April 2003 Commit Log

Number of Commits:
57
Number of Active Developers:
8
baderk 2003-04-30 18:14 Rev.: 1339

ca_probe.cxx modified - bugfix
KB

1 lines of code changed in 1 file:

westram 2003-04-30 17:27 Rev.: 1338

* EDIT4/ED4_root.cxx: - fixed a bug causing EDIT4 startup crash when alignment name
was longer than about 12 chars

19 lines of code changed in 1 file:

westram 2003-04-30 17:26 Rev.: 1337

- flushes stderr
- function for pointers XXX_DUMP_PTR

12 lines of code changed in 1 file:

westram 2003-04-30 17:23 Rev.: 1336

* Makefile: - DEVEL_XXX also defined in NDEBUG version
- DEVEL_ANY never defined

14 lines of code changed in 1 file:

westram 2003-04-30 11:10 Rev.: 1335

added BUGEX

1 lines of code changed in 1 file:

westram 2003-04-30 11:08 Rev.: 1334

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197 lines of code changed in 1 file:

baderk 2003-04-30 02:51 Rev.: 1333

einige updates an ca_probe (vermeidung fehlerhafter chars)
KB

32 lines of code changed in 1 file:

westram 2003-04-29 16:29 Rev.: 1332

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4 lines of code changed in 1 file:

thomasw 2003-04-29 16:22 Rev.: 1331

CHIP/ca_probe.cxx: probe_match sucht jetzt auch nach complement, WT

14 lines of code changed in 1 file:

foerster 2003-04-26 09:18 Rev.: 1330

last program .. back to the ARB-Databases
1. open final-candidates-paths-file (from ps_eval)
2. open temp output file
3. handle all candidates of ONE probe length each run
- for each candidate in source file that was handled yet -> store unchanged
- at first unhandled candidate
* remember probe length
* open the ARB-Database file that holds probes of that length
- for remaining unhandled candidates
* if probe length equals probe length of first unhandled candidate
-> look it up in ARB-DB
-> store with probe sequence data
* store other candidate unchanged

278 lines of code changed in 1 file:

foerster 2003-04-26 09:05 Rev.: 1329

added storing of used probe lengths
bug fix : forgot to invert path for 'inverse probes' before storing them to file

63 lines of code changed in 1 file:

foerster 2003-04-26 09:03 Rev.: 1328

new core program ps_get_probes

6 lines of code changed in 1 file:

foerster 2003-04-25 23:06 Rev.: 1327

1. get leaf nodes of candidates tree
2. examine paths from leaf candidates to root of candidates tree
- store PS_NodePtrs of candidates in a path that are no permutation of PS_NodePtrs of another path
3. examine the probes of the PS_Nodes of stored paths
- for each combination of the probes of the PS_Nodes in a path calculate the average probe temperature
- for each average probe temperature calculate the sum of square distances of probes temperatures for all combinations of probes of the PS_Nodes in a path
- find the path with the minimum of those sums and its associated average temperature
4. in the path with the minimum sum
- in each node remove all probes except the one that is closest to average temperature in the path with minimum sum and has the greatest length
5. for each PS_Candidate-node in path with minimum sum
- write the length and the GC-content of the probe of the PS_Node of the PS_Candidate
- write the set of SpeciesIDs that lead to PS_Node of the PS_Candidate

541 lines of code changed in 1 file:

foerster 2003-04-25 22:38 Rev.: 1326

*** empty log message ***

380 lines of code changed in 1 file:

foerster 2003-04-25 22:36 Rev.: 1325

new core program ps_eval_candidates.cxx

21 lines of code changed in 1 file:

foerster 2003-04-25 22:35 Rev.: 1324

hopefully last major changes

662 lines of code changed in 1 file:

foerster 2003-04-25 22:31 Rev.: 1323

renamed *Iterator to *Iter to match naming conventions

19 lines of code changed in 2 files:

foerster 2003-04-25 22:29 Rev.: 1322

new global variable __NODES_LEFT stores the count of nodes
to be examines per depth for depths < 60
used to visualize the process of PS_dect_weak_differences_stepdown

45 lines of code changed in 1 file:

foerster 2003-04-25 22:25 Rev.: 1321

fixed getSpeciesCount()

1 lines of code changed in 1 file:

foerster 2003-04-25 22:24 Rev.: 1320

new functions PS_BitMap_Counted::get(True|False)IndicesForRow()

fixed functions in PS_BitMap_Counted : set,get,setTrue,setFalse,recalcCounters
the diagonal locations are now accessible
recalcCounters doesnt count diagonal locations twice

28 lines of code changed in 1 file:

yadhu 2003-04-25 15:35 Rev.: 1319

*** empty log message ***

10 lines of code changed in 3 files:

westram 2003-04-25 15:16 Rev.: 1318

fixed bug which caused editor crash

7 lines of code changed in 2 files:

westram 2003-04-25 15:16 Rev.: 1317

* ED4_main.cxx: fixed malformed ED4_root ctor call

2 lines of code changed in 1 file:

richter 2003-04-25 14:55 Rev.: 1316

intro names adjusted

1 lines of code changed in 1 file:

baderk 2003-04-25 12:56 Rev.: 1315

ca_mark & ca_probe: corrected faulty EOF
KB

8 lines of code changed in 2 files:

westram 2003-04-25 09:50 Rev.: 1314

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7 lines of code changed in 2 files:

richter 2003-04-24 14:32 Rev.: 1313

latest version; aw_file_selection removed again, because it didn't work

11 lines of code changed in 1 file:

richter 2003-04-24 13:34 Rev.: 1312

import function: valid names file path now relative to $ARBHOME

12 lines of code changed in 1 file:

baderk 2003-04-22 23:02 Rev.: 1311

reworked version of ca_mark (now without compilation errors).
[baderk]

52 lines of code changed in 1 file:

westram 2003-04-22 17:19 Rev.: 1310

chip analyzer not build by make all

1 lines of code changed in 1 file:

westram 2003-04-22 17:16 Rev.: 1308

LIBLINK inserted as full path (prefixed with ARBHOME)

2 lines of code changed in 1 file:

westram 2003-04-22 17:15 Rev.: 1307

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2 lines of code changed in 1 file:

baderk 2003-04-22 16:48 Rev.: 1306

versuch von kai und wolfi

2 lines of code changed in 1 file:

baderk 2003-04-22 16:45 Rev.: 1305

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312 lines of code changed in 5 files:

yadhu 2003-04-16 13:07 Rev.: 1304

Description on using Visualise SAI function in Primary structure and Secondary structure editor windows.

5 lines of code changed in 1 file:

yadhu 2003-04-15 18:02 Rev.: 1303

Description on using Visualise SAI function in Primary structure and Secondary structure editor windows.

38 lines of code changed in 1 file:

yadhu 2003-04-15 17:54 Rev.: 1302

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1 lines of code changed in 1 file:

yadhu 2003-04-15 17:35 Rev.: 1301

*** empty log message ***

271 lines of code changed in 8 files:

foerster 2003-04-15 12:55 Rev.: 1300

* now uses PS_Candidate to build a tree of candidates
max depth of the tree depends on the number of species in the DB
* added functions to measure execution time

428 lines of code changed in 1 file:

foerster 2003-04-15 12:52 Rev.: 1299

new function getConstRootNode() .. const version of existing getRootNode()

106 lines of code changed in 2 files:

foerster 2003-04-15 12:50 Rev.: 1298

added functions to measure execution time

132 lines of code changed in 3 files:

foerster 2003-04-15 12:49 Rev.: 1297

removed comment on top

0 lines of code changed in 1 file:

foerster 2003-04-15 12:48 Rev.: 1296

testing of timing function

15 lines of code changed in 1 file:

westram 2003-04-10 14:42 Rev.: 1295

Enabled Valid-Names-Menu for NDEBUG version

1 lines of code changed in 1 file:

foerster 2003-04-10 09:17 Rev.: 1294

definition of a node for candidates to build a tree of candidates
PS_Candidate::addChild() is used to add a child (if child with same gain exists it is updated if the distance of new child is lower)
PS_Candidate::reduce() is used to ensure that a node has max. 3 childs (best/worst/middle gain)

114 lines of code changed in 1 file:

foerster 2003-04-10 09:15 Rev.: 1293

added ps_candidate.hxx to dependencies of ps_find_probes.cxx

1 lines of code changed in 1 file:

foerster 2003-04-10 09:14 Rev.: 1292

new functions: PS_Bit(Set|Map)::copy( PS_Bit(Set|Map)* ) : copy an existing Set|Map

121 lines of code changed in 2 files:

foerster 2003-04-10 09:12 Rev.: 1291

paths no longer begin with ID 0 but with the lowest ID that was found in the shortname-to-ID mapping

7 lines of code changed in 1 file:

foerster 2003-04-10 09:11 Rev.: 1290

new functions : (re)store_pos

18 lines of code changed in 1 file:

westram 2003-04-08 15:20 Rev.: 1289

changed remote shell to ssh

3 lines of code changed in 1 file:

richter 2003-04-08 13:20 Rev.: 1288

belogs to manual selection of valid name

25 lines of code changed in 1 file:

richter 2003-04-08 13:15 Rev.: 1287

path for names file changed

1 lines of code changed in 1 file:

richter 2003-04-08 13:13 Rev.: 1286

valid names file add

8474 lines of code changed in 1 file:

littschw 2003-04-08 12:33 Rev.: 1285

gene_probe linkeroptions modified

1 lines of code changed in 1 file:

spanfeln 2003-04-08 11:58 Rev.: 1284

added gene probe tool

11 lines of code changed in 1 file:

richter 2003-04-08 10:48 Rev.: 1283

first version of functional valid names tool finished

144 lines of code changed in 3 files:

yadhu 2003-04-01 18:16 Rev.: 1282

Added new feature to visualise sequence associated information (SAI) in
primary structure and secondary structure editors.

135 lines of code changed in 9 files:

March 2003 »

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