/trunk Developers: foerster

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foerster 2003-04-26 10:18 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:

• PROBE_SET: ps_get_probes.cxx (new 278)

foerster 2003-04-26 10:05 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:

• PROBE_SET: ps_eval_candidates.cxx (+63 -14)

foerster 2003-04-26 10:03 Rev.: 1328

new core program ps_get_probes

6 lines of code changed in 1 file:

• PROBE_SET: Makefile (+6)

foerster 2003-04-26 00:06 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:

• PROBE_SET: ps_eval_candidates.cxx (new 541)

foerster 2003-04-25 23:38 Rev.: 1326

*** empty log message ***

380 lines of code changed in 1 file:

• PROBE_SET: ps_candidate.hxx (+380 -50)

foerster 2003-04-25 23:36 Rev.: 1325

new core program ps_eval_candidates.cxx

21 lines of code changed in 1 file:

• PROBE_SET: Makefile (+21 -9)

foerster 2003-04-25 23:35 Rev.: 1324

hopefully last major changes

662 lines of code changed in 1 file:

• PROBE_SET: ps_find_probes.cxx (+662 -132)

foerster 2003-04-25 23:31 Rev.: 1323

renamed *Iterator to *Iter to match naming conventions

19 lines of code changed in 2 files:

• PROBE_SET: ps_node.cxx (+2 -2), ps_node.hxx (+17 -18)

foerster 2003-04-25 23:29 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:

• PROBE_SET: ps_detect_weak_differences.cxx (+45 -20)

foerster 2003-04-25 23:25 Rev.: 1321

fixed getSpeciesCount()

1 lines of code changed in 1 file:

• PROBE_SET: ps_database.hxx (+1 -1)

foerster 2003-04-25 23:24 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:

• PROBE_SET: ps_bitmap.hxx (+28 -6)

foerster 2003-04-15 13:55 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:

• PROBE_SET: ps_find_probes.cxx (+428 -177)

foerster 2003-04-15 13:52 Rev.: 1299

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

106 lines of code changed in 2 files:

• PROBE_SET: ps_candidate.hxx (+103 -32), ps_database.hxx (+3)

foerster 2003-04-15 13:50 Rev.: 1298

added functions to measure execution time

132 lines of code changed in 3 files:

• PROBE_SET: ps_convert_db.cxx (+55 -6), ps_detect_weak_differences.cxx (+44 -5), ps_merge_my_dbs.cxx (+33 -2)

foerster 2003-04-15 13:49 Rev.: 1297

removed comment on top

0 lines of code changed in 1 file:

• PROBE_SET: ps_node.cxx (-12)

foerster 2003-04-15 13:48 Rev.: 1296

testing of timing function

15 lines of code changed in 1 file:

• PROBE_SET: fb_test.cxx (+15 -1)

foerster 2003-04-10 10:17 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:

• PROBE_SET: ps_candidate.hxx (new 114)

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

added ps_candidate.hxx to dependencies of ps_find_probes.cxx

1 lines of code changed in 1 file:

• PROBE_SET: Makefile (+1)

foerster 2003-04-10 10:14 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:

• PROBE_SET: ps_bitmap.hxx (+77), ps_bitset.hxx (+44 -2)

foerster 2003-04-10 10:12 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:

• PROBE_SET: ps_convert_db.cxx (+7 -3)

(58 more)