This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository hyphy.
commit 631cadd83629d024b530aac7889d0cbf78bbc586 Merge: 52eb267 f517b2a Author: Andreas Tille <[email protected]> Date: Sat Jul 11 06:42:29 2015 +0200 Merge tag 'upstream/2.2.5+dfsg' Upstream version 2.2.5+dfsg LICENSE | 34 ++ 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, 3172 insertions(+), 2003 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/hyphy.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
