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tille pushed a change to branch upstream
in repository hyphy.
from 248b8de Imported Upstream version 2.2.4+dfsg
new f517b2a Imported Upstream version 2.2.5+dfsg
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
src/gui/qt/include/hyphymessageoutput.h => LICENSE | 33 +-
res/TemplateBatchFiles/GARDProcessor.bf | 26 +-
res/TemplateBatchFiles/lib2014/IOFunctions.bf | 47 ++
res/TemplateBatchFiles/lib2014/UtilityFunctions.bf | 28 +-
res/TemplateBatchFiles/lib2014/models/DNA/GTR.bf | 3 +-
.../lib2014/models/frequencies.bf | 43 +-
.../lib2014/models/model_functions.bf | 12 +-
.../lib2014/models/parameters.bf | 9 +-
.../lib2014/models/rate_variation.bf | 98 ++++
res/TemplateBatchFiles/lib2014/models/terms.bf | 5 +
res/TemplateBatchFiles/lib2014/tasks/estimators.bf | 78 ++-
src/core/_hyExecutionContext.cpp | 64 ++-
src/core/alignment.cpp | 38 ++
src/core/avllist.cpp | 67 ++-
src/core/avllistx.cpp | 67 ++-
src/core/avllistxl.cpp | 67 ++-
src/core/baseobj.cpp | 69 +--
src/core/batchlan.cpp | 28 +-
src/core/batchlan2.cpp | 34 --
src/core/calcnode.cpp | 85 +--
src/core/calcnode2.cpp | 40 +-
src/core/category.cpp | 64 ++-
src/core/error.cpp | 64 ++-
src/core/formula.cpp | 40 +-
src/core/include/alignment.h | 38 ++
src/core/include/batchlan.h | 2 -
src/core/include/mypthread.h | 2 +-
src/core/likefunc.cpp | 110 +++-
src/core/list.cpp | 67 ++-
src/core/mathobj.cpp | 39 ++
src/core/matrix.cpp | 64 ++-
src/core/nexus.cpp | 63 ++-
src/core/parser.cpp | 64 ++-
src/core/parser2.cpp | 64 ++-
src/core/polynoml.cpp | 64 ++-
src/core/sequence.cpp | 64 ++-
src/core/simplelist.cpp | 65 ++-
src/core/site.cpp | 64 ++-
src/core/strings.cpp | 65 ++-
src/gui/Components/HYButton.cpp | 2 +-
src/gui/Components/HYButtonBar.cpp | 43 +-
src/gui/Components/HYCheckBox.cpp | 2 +-
src/gui/Components/HYLabel.cpp | 2 +-
src/gui/Components/HYPullDown.cpp | 43 +-
src/gui/Components/HYSequencePanel.cpp | 43 +-
src/gui/Components/HYTable.cpp | 2 +-
src/gui/Components/HYTextBox.cpp | 2 +-
src/gui/gtk/Components/HYPlatformButton.cpp | 41 +-
src/gui/gtk/Components/HYPlatformButtonBar.cpp | 43 +-
src/gui/gtk/Components/HYPlatformCheckBox.cpp | 43 +-
src/gui/gtk/Components/HYPlatformLabel.cpp | 43 +-
src/gui/gtk/Components/HYPlatformPullDown.cpp | 43 +-
src/gui/gtk/Components/HYPlatformSequencePane.cpp | 43 +-
src/gui/gtk/Components/HYPlatformTable.cpp | 43 +-
src/gui/gtk/Components/HYPlatformTextBox.cpp | 43 +-
src/gui/gtk/HYPlatformComponent.cpp | 40 ++
src/gui/gtk/HYPlatformGraphicPane.cpp | 42 +-
src/gui/gtk/HYPlatformUtils.cpp | 40 ++
src/gui/gtk/HYPlatformWindow.cpp | 42 +-
.../gtk/WindowClasses/HYPlatformBootsrapWindow.cpp | 41 +-
.../gtk/WindowClasses/HYPlatformChartWindow.cpp | 41 +-
.../gtk/WindowClasses/HYPlatformConsoleWindow.cpp | 39 ++
src/gui/gtk/WindowClasses/HYPlatformDBWindow.cpp | 2 +-
src/gui/gtk/WindowClasses/HYPlatformDataPanel.cpp | 42 +-
src/gui/gtk/WindowClasses/HYPlatformGWindow.cpp | 42 +-
.../gtk/WindowClasses/HYPlatformModelWindow.cpp | 42 +-
src/gui/gtk/WindowClasses/HYPlatformPWindow.cpp | 42 +-
.../gtk/WindowClasses/HYPlatformParameterTable.cpp | 42 +-
src/gui/gtk/WindowClasses/HYPlatformTWindow.cpp | 42 +-
src/gui/gtk/WindowClasses/HYPlatformTreePanel.cpp | 42 +-
src/gui/gtk/include/Components/HYPlatformButton.h | 43 +-
.../gtk/include/Components/HYPlatformButtonBar.h | 43 +-
.../gtk/include/Components/HYPlatformCheckbox.h | 43 +-
src/gui/gtk/include/Components/HYPlatformLabel.h | 43 +-
.../gtk/include/Components/HYPlatformPullDown.h | 43 +-
src/gui/gtk/include/Components/HYPlatformTable.h | 43 +-
src/gui/gtk/include/Components/HYPlatformTextbox.h | 43 +-
src/gui/gtk/include/HYPlatformComponent.h | 43 +-
src/gui/gtk/include/HYPlatformGraphicPane.h | 43 +-
src/gui/gtk/include/HYPlatformWindow.h | 42 +-
src/gui/preferences.cpp | 71 +--
src/mains/mac.cpp | 64 ++-
src/new/HYNetInterface.cpp | 375 -------------
src/new/Net.cpp | 606 ---------------------
src/new/bgm.cpp | 68 +--
src/new/bgm2.cpp | 42 +-
src/new/include/HYNetInterface.h | 40 --
src/new/include/SerangNet.h | 95 ----
src/new/include/bgm.h | 43 +-
src/new/include/scfg.h | 44 +-
src/new/scfg.cpp | 42 +-
src/ocl/opencl_kernels.cl | 40 ++
src/utils/hyphyunixutils.cpp | 39 ++
tests/gtests/ut_avllists.cpp | 42 +-
tests/gtests/ut_list.cpp | 41 +-
tests/gtests/ut_simplelists.cpp | 42 +-
tests/gtests/ut_strings.cpp | 42 +-
tests/hbltests/SimpleOptimizations/SmallCodon.bf | 2 +
.../hbltests/UnitTests/HBLCommands/AllCommands.bf | 1 -
99 files changed, 3146 insertions(+), 2028 deletions(-)
copy src/gui/qt/include/hyphymessageoutput.h => LICENSE (70%)
create mode 100644 res/TemplateBatchFiles/lib2014/models/rate_variation.bf
delete mode 100644 src/new/HYNetInterface.cpp
delete mode 100644 src/new/Net.cpp
delete mode 100644 src/new/include/HYNetInterface.h
delete mode 100644 src/new/include/SerangNet.h
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