|
|
|
@3649
|
[3649]
|
7 months |
pakanati |
fixed small bug in viewer where reactions had to ALL have resources or …
|
|
|
|
@3648
|
[3648]
|
7 months |
goingssh |
Added SetMigrant?() call to cell chosen for migration when using …
|
|
|
|
@3647
|
[3647]
|
7 months |
ruppmatt |
Updating to make cPopulation.h compatible with alice.
|
|
|
|
@3646
|
[3646]
|
7 months |
ruppmatt |
Fixed bug in InheritInstSet? code that would cause instructions to almost …
|
|
|
|
@3645
|
[3645]
|
7 months |
hjg |
Added support for an inject deme event that injects a deme with an …
|
|
|
|
@3644
|
[3644]
|
7 months |
ruppmatt |
Got deme scheduler working.
|
|
|
|
@3643
|
[3643]
|
7 months |
ruppmatt |
Removing unnecessary action fields.
|
|
|
|
@3642
|
[3642]
|
7 months |
dk |
bugfix: hgt fragment transformation was broken; added error checking on …
|
|
|
|
@3641
|
[3641]
|
7 months |
dk |
Added post-selection HGT fragment transformations.
|
|
|
|
@3640
|
[3640]
|
7 months |
ruppmatt |
Removed debug output.
|
|
|
|
@3639
|
[3639]
|
7 months |
ruppmatt |
Fixed bug with event parsing.
|
|
|
|
@3638
|
[3638]
|
7 months |
dk |
Added option to scramble HGT fragments prior to insertion or replacement.
|
|
|
|
@3637
|
[3637]
|
7 months |
ruppmatt |
Fixed bug to keep mutating inst set ids positive.
|
|
|
|
@3636
|
[3636]
|
7 months |
ruppmatt |
Bug fixes.
|
|
|
|
@3635
|
[3635]
|
7 months |
ruppmatt |
Updating to include some deme actions for altering instset id and print …
|
|
|
|
@3634
|
[3634]
|
7 months |
dk |
added missing include for std::random_shuffle.
|
|
|
|
@3633
|
[3633]
|
7 months |
dk |
Added print action to calculate average edit distance, enabled …
|
|
|
|
@3632
|
[3632]
|
7 months |
dk |
Added neighborhood-based HGT conjugation.
|
|
|
|
@3631
|
[3631]
|
7 months |
blwalker |
Hey, check it out, I fail at not deleting random sections of code. Fixed …
|
|
|
|
@3630
|
[3630]
|
7 months |
blwalker |
Fixed some comments. Clearly copy-paste had been abused…
|
|
|
|
@3629
|
[3629]
|
7 months |
dk |
Added hgt conjugation, refactored genome splitting.
|
|
|
|
@3628
|
[3628]
|
7 months |
ruppmatt |
Got EventTriggers? with state information using flex vars working.
|
|
|
|
@3627
|
[3627]
|
7 months |
ruppmatt |
Incremental update. Still fussing with triggerable events.
|
|
|
|
@3626
|
[3626]
|
7 months |
blwalker |
Moved lineage label to the last column of SaveStructuredPopulation? so it …
|
|
|
|
@3625
|
[3625]
|
7 months |
blwalker |
I ran the long tests and didn't even notice I'd broken this one. …
|
|
|
|
@3624
|
[3624]
|
7 months |
ruppmatt |
Incremental changes including addition of triggered event handling via …
|
|
|
|
@3623
|
[3623]
|
7 months |
blwalker |
Added "lineage" option to DETAIL documentation (the option was already …
|
|
|
|
@3622
|
[3622]
|
7 months |
dk |
Added HGT source option.
|
|
|
|
@3621
|
[3621]
|
7 months |
ruppmatt |
Incremental update to include deme actions, pre and post replacement …
|
|
|
|
@3620
|
[3620]
|
7 months |
ruppmatt |
Adding configuration options to handle additional schedulers.
|
|
|
|
@3619
|
[3619]
|
7 months |
ruppmatt |
Adding Art's deme-based schedulers.
|
|
|
|
@3618
|
[3618]
|
7 months |
beckma24 |
Rework of active messages. Active messages no longer casue interrupts. …
|
|
|
|
@3617
|
[3617]
|
7 months |
ruppmatt |
Updating to fix some bugs. Should be relatively stable now.
|
|
|
|
@3616
|
[3616]
|
8 months |
ruppmatt |
Adding missing files.
|
|
|
|
@3615
|
[3615]
|
8 months |
ruppmatt |
Done implementing deme manager structural changes. Still need to put some …
|
|
|
|
@3614
|
[3614]
|
8 months |
connel42 |
Fixed logic error in my MeanKill? event
|
|
|
|
@3613
|
[3613]
|
8 months |
covertar |
Short and long consitency tests for:
MIGRATION_RATE -- random migration …
|
|
|
|
@3612
|
[3612]
|
8 months |
ruppmatt |
Incomplete incremental update.
|
|
|
|
@3611
|
[3611]
|
8 months |
covertar |
Added consistency test for replace deleterious.
|
|
|
|
@3610
|
[3610]
|
8 months |
ruppmatt |
Incremental update-- with a number of problems fixed.
|
|
|
|
@3609
|
[3609]
|
8 months |
pakanati |
population = dead (mostly). topology = mess …
|
|
|
|
@3608
|
[3608]
|
8 months |
pakanati |
nearly done liquidating cPopulation, a commit before trying to kill it …
|
|
|
|
@3607
|
[3607]
|
8 months |
pakanati |
pre-cell array movage, post other stuff breakage
|
|
|
|
@3606
|
[3606]
|
8 months |
baerb |
Finished first draft of the Text-View Documentation
|
|
|
|
@3605
|
[3605]
|
8 months |
ruppmatt |
Incremental update to handle deme manager modifications.
|
|
|
|
@3604
|
[3604]
|
8 months |
baerb |
Update of the text viewer documentation. Corrected errors in the text, …
|
|
|
|
@3603
|
[3603]
|
8 months |
ruppmatt |
Renaming a cpp to cc file.
|
|
|
|
@3602
|
[3602]
|
8 months |
ruppmatt |
Renaming a cpp to cc file.
|
|
|
|
@3601
|
[3601]
|
8 months |
ruppmatt |
Updating to include a deme manager for my own sanity.
|
|
|
|
@3600
|
[3600]
|
8 months |
baerb |
Started translating the text view manual from Chri Adami's Alife to …
|
|
|
|
@3599
|
[3599]
|
8 months |
pakanati |
working version, flipped topologymanager and population objects
|
|
|
|
@3598
|
[3598]
|
8 months |
goingssh |
updated reset function so doesn't reset parent rewards, only model stuff
|
|
|
|
@3597
|
[3597]
|
8 months |
goingssh |
last few changes to reset models for each org
|
|
|
|
@3596
|
[3596]
|
8 months |
goingssh |
more updates
|
|
|
|
@3595
|
[3595]
|
8 months |
goingssh |
New UML stuff
|
|
|
|
@3594
|
[3594]
|
8 months |
beckma24 |
Enhanced interrupt.dat
|
|
|
|
@3593
|
[3593]
|
8 months |
ruppmatt |
Added ability to calculate most likely genotype merit via test CPU …
|
|
|
|
@3592
|
[3592]
|
8 months |
ruppmatt |
Updated inst set redundancy print actions to handle situations when …
|
|
|
|
@3591
|
[3591]
|
8 months |
ruppmatt |
Updated branch to allow for maximally fit ancestor comparisons for …
|
|
|
|
@3590
|
[3590]
|
8 months |
beckma24 |
Push data of message being sent into organism's output buffer so that …
|
|
|
|
@3589
|
[3589]
|
8 months |
beckma24 |
Sending a message is an output, so call to DoOutput? method has be …
|
|
|
|
@3588
|
[3588]
|
8 months |
ruppmatt |
Added instset redundancy dump print actions.
|
|
|
|
@3587
|
[3587]
|
8 months |
blwalker |
Make destroy instruction actually destroy resources.
|
|
|
|
@3586
|
[3586]
|
8 months |
ruppmatt |
Done with initial implementation of inherited instruction sets. Memory …
|
|
|
|
@3585
|
[3585]
|
8 months |
ruppmatt |
Changing filename from cpp to cc.
|
|
|
|
@3584
|
[3584]
|
8 months |
ruppmatt |
Fixing some casting issues.
|
|
|
|
@3583
|
[3583]
|
8 months |
ruppmatt |
Added backend inheritence functionality.
|
|
|
|
@3582
|
[3582]
|
8 months |
beckma24 |
Added a few more message types, 6 total. Fixed …
|
|
|
|
@3581
|
[3581]
|
8 months |
beckma24 |
Active messages can now trigger thread-based interrupts. Interrupts …
|
|
|
|
@3580
|
[3580]
|
8 months |
beckma24 |
Added instructions and config options for thread-centric version of the …
|
|
|
|
@3579
|
[3579]
|
9 months |
pakanati |
inline problem
|
|
|
|
@3578
|
[3578]
|
9 months |
jbarrick |
New BASE_MERIT_METHOD 7 = assign merit from gestation time. Fixed …
|
|
|
|
@3577
|
[3577]
|
9 months |
beckma24 |
Added cHardwareCPU::InterruptThread? that is called to start an interrupt.
|
|
|
|
@3576
|
[3576]
|
9 months |
beckma24 |
Initial step toward incorporating active messages and interrupts. Added …
|
|
|
|
@3575
|
[3575]
|
9 months |
brysonda |
Add stub files for cBGSpecies and cBGSpeciesManager classes.
Add interface …
|
|
|
|
@3574
|
[3574]
|
9 months |
brysonda |
Begin the work of excising the old cGenotype class.
|
|
|
|
@3573
|
[3573]
|
9 months |
connel42 |
Changed some stats associated to organism kill events. Removed …
|
|
|
|
@3572
|
[3572]
|
9 months |
brysonda |
Properly initialize parasite generation in cParasite's cPhenotype object. …
|
|
|
|
@3571
|
[3571]
|
9 months |
brysonda |
Update CMakeLists.txt to support new BioGroup? classes.
|
|
|
|
@3570
|
[3570]
|
9 months |
brysonda |
Parasite genotypes are now output by SaveStructuredPopulationBG.
Enhance …
|
|
|
|
@3569
|
[3569]
|
9 months |
goingssh |
Added reaction requesite for total number of reactions completed (max and …
|
|
|
|
@3568
|
[3568]
|
9 months |
brysonda |
Properly verify parasite target organism hardware type and instruction …
|
|
|
|
@3567
|
[3567]
|
9 months |
brysonda |
Clean up a couple of todo items.
|
|
|
|
@3566
|
[3566]
|
9 months |
brysonda |
Parasites should now be properly tracked via biogroup based genotypes.
|
|
|
|
@3565
|
[3565]
|
9 months |
connel42 |
Added additional kill event that looks at the mean resource levels
|
|
|
|
@3564
|
[3564]
|
9 months |
brysonda |
Work towards biounit based tracking of parasite genotypes. This is …
|
|
|
|
@3563
|
[3563]
|
9 months |
brysonda |
Add new tBufferedList class to the tools. This class functions similar …
|
|
|
|
@3562
|
[3562]
|
9 months |
brysonda |
Remove defunct developers branch holding directory.
|
|
|
|
@3561
|
[3561]
|
9 months |
brysonda |
Move Avida-ED branch to the top level of the repository.
|
|
|
|
@3560
|
[3560]
|
9 months |
brysonda |
Alter svn properties inherited from branches/parasites to be generic.
|
|
|
|
@3559
|
[3559]
|
9 months |
brysonda |
Merge r3507:3558 from branches/parasites into branches/biounit. Includes …
|
|
|
|
@3558
|
[3558]
|
9 months |
brysonda |
Merge r3507:3557 from development into branches/parasites
|
|
|
|
@3557
|
[3557]
|
9 months |
zaman |
added option to kill host
|
|
|
|
@3556
|
[3556]
|
9 months |
dk |
HGT refactoring.
|
|
|
|
@3555
|
[3555]
|
9 months |
brysonda |
Merge r3501:3554 from development into branches/biounit
|
|
|
|
@3554
|
[3554]
|
9 months |
brysonda |
Add generation born tracking to cBGGenotype. Output genotype source. …
|
|
|
|
@3553
|
[3553]
|
9 months |
beckma24 |
Added event KillWithinRadiusBelowResourceThresholdTestAll?
|
|
|
|
@3552
|
[3552]
|
9 months |
brysonda |
Active and passive reference counting fixes. Size parameter passing to …
|
|
|
|
@3551
|
[3551]
|
9 months |
brysonda |
Add basic support for saving bio group based genotypes.
|
|
|
|
@3550
|
[3550]
|
9 months |
brysonda |
cBGGenotypeManager coalescent and best handling.
|
|
|
|
