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tille pushed a change to branch master
in repository hyphy.
from d48d988 Merge tag 'upstream/2.2.4+dfsg'
new 52eb267 Fix d/watch
new f517b2a Imported Upstream version 2.2.5+dfsg
new 631cadd Merge tag 'upstream/2.2.5+dfsg'
new d65b5ce New upstream release with fixed licenses
The 4 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 +-
debian/changelog | 4 +-
debian/watch | 2 +-
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 -
101 files changed, 3149 insertions(+), 2031 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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