Directory src/dr/app/bss/

Total Files:
34
Deleted Files:
17
Lines of Code:
619

[root]/src/dr/app/bss
                    directory in repo icons (8 files, 0 lines)
                    directory in repo test (1 files, -5 lines)

Lines of Code

src/dr/app/bss/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 648 (100.0%) 20193 (100.0%) 31.1
fbielejec 645 (99.5%) 20184 (100.0%) 31.2
rambaut 3 (0.5%) 9 (0.0%) 3.0

Most Recent Commits

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

simulate under implemented models only

102 lines of code changed in 10 files:

  • src/dr/app/bss: MainFrame.java (new), PartitionData.java (+88 -64), PartitionDataList.java (new), TreesTableModel.java (+6 -2), Utils.java (new)
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

520 lines of code changed in 14 files:

  • 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 (+18 -14), TreesTableModel.java (+58 -27), Utils.java (+97 -65), XMLGenerator.java (new)
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 3 files:

  • src/dr/app/bss: AboutDialog.java (+12 -19), BeagleSequenceSimulatorApp.java (new)
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

39 lines of code changed in 5 files:

  • 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

8 lines of code changed in 1 file:

  • 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)
fbielejec 2013-04-11 00:13 Rev.: 5580

working on multiple partitions in CLI.

14 lines of code changed in 1 file:

  • src/dr/app/bss: BeagleSequenceSimulatorConsoleApp.java (+14 -7)
fbielejec 2013-04-11 00:02 Rev.: 5579

multiple partitions in CLI.

38 lines of code changed in 1 file:

  • src/dr/app/bss: BeagleSequenceSimulatorConsoleApp.java (+38 -41)
fbielejec 2013-04-10 23:39 Rev.: 5576

working on multiple partitions in CLI.

350 lines of code changed in 9 files:

  • src/dr/app/bss: BeagleSequenceSimulatorApp.java (+3 -6), BeagleSequenceSimulatorConsoleApp.java (+279 -208), PartitionData.java (+26 -27), PartitionTableModel.java (+22 -18), PartitionsPanel.java (new), README.textile (-2), Utils.java (+1 -1), XMLGenerator.java (+10 -5)
fbielejec 2013-04-09 00:37 Rev.: 5567

Parameter values in CLI.

185 lines of code changed in 2 files:

  • src/dr/app/bss: BeagleSequenceSimulatorConsoleApp.java (+183 -49), README.textile (+2 -3)
fbielejec 2013-03-28 23:48 Rev.: 5552

basic CLI options with some exception handling. Moving to parameter values.

208 lines of code changed in 5 files:

  • src/dr/app/bss: BeagleSequenceSimulatorConsoleApp.java (+203 -86), MainFrame.java (+1 -1), PartitionData.java (+1 -1), README.textile (+1), Utils.java (+2 -2)
fbielejec 2013-03-28 02:55

starting to implement CLI

201 lines of code changed in 5 files:

  • src/dr/app/bss: BeagleSequenceSimulatorApp.java (+7 -3), BeagleSequenceSimulatorConsoleApp.java (+187), MainFrame.java (+1 -69), PartitionData.java (+3 -3), README.textile (+3)
fbielejec 2013-03-26 02:24 Rev.: 5539

fixed small bug

24 lines of code changed in 7 files:

  • src/dr/app/bss: JTableButtonCellRenderer.java (new), PartitionDataList.java (+4 -2), README.textile (+2 -2), TreesPanel.java (+2), TreesTableModel.java (+11 -22), Utils.java (+3 -9)
fbielejec 2013-03-26 01:43 Rev.: 5538

loading saved data with new trees panel

135 lines of code changed in 17 files:

  • src/dr/app/bss: BeagleSequenceSimulatorApp.java (+1 -1), BranchSubstitutionModelEditor.java (-10), ClockRateModelEditor.java (+1 -2), ColumnResizer.java (new), JTableButtonCellRenderer.java (-1), MainFrame.java (+77 -215), PartitionDataList.java (+3 -5), PartitionTableModel.java (-11), PartitionsPanel.java (+1 -14), README.textile (+1 -1), SimulationPanel.java (+5 -131), TaxaTableModel.java (new), TreesPanel.java (+29 -10), TreesTableModel.java (+9 -23), XMLGenerator.java (-2)
fbielejec 2013-03-25 22:44 Rev.: 5537

update taxa column when data changes

51 lines of code changed in 4 files:

  • src/dr/app/bss: BeagleSequenceSimulatorApp.java (+11 -9), MainFrame.java (+1 -1), TreesTableModel.java (+22 -7), Utils.java (+17)
fbielejec 2013-03-25 11:37 Rev.: 5536

remove unwanted taxa when tree table changes

48 lines of code changed in 7 files:

  • src/dr/app/bss: MainFrame.java (+17 -18), PartitionData.java (+1 -3), PartitionDataList.java (+1 -6), README.textile (+1 -1), TreePanel.java (del), TreesPanel.java (-25), TreesTableModel.java (+28 -6)
fbielejec 2013-03-25 09:14 Rev.: 5535

some updates to UI

33 lines of code changed in 5 files:

  • src/dr/app/bss: PartitionDataList.java (+1 -1), TaxaPanel.java (-1), TreesPanel.java (+2), TreesTableModel.java (+30 -5)
fbielejec 2013-03-25 08:43 Rev.: 5534

new tree table

225 lines of code changed in 8 files:

  • src/dr/app/bss: MainFrame.java (+2 -2), PartitionDataList.java (+2 -2), TaxaPanel.java (+8), TaxaTableModel.java (+45 -21), TreePanel.java (new 52), TreesPanel.java (+51 -67), TreesTableModel.java (+39 -29), Utils.java (+26 -9)
fbielejec 2013-03-25 04:18 Rev.: 5533

labels on buttons

174 lines of code changed in 7 files:

  • src/dr/app/bss: JTableButtonCellRenderer.java (+42 -6), MainFrame.java (+4 -6), PartitionsPanel.java (+5 -108), TreePanel.java (+3 -2), TreesPanel.java (+27 -27), TreesTableModel.java (+92 -15), Utils.java (+1)
fbielejec 2013-03-23 04:03 Rev.: 5528

working on new trees panel

97 lines of code changed in 7 files:

  • src/dr/app/bss: MainFrame.java (-1), PartitionDataList.java (+2 -1), PartitionTableModel.java (+10 -10), PartitionsPanel.java (+2 -2), TreesPanel.java (+21 -19), TreesTableModel.java (+54 -38), Utils.java (+8)
fbielejec 2013-03-23 03:20 Rev.: 5527

improved rendering of tables

111 lines of code changed in 7 files:

  • src/dr/app/bss: MainFrame.java (+3), PartitionTableModel.java (+2 -1), PartitionsPanel.java (+33 -10), TaxaPanel.java (+20 -20), TaxaTableModel.java (+6 -3), TreesPanel.java (+41 -8), TreesTableModel.java (+6 -4)
fbielejec 2013-03-23 02:24 Rev.: 5525

working on new trees panel

498 lines of code changed in 11 files:

  • src/dr/app/bss: JTableButtonCellEditor.java (new 65), JTableButtonCellRenderer.java (+34), JTableButtonMouseListener.java (new 35), MainFrame.java (+5 -2), PartitionData.java (-1), PartitionDataList.java (+3), PartitionTableModel.java (+1 -1), PartitionsPanel.java (+104 -109), README.textile (+1 -3), TreesPanel.java (+128), TreesTableModel.java (+122)
fbielejec 2013-03-23 00:04 Rev.: 5524

reset idrefs after writing to XML

91 lines of code changed in 6 files:

  • src/dr/app/bss: MainFrame.java (+1 -4), PartitionData.java (+77 -41), PartitionDataList.java (+3 -2), README.textile (-1), Utils.java (+3 -1), XMLGenerator.java (+7)
fbielejec 2013-03-22 09:07 Rev.: 5522

removing siteCount from UI

24 lines of code changed in 3 files:

  • src/dr/app/bss: MainFrame.java (+18 -10), README.textile (+2 -5), XMLGenerator.java (+4 -6)
fbielejec 2013-03-22 00:33 Rev.: 5521

removing siteCount from UI

146 lines of code changed in 6 files:

  • src/dr/app/bss: MainFrame.java (+1 -2), PartitionData.java (+4), PartitionDataList.java (+1 -2), SimulationPanel.java (+7 -7), Utils.java (+12 -3), XMLGenerator.java (+121 -168)
fbielejec 2013-03-22 00:10 Rev.: 5519

no need for site count, this information can be parsed from partitions

11 lines of code changed in 2 files:

  • src/dr/app/bss: MainFrame.java (+6 -2), XMLGenerator.java (+5 -4)

(94 more)

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