10-23 12:49 Rev.: 5550

Auto version upgrade by devel@arb-home.de

2 lines of code changed in 1 file:

westram 2008-10-23 12:29 Rev.: 5549


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

36 lines of code changed in 1 file:

westram 2008-10-22 16:53 Rev.: 5548


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



10 lines of code changed in 1 file:

westram 2008-10-22 16:24 Rev.: 5547


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


3 lines of code changed in 1 file:

baderk 2008-10-22 15:11 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:

westram 2008-10-22 14:40 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:

westram 2008-10-22 14:15 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:

westram 2008-10-22 13:42 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:

westram 2008-10-22 13:27 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:

westram 2008-10-22 10:56 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:

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


- prototypes and dependencies updated

40 lines of code changed in 6 files:

westram 2008-10-22 10:38 Rev.: 5539


- corrected indented defines

3 lines of code changed in 1 file:

westram 2008-10-22 10:22 Rev.: 5538


erm.. + help

0 lines of code changed in 1 file:

westram 2008-10-22 10:21 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:

westram 2008-10-22 10:19 Rev.: 5536


- added item mode AWM_DISABLED (used for dynamic items)

12 lines of code changed in 1 file:

westram 2008-10-22 10:19 Rev.: 5535


- renamed search_executable into GB_executable (to make it public)

4 lines of code changed in 2 files:

westram 2008-10-22 09:26 Rev.: 5534


ignore subdir 'patches'

1 lines of code changed in 1 file:

westram 2008-10-22 09:10


TAB

4 lines of code changed in 2 files:

westram 2008-10-22 09:09 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:

westram 2008-10-16 12:44 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:

westram 2008-10-16 10:56 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:

boehnel 2008-10-14 04:35 Rev.: 5528

added some comments

added code for long diffs


31 lines of code changed in 1 file:

boehnel 2008-10-14 04:34 Rev.: 5527

added a comment

2 lines of code changed in 1 file:

boehnel 2008-10-14 04:29 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:

boehnel 2008-10-14 01:28 Rev.: 5525

0 -> NULL


89 lines of code changed in 4 files:

boehnel 2008-10-10 18:58 Rev.: 5524

added two assertions


2 lines of code changed in 1 file:

westram 2008-10-08 10:33 Rev.: 5523

5 lines of code changed in 1 file:

boehnel 2008-10-07 06:28 Rev.: 5522

added some comments

added code for long diffs


135 lines of code changed in 2 files:

boehnel 2008-10-06 23:26 Rev.: 5521

added stats for long diffs

15 lines of code changed in 1 file:

boehnel 2008-10-05 21:13 Rev.: 5520

added some comments

added code to handle long diffs

46 lines of code changed in 1 file:

boehnel 2008-10-05 19:51 Rev.: 5519

added some comments


7 lines of code changed in 1 file:

boehnel 2008-10-02 00:35 Rev.: 5518

added some comments...

9 lines of code changed in 2 files:

September 2008 »

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