/trunk Developers: fbielejec

Login name:
fbielejec
Total Commits:
952 (4.0%)
Lines of Code:
31,740 (2.8%)
Most Recent Commit:
2013-05-07 02:44
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Activity in Directories

Directory Changes Lines of Code Lines per Change
Totals 952 (100.0%) 31740 (100.0%) 33.3
src/dr/app/bss/ 645 (67.8%) 20184 (63.6%) 31.2
src/dr/app/beagle/tools/ 91 (9.6%) 4981 (15.7%) 54.7
src/dr/app/beagle/evomodel/sitemodel/ 49 (5.1%) 2805 (8.8%) 57.2
src/dr/app/beauti/siteModelsPanel/ 7 (0.7%) 809 (2.5%) 115.5
src/dr/app/beagle/tools/parsers/ 35 (3.7%) 541 (1.7%) 15.4
src/dr/app/beauti/components/dnds/ 11 (1.2%) 480 (1.5%) 43.6
/ 11 (1.2%) 462 (1.5%) 42.0
src/dr/app/bss/test/ 8 (0.8%) 446 (1.4%) 55.7
src/dr/app/beagle/evomodel/parsers/ 22 (2.3%) 313 (1.0%) 14.2
src/dr/app/beagle/evomodel/treelikelihood/ 15 (1.6%) 300 (0.9%) 20.0
src/dr/app/beauti/generator/ 9 (0.9%) 159 (0.5%) 17.6
src/dr/app/seqgen/ 4 (0.4%) 101 (0.3%) 25.2
src/dr/app/beauti/util/ 1 (0.1%) 53 (0.2%) 53.0
src/dr/evomodel/substmodel/ 2 (0.2%) 31 (0.1%) 15.5
src/dr/app/beauti/components/ancestralstates/ 3 (0.3%) 23 (0.1%) 7.6
src/dr/evolution/alignment/ 6 (0.6%) 17 (0.1%) 2.8
src/dr/app/beast/ 6 (0.6%) 13 (0.0%) 2.1
src/dr/app/tools/ 2 (0.2%) 6 (0.0%) 3.0
src/dr/evolution/util/ 2 (0.2%) 5 (0.0%) 2.5
src/dr/app/beagle/evomodel/branchmodel/ 2 (0.2%) 4 (0.0%) 2.0
src/dr/app/beauti/ancestralStatesPanel/ 1 (0.1%) 3 (0.0%) 3.0
src/dr/evoxml/ 1 (0.1%) 1 (0.0%) 1.0
src/dr/evomodelxml/treelikelihood/ 1 (0.1%) 1 (0.0%) 1.0
src/dr/evomodel/coalescent/ 1 (0.1%) 1 (0.0%) 1.0
src/dr/app/beagle/evomodel/substmodel/ 1 (0.1%) 1 (0.0%) 1.0
src/dr/app/bss/icons/ 12 (1.3%) 0 (0.0%) 0.0
lib/ 4 (0.4%) 0 (0.0%) 0.0

Activity of fbielejec

Most Recent Commits

fbielejec 2013-05-07 02:44 Rev.: 5634

simulate under implemented models only

102 lines of code changed in 12 files:

  • src/dr/app/bss: MainFrame.java (new), PartitionData.java (+88 -64), PartitionDataList.java (new), TreesTableModel.java (+6 -2), Utils.java (new)
  • src/dr/app/bss/test: BeagleSeqSimTest.java (-5)
fbielejec 2013-05-07 01:46 Rev.: 5633

create demo models

48 lines of code changed in 1 file:

  • src/dr/app/bss: PartitionData.java (+48 -68)
fbielejec 2013-05-07 01:06 Rev.: 5632

adding demography models

879 lines of code changed in 18 files:

  • src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+4 -390)
  • src/dr/app/bss: AboutDialog.java (+8 -1), BeagleSequenceSimulatorConsoleApp.java (+1 -1), DemographicModelEditor.java (new 161), PartitionData.java (+163 -8), PartitionTableModel.java (+11 -11), TreesPanel.java (new), TreesTableModel.java (+58 -27), Utils.java (+97 -65), XMLGenerator.java (new)
  • src/dr/app/bss/test: BeagleSeqSimTest.java (+355), Test.java (del)
fbielejec 2013-04-26 04:45 Rev.: 5613

static access to indices

14 lines of code changed in 9 files:

  • src/dr/app/bss: BeagleSequenceSimulatorConsoleApp.java (+4 -4), BranchSubstitutionModelEditor.java (+2 -2), ClockRateModelEditor.java (+2 -2), PartitionData.java (+2 -2), README.textile (new), Utils.java (+4 -4)
fbielejec 2013-04-26 04:42 Rev.: 5612

checks on values

81 lines of code changed in 11 files:

  • src/dr/app/bss: BeagleSequenceSimulatorConsoleApp.java (+2 -2), BranchSubstitutionModelEditor.java (+1 -1), ClockRateModelEditor.java (+43 -1), FrequencyModelEditor.java (+2 -1), PartitionData.java (+2 -3), README.textile (+2 -4), SiteRateModelEditor.java (+23 -4), TreesTableModel.java (+4 -4), Utils.java (+2 -2)
fbielejec 2013-04-25 22:57 Rev.: 5611

gamma + inv

21 lines of code changed in 4 files:

  • src/dr/app/bss: PartitionData.java (+11 -7), PartitionDataList.java (+2 -2), README.textile (-1), XMLGenerator.java (+8)
fbielejec 2013-04-25 03:39 Rev.: 5609

new icon

13 lines of code changed in 5 files:

  • src/dr/app/bss: AboutDialog.java (+12 -19), BeagleSequenceSimulatorApp.java (new)
  • src/dr/app/bss/icons: biohazard.png (changed)
fbielejec 2013-04-25 03:33 Rev.: 5608

use those icons

56 lines of code changed in 13 files:

  • src/dr/app/bss: AboutDialog.java (+1 -1), BeagleSequenceSimulatorApp.java (+2 -41), BranchSubstitutionModelEditor.java (+2 -2), ClockRateModelEditor.java (+2 -2), DefaultFileMenuFactory.java (+6 -6), ExceptionHandler.java (new), FrequencyModelEditor.java (+2 -2), SimulationPanel.java (new), SiteRateModelEditor.java (+2 -2), Utils.java (+36 -5)
fbielejec 2013-04-25 02:59 Rev.: 5607

take max TO value as site count to avoid exceptions being thrown

53 lines of code changed in 8 files:

  • src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+14 -6), Partition.java (-2)
  • src/dr/app/bss: BeagleSequenceSimulatorConsoleApp.java (+1 -2), MainFrame.java (+18 -14), PartitionTableModel.java (+8 -9), TreesPanel.java (-2), Utils.java (+12 -21)
fbielejec 2013-04-24 21:29 Rev.: 5606

bug fixes in codon model XML generation

15 lines of code changed in 3 files:

  • src/dr/app/bss: README.textile (+9 -9), Utils.java (+1), XMLGenerator.java (+5 -7)
fbielejec 2013-04-20 02:21 Rev.: 5601

updated buildfile

12 lines of code changed in 4 files:

  • build_bss.xml (+2)
  • src/dr/app/beagle/tools: BeagleSequenceSimulator.java (+2 -2)
  • src/dr/app/bss: README.textile (+8 -2)
fbielejec 2013-04-18 22:28 Rev.: 5596

added inverse gaussian clock and offset parameters to relaxed clocks. Still needs to be tested

92 lines of code changed in 3 files:

  • src/dr/app/bss: BeagleSequenceSimulatorConsoleApp.java (+20 -4), PartitionData.java (+17 -56), XMLGenerator.java (+55 -5)
fbielejec 2013-04-17 02:41 Rev.: 5593

Inverse gaussian model in UI. Need to implement XML and command line options

28 lines of code changed in 2 files:

  • src/dr/app/bss: BeagleSequenceSimulatorConsoleApp.java (-1), PartitionData.java (+28 -5)
fbielejec 2013-04-13 01:48 Rev.: 5588

help menu about dialog

42 lines of code changed in 4 files:

  • src/dr/app/bss: AboutDialog.java (+2 -2), DefaultHelpMenuFactory.java (+40 -12), README.textile (-1)
fbielejec 2013-04-13 01:37 Rev.: 5587

help menu

317 lines of code changed in 8 files:

  • src/dr/app/bss: AboutDialog.java (+257), BeagleSequenceSimulatorApp.java (+8 -4), DefaultHelpMenuFactory.java (+36 -11), MenuBarFactory.java (new), SimulationPanel.java (+1 -1), Utils.java (+14), XMLGenerator.java (+1 -1)
fbielejec 2013-04-12 21:03 Rev.: 5585

custom edit menu

91 lines of code changed in 4 files:

  • src/dr/app/bss: BeagleSequenceSimulatorApp.java (+3 -4), DefaultEditMenuFactory.java (new 59), DefaultHelpMenuFactory.java (+28), MenuBarFactory.java (+1 -1)
fbielejec 2013-04-12 20:33 Rev.: 5584

custom edit menu

4 lines of code changed in 4 files:

  • src/dr/app/bss: BeagleSequenceSimulatorApp.java (+1 -1), MenuBarFactory.java (+1 -1), README.textile (+1 -1), SimulationPanel.java (+1 -1)
fbielejec 2013-04-12 04:18 Rev.: 5583

fixed small bug in XML generator

13 lines of code changed in 2 files:

  • src/dr/app/bss: README.textile (+11 -5), XMLGenerator.java (+2 -2)
fbielejec 2013-04-12 03:18 Rev.: 5582

seed setting in CLI

21 lines of code changed in 1 file:

  • src/dr/app/bss: BeagleSequenceSimulatorConsoleApp.java (+21 -9)
fbielejec 2013-04-11 22:59 Rev.: 5581

seed setting in UI

72 lines of code changed in 6 files:

  • src/dr/app/bss: BeagleSequenceSimulatorConsoleApp.java (+5 -1), MainFrame.java (+10 -1), PartitionDataList.java (+7), README.textile (+1 -1), SimulationPanel.java (+39 -5), Utils.java (+10 -1)

(270 more)

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