├── README ├── .gitignore ├── doc ├── html │ ├── bc_s.png │ ├── bdwn.png │ ├── open.png │ ├── closed.png │ ├── ftv2cl.png │ ├── ftv2mo.png │ ├── ftv2ns.png │ ├── nav_f.png │ ├── nav_g.png │ ├── nav_h.png │ ├── tab_a.png │ ├── tab_b.png │ ├── tab_h.png │ ├── tab_s.png │ ├── doxygen.png │ ├── ftv2blank.png │ ├── ftv2doc.png │ ├── ftv2link.png │ ├── ftv2mnode.png │ ├── ftv2node.png │ ├── ftv2pnode.png │ ├── sync_off.png │ ├── sync_on.png │ ├── ftv2folderopen.png │ ├── ftv2lastnode.png │ ├── ftv2mlastnode.png │ ├── ftv2plastnode.png │ ├── ftv2splitbar.png │ ├── ftv2vertline.png │ ├── search │ │ ├── close.png │ │ ├── mag_sel.png │ │ ├── search_l.png │ │ ├── search_m.png │ │ ├── search_r.png │ │ ├── pages_69.js │ │ ├── pages_6d.js │ │ ├── files_6d.js │ │ ├── classes_6.js │ │ ├── classes_72.js │ │ ├── files_3.js │ │ ├── classes_4.js │ │ ├── pages_0.js │ │ ├── classes_63.js │ │ ├── classes_6c.js │ │ ├── classes_5.js │ │ ├── classes_66.js │ │ ├── classes_6e.js │ │ ├── classes_70.js │ │ ├── pages_1.js │ │ ├── pages_73.js │ │ ├── classes_0.js │ │ ├── classes_6d.js │ │ ├── classes_61.js │ │ ├── functions_7.js │ │ ├── classes_75.js │ │ ├── defines_2.js │ │ ├── defines_6f.js │ │ ├── defines_1.js │ │ ├── defines_6d.js │ │ ├── defines_0.js │ │ ├── defines_62.js │ │ ├── functions_4.js │ │ ├── files_0.js │ │ ├── files_61.js │ │ ├── functions_66.js │ │ ├── variables_73.js │ │ ├── variables_2.js │ │ ├── variables_7.js │ │ ├── variables_66.js │ │ ├── variables_72.js │ │ ├── files_1.js │ │ ├── files_65.js │ │ ├── files_2.js │ │ ├── files_67.js │ │ ├── classes_2.js │ │ ├── classes_65.js │ │ ├── classes_3.js │ │ ├── classes_67.js │ │ ├── functions_8.js │ │ ├── functions_6d.js │ │ ├── variables_4.js │ │ ├── all_5.js │ │ ├── variables_3.js │ │ ├── variables_1.js │ │ ├── variables_69.js │ │ ├── variables_6c.js │ │ ├── all_66.js │ │ ├── files_74.js │ │ ├── variables_63.js │ │ ├── variables_5.js │ │ ├── variables_6f.js │ │ ├── all_13.js │ │ ├── functions_12.js │ │ ├── all_7e.js │ │ ├── functions_7e.js │ │ ├── all_6c.js │ │ ├── files_5.js │ │ ├── all_9.js │ │ ├── all_6d.js │ │ ├── variables_6.js │ │ ├── classes_5f.js │ │ ├── classes_8.js │ │ ├── variables_70.js │ │ ├── classes_74.js │ │ ├── functions_9.js │ │ ├── all_8.js │ │ ├── functions_6e.js │ │ ├── nomatches.html │ │ ├── all_71.js │ │ ├── all_d.js │ │ ├── functions_c.js │ │ ├── functions_71.js │ │ ├── all_12.js │ │ ├── functions_11.js │ │ ├── all_76.js │ │ ├── functions_76.js │ │ ├── all_a.js │ │ ├── all_6e.js │ │ ├── functions_3.js │ │ ├── functions_65.js │ │ ├── classes_1.js │ │ ├── files_4.js │ │ ├── files_73.js │ │ ├── classes_7.js │ │ ├── functions_6.js │ │ ├── functions_d.js │ │ ├── functions_72.js │ │ ├── functions_1.js │ │ ├── functions_69.js │ │ ├── classes_73.js │ │ ├── functions_62.js │ │ ├── all_2.js │ │ ├── all_62.js │ │ ├── functions_a.js │ │ ├── functions_6f.js │ │ ├── all_4.js │ │ ├── all_72.js │ │ ├── all_65.js │ │ ├── all_7.js │ │ ├── all_e.js │ │ ├── all_69.js │ │ ├── all_0.html │ │ ├── all_1.html │ │ ├── all_10.html │ │ ├── all_11.html │ │ ├── all_12.html │ │ ├── all_13.html │ │ ├── all_2.html │ │ ├── all_3.html │ │ ├── all_4.html │ │ ├── all_5.html │ │ ├── all_5f.html │ │ ├── all_6.html │ │ ├── all_61.html │ │ ├── all_62.html │ │ ├── all_63.html │ │ ├── all_65.html │ │ ├── all_66.html │ │ ├── all_67.html │ │ ├── all_69.html │ │ ├── all_6c.html │ │ ├── all_6d.html │ │ ├── all_6e.html │ │ ├── all_6f.html │ │ ├── all_7.html │ │ ├── all_70.html │ │ ├── all_71.html │ │ ├── all_72.html │ │ ├── all_73.html │ │ ├── all_74.html │ │ ├── all_75.html │ │ ├── all_76.html │ │ ├── all_7e.html │ │ ├── all_8.html │ │ └── all_9.html │ ├── ftv2folderclosed.png │ ├── class_faulting_traverser.png │ ├── class_simple_tree_node.png │ ├── class_edge_print_traverser.png │ ├── class_node_print_traverser.png │ ├── class_print_data_traverser.png │ ├── class_tree_print_traverser.png │ ├── class_subclone_seeker_1_1_c_n_v.png │ ├── class_subclone_seeker_1_1_l_o_h.png │ ├── class_subclone_seeker_1_1_s_n_p.png │ ├── class_subclone_explorer_1_1_c_n_v.png │ ├── class_subclone_explorer_1_1_l_o_h.png │ ├── class_subclone_explorer_1_1_s_n_p.png │ ├── class_subclone_seeker_1_1_subclone.png │ ├── classqiaoy_1_1_mutation_tree_node.png │ ├── class_coexistance_traverse_delegate.png │ ├── class_subclone_explorer_1_1_subclone.png │ ├── class_subclone_seeker_1_1_archivable.png │ ├── class_subclone_seeker_1_1_tree_node.png │ ├── class_tree_merge_traverse_secondary.png │ ├── class_subclone_explorer_1_1_archivable.png │ ├── class_subclone_explorer_1_1_tree_node.png │ ├── class_subclone_seeker_1_1_event_cluster.png │ ├── class_subclone_seeker_1_1_genomic_range.png │ ├── class_subclone_seeker_1_1_somatic_event.png │ ├── class_subclone_explorer_1_1_event_cluster.png │ ├── class_subclone_explorer_1_1_genomic_range.png │ ├── class_subclone_explorer_1_1_somatic_event.png │ ├── class_subclone_explorer_1_1_genomic_location.png │ ├── class_subclone_seeker_1_1_genomic_location.png │ ├── class_subclone_seeker_1_1_segmental_mutation.png │ ├── class_subclone_explorer_1_1_segmental_mutation.png │ ├── class_subclone_seeker_1_1_tree_traverse_delegate.png │ ├── class_subclone_explorer_1_1_tree_traverse_delegate.png │ ├── class_edge_print_traverser.js │ ├── class_node_print_traverser.js │ ├── class_subclone_seeker_1_1_subclone_load_tree_traverser.png │ ├── class_subclone_seeker_1_1_subclone_save_tree_traverser.png │ ├── class_subclone_explorer_1_1_subclone_load_tree_traverser.png │ ├── class_subclone_explorer_1_1_subclone_save_tree_traverser.png │ ├── class_subclone_seeker_1_1_l_o_h.js │ ├── class_subclone_explorer_1_1_l_o_h.js │ ├── files.js │ ├── _archivable_8h.js │ ├── _event_cluster_8h.js │ ├── _somatic_event_8h.js │ ├── navtreeindex1.js │ ├── class_subclone_seeker_1_1_c_n_v.js │ ├── class_subclone_explorer_1_1_c_n_v.js │ ├── dir_cbdb8362360e11eafe2fa3bc74cf0ffd.js │ ├── _tree_node_8h.js │ ├── class_coexistance_traverse_delegate.js │ ├── class_subclone_seeker_1_1_subclone_load_tree_traverser.js │ ├── class_subclone_explorer_1_1_subclone_load_tree_traverser.js │ ├── class_tree_merge_traverse_secondary.js │ ├── class_subclone_seeker_1_1_genomic_range.js │ ├── class_subclone_explorer_1_1_genomic_range.js │ ├── _subclone_8h.js │ ├── class_subclone_seeker_1_1_subclone_save_tree_traverser.js │ ├── class_subclone_explorer_1_1_subclone_save_tree_traverser.js │ ├── class_subclone_seeker_1_1_genomic_location.js │ ├── class_tree_print_traverser.js │ ├── class_subclone_explorer_1_1_genomic_location.js │ ├── treemerge__p_8h.js │ ├── class_subclone_seeker_1_1_s_n_p.js │ ├── class_subclone_explorer_1_1_s_n_p.js │ ├── treemerge__p_8cc.js │ ├── class_ref_genome.js │ ├── class_subclone_seeker_1_1_segmental_mutation.js │ ├── class_subclone_explorer_1_1_segmental_mutation.js │ ├── class_subclone_seeker_1_1_somatic_event.js │ ├── class_subclone_explorer_1_1_somatic_event.js │ └── class_subclone_seeker_1_1_tree_traverse_delegate.js └── extra │ └── mainpage_header.md ├── examples.tar.gz ├── vendor └── UnitTest++ │ ├── src │ ├── .svn │ │ ├── dir-prop-base │ │ ├── prop-base │ │ │ ├── Checks.h.svn-base │ │ │ ├── Config.h.svn-base │ │ │ ├── Test.cpp.svn-base │ │ │ ├── Test.h.svn-base │ │ │ ├── CheckMacros.h.svn-base │ │ │ ├── Checks.cpp.svn-base │ │ │ ├── TestDetails.h.svn-base │ │ │ ├── TestList.cpp.svn-base │ │ │ ├── TestList.h.svn-base │ │ │ ├── TestMacros.h.svn-base │ │ │ ├── TestResults.h.svn-base │ │ │ ├── TestRunner.h.svn-base │ │ │ ├── TestSuite.h.svn-base │ │ │ ├── TimeHelpers.h.svn-base │ │ │ ├── UnitTest++.h.svn-base │ │ │ ├── AssertException.h.svn-base │ │ │ ├── MemoryOutStream.h.svn-base │ │ │ ├── ReportAssert.cpp.svn-base │ │ │ ├── ReportAssert.h.svn-base │ │ │ ├── TestDetails.cpp.svn-base │ │ │ ├── TestReporter.cpp.svn-base │ │ │ ├── TestReporter.h.svn-base │ │ │ ├── TestResults.cpp.svn-base │ │ │ ├── TestRunner.cpp.svn-base │ │ │ ├── TimeConstraint.cpp.svn-base │ │ │ ├── TimeConstraint.h.svn-base │ │ │ ├── XmlTestReporter.h.svn-base │ │ │ ├── AssertException.cpp.svn-base │ │ │ ├── DeferredTestReporter.h.svn-base │ │ │ ├── DeferredTestResult.cpp.svn-base │ │ │ ├── DeferredTestResult.h.svn-base │ │ │ ├── MemoryOutStream.cpp.svn-base │ │ │ ├── TestReporterStdout.cpp.svn-base │ │ │ ├── TestReporterStdout.h.svn-base │ │ │ ├── XmlTestReporter.cpp.svn-base │ │ │ └── DeferredTestReporter.cpp.svn-base │ │ └── text-base │ │ │ ├── TestReporter.cpp.svn-base │ │ │ ├── TimeHelpers.h.svn-base │ │ │ ├── ReportAssert.h.svn-base │ │ │ ├── TestSuite.h.svn-base │ │ │ ├── ReportAssert.cpp.svn-base │ │ │ ├── CurrentTest.h.svn-base │ │ │ ├── UnitTest++.h.svn-base │ │ │ ├── CurrentTest.cpp.svn-base │ │ │ ├── TestList.h.svn-base │ │ │ ├── DeferredTestResult.cpp.svn-base │ │ │ ├── TestDetails.cpp.svn-base │ │ │ ├── TestReporter.h.svn-base │ │ │ ├── TestReporterStdout.h.svn-base │ │ │ ├── AssertException.h.svn-base │ │ │ ├── TestList.cpp.svn-base │ │ │ ├── TestDetails.h.svn-base │ │ │ ├── Test.h.svn-base │ │ │ ├── AssertException.cpp.svn-base │ │ │ ├── DeferredTestResult.h.svn-base │ │ │ ├── DeferredTestReporter.h.svn-base │ │ │ ├── TimeConstraint.cpp.svn-base │ │ │ ├── TimeConstraint.h.svn-base │ │ │ ├── Test.cpp.svn-base │ │ │ ├── TestResults.h.svn-base │ │ │ └── DeferredTestReporter.cpp.svn-base │ ├── Posix │ │ ├── .svn │ │ │ ├── dir-prop-base │ │ │ ├── prop-base │ │ │ │ ├── TimeHelpers.cpp.svn-base │ │ │ │ ├── TimeHelpers.h.svn-base │ │ │ │ ├── SignalTranslator.cpp.svn-base │ │ │ │ └── SignalTranslator.h.svn-base │ │ │ ├── text-base │ │ │ │ ├── TimeHelpers.h.svn-base │ │ │ │ └── TimeHelpers.cpp.svn-base │ │ │ └── all-wcprops │ │ ├── TimeHelpers.h │ │ └── TimeHelpers.cpp │ ├── tests │ │ ├── .svn │ │ │ ├── dir-prop-base │ │ │ ├── prop-base │ │ │ │ ├── Main.cpp.svn-base │ │ │ │ ├── TestTest.cpp.svn-base │ │ │ │ ├── TestChecks.cpp.svn-base │ │ │ │ ├── TestTestList.cpp.svn-base │ │ │ │ ├── TestTestSuite.cpp.svn-base │ │ │ │ ├── RecordingReporter.h.svn-base │ │ │ │ ├── TestAssertHandler.cpp.svn-base │ │ │ │ ├── TestCheckMacros.cpp.svn-base │ │ │ │ ├── TestTestMacros.cpp.svn-base │ │ │ │ ├── TestTestResults.cpp.svn-base │ │ │ │ ├── TestTestRunner.cpp.svn-base │ │ │ │ ├── TestTimeConstraint.cpp.svn-base │ │ │ │ ├── TestUnitTest++.cpp.svn-base │ │ │ │ ├── TestMemoryOutStream.cpp.svn-base │ │ │ │ ├── TestTimeConstraintMacro.cpp.svn-base │ │ │ │ ├── TestXmlTestReporter.cpp.svn-base │ │ │ │ └── TestDeferredTestReporter.cpp.svn-base │ │ │ └── text-base │ │ │ │ ├── Main.cpp.svn-base │ │ │ │ ├── TestTestSuite.cpp.svn-base │ │ │ │ ├── TestCurrentTest.cpp.svn-base │ │ │ │ ├── TestAssertHandler.cpp.svn-base │ │ │ │ └── TestTestList.cpp.svn-base │ │ ├── Main.cpp │ │ ├── TestTestSuite.cpp │ │ ├── TestCurrentTest.cpp │ │ ├── TestAssertHandler.cpp │ │ └── TestTestList.cpp │ ├── Win32 │ │ ├── .svn │ │ │ ├── prop-base │ │ │ │ ├── TimeHelpers.cpp.svn-base │ │ │ │ └── TimeHelpers.h.svn-base │ │ │ ├── all-wcprops │ │ │ ├── text-base │ │ │ │ └── TimeHelpers.h.svn-base │ │ │ └── entries │ │ └── TimeHelpers.h │ ├── TestReporter.cpp │ ├── TimeHelpers.h │ ├── ReportAssert.h │ ├── TestSuite.h │ ├── ReportAssert.cpp │ ├── CurrentTest.h │ ├── UnitTest++.h │ ├── CurrentTest.cpp │ ├── TestList.h │ ├── DeferredTestResult.cpp │ ├── TestDetails.cpp │ ├── TestReporter.h │ ├── TestReporterStdout.h │ ├── AssertException.h │ ├── TestList.cpp │ ├── TestDetails.h │ ├── Test.h │ ├── AssertException.cpp │ ├── DeferredTestResult.h │ ├── DeferredTestReporter.h │ ├── TimeConstraint.cpp │ ├── TimeConstraint.h │ ├── Test.cpp │ ├── TestResults.h │ ├── DeferredTestReporter.cpp │ └── Config.h │ ├── .svn │ ├── prop-base │ │ ├── COPYING.svn-base │ │ ├── README.svn-base │ │ ├── Makefile.svn-base │ │ ├── UnitTest++.vsnet2003.sln.svn-base │ │ ├── UnitTest++.vsnet2003.vcproj.svn-base │ │ ├── UnitTest++.vsnet2005.sln.svn-base │ │ ├── UnitTest++.vsnet2005.vcproj.svn-base │ │ ├── TestUnitTest++.vsnet2003.vcproj.svn-base │ │ └── TestUnitTest++.vsnet2005.vcproj.svn-base │ ├── dir-prop-base │ └── text-base │ │ ├── UnitTestPP_vs6.dsp.svn-base │ │ ├── UnitTestPP_vs6.dsw.svn-base │ │ └── TestUnitTestPP_vs6.dsp.svn-base │ ├── docs │ └── .svn │ │ ├── prop-base │ │ └── UnitTest++.html.svn-base │ │ ├── all-wcprops │ │ └── entries │ ├── UnitTestPP_vs6.dsp │ ├── UnitTestPP_vs6.dsw │ └── TestUnitTestPP_vs6.dsp ├── Makefile ├── src └── Makefile ├── utils └── CoexistanceTable.h └── test └── Makefile /README: -------------------------------------------------------------------------------- 1 | see README.md 2 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | *.o 3 | doc/latex 4 | -------------------------------------------------------------------------------- /doc/html/bc_s.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yiq/SubcloneSeeker/HEAD/doc/html/bc_s.png 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-------------------------------------------------------------------------------- /doc/html/class_node_print_traverser.js: -------------------------------------------------------------------------------- 1 | var class_node_print_traverser = 2 | [ 3 | [ "processNode", "class_node_print_traverser.html#ae62459af6a4d939021dc081dfdad55d8", null ] 4 | ]; -------------------------------------------------------------------------------- /doc/html/class_subclone_seeker_1_1_subclone_load_tree_traverser.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yiq/SubcloneSeeker/HEAD/doc/html/class_subclone_seeker_1_1_subclone_load_tree_traverser.png -------------------------------------------------------------------------------- /doc/html/class_subclone_seeker_1_1_subclone_save_tree_traverser.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yiq/SubcloneSeeker/HEAD/doc/html/class_subclone_seeker_1_1_subclone_save_tree_traverser.png -------------------------------------------------------------------------------- /doc/html/class_subclone_explorer_1_1_subclone_load_tree_traverser.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yiq/SubcloneSeeker/HEAD/doc/html/class_subclone_explorer_1_1_subclone_load_tree_traverser.png -------------------------------------------------------------------------------- /doc/html/class_subclone_explorer_1_1_subclone_save_tree_traverser.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yiq/SubcloneSeeker/HEAD/doc/html/class_subclone_explorer_1_1_subclone_save_tree_traverser.png -------------------------------------------------------------------------------- /doc/html/search/defines_1.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['min_5fclone_5ffrac',['MIN_CLONE_FRAC',['../treemerge__p_8cc.html#a83c5ed1b565344d61820946b9ad203ce',1,'treemerge_p.cc']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /doc/html/search/defines_6d.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['min_5fclone_5ffrac',['MIN_CLONE_FRAC',['../treemerge__p_8cc.html#a83c5ed1b565344d61820946b9ad203ce',1,'treemerge_p.cc']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /doc/html/search/defines_0.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['boundry_5fresolution',['BOUNDRY_RESOLUTION',['../treemerge__p_8h.html#a63777350dacef4ba0869630657870963',1,'treemerge_p.h']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /doc/html/search/defines_62.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['boundry_5fresolution',['BOUNDRY_RESOLUTION',['../treemerge__p_8h.html#a63777350dacef4ba0869630657870963',1,'treemerge_p.h']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/TimeHelpers.h: -------------------------------------------------------------------------------- 1 | #include "Config.h" 2 | 3 | #if defined UNITTEST_POSIX 4 | #include "Posix/TimeHelpers.h" 5 | #else 6 | #include "Win32/TimeHelpers.h" 7 | #endif 8 | -------------------------------------------------------------------------------- /doc/html/class_subclone_seeker_1_1_l_o_h.js: -------------------------------------------------------------------------------- 1 | var class_subclone_seeker_1_1_l_o_h = 2 | [ 3 | [ "getTableName", "class_subclone_seeker_1_1_l_o_h.html#abb2d9b24f9879043b8f3e2114284fca7", null ] 4 | ]; -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/TestReporter.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "TestReporter.h" 2 | 3 | namespace UnitTest { 4 | 5 | 6 | TestReporter::~TestReporter() 7 | { 8 | } 9 | 10 | } 11 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/tests/Main.cpp: -------------------------------------------------------------------------------- 1 | #include "../UnitTest++.h" 2 | #include "../TestReporterStdout.h" 3 | 4 | 5 | int main(int, char const *[]) 6 | { 7 | return UnitTest::RunAllTests(); 8 | } 9 | -------------------------------------------------------------------------------- /doc/html/class_subclone_explorer_1_1_l_o_h.js: -------------------------------------------------------------------------------- 1 | var class_subclone_explorer_1_1_l_o_h = 2 | [ 3 | [ "getTableName", "class_subclone_explorer_1_1_l_o_h.html#abb2d9b24f9879043b8f3e2114284fca7", null ] 4 | ]; -------------------------------------------------------------------------------- /doc/html/search/functions_4.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['fraction',['fraction',['../class_subclone_seeker_1_1_subclone.html#ad250d3e7338d579a98e9b0a1cb66d1ea',1,'SubcloneSeeker::Subclone']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /doc/html/search/files_0.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['archivable_2ecc',['Archivable.cc',['../_archivable_8cc.html',1,'']]], 4 | ['archivable_2eh',['Archivable.h',['../_archivable_8h.html',1,'']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/search/files_61.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['archivable_2ecc',['Archivable.cc',['../_archivable_8cc.html',1,'']]], 4 | ['archivable_2eh',['Archivable.h',['../_archivable_8h.html',1,'']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/search/functions_66.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['fraction',['fraction',['../class_subclone_explorer_1_1_subclone.html#ade2f888fe51eac039f7cc0de2930dc97',1,'SubcloneExplorer::Subclone']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /doc/html/search/variables_73.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['start',['start',['../class_subclone_explorer_1_1_genomic_range.html#a496b88dee59d000b18396bd6ee540a81',1,'SubcloneExplorer::GenomicRange']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /doc/html/search/variables_2.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['frequency',['frequency',['../class_subclone_seeker_1_1_somatic_event.html#aef56c53d7eb294a6063b4a5043a0ed87',1,'SubcloneSeeker::SomaticEvent']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /doc/html/search/variables_7.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['range',['range',['../class_subclone_seeker_1_1_segmental_mutation.html#a03db5155dd9091e8a142877df83cd7ce',1,'SubcloneSeeker::SegmentalMutation']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/TimeHelpers.h.svn-base: -------------------------------------------------------------------------------- 1 | #include "Config.h" 2 | 3 | #if defined UNITTEST_POSIX 4 | #include "Posix/TimeHelpers.h" 5 | #else 6 | #include "Win32/TimeHelpers.h" 7 | #endif 8 | -------------------------------------------------------------------------------- /doc/html/search/variables_66.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['frequency',['frequency',['../class_subclone_explorer_1_1_somatic_event.html#a42f108dc0bc7bc0119bb6e0da2af32f3',1,'SubcloneExplorer::SomaticEvent']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /doc/html/search/variables_72.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['range',['range',['../class_subclone_explorer_1_1_segmental_mutation.html#a126dc16608ec7cc57f5f890ec498a7dc',1,'SubcloneExplorer::SegmentalMutation']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /doc/html/search/files_1.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['eventcluster_2ecc',['EventCluster.cc',['../_event_cluster_8cc.html',1,'']]], 4 | ['eventcluster_2eh',['EventCluster.h',['../_event_cluster_8h.html',1,'']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/search/files_65.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['eventcluster_2ecc',['EventCluster.cc',['../_event_cluster_8cc.html',1,'']]], 4 | ['eventcluster_2eh',['EventCluster.h',['../_event_cluster_8h.html',1,'']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/tests/.svn/text-base/Main.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "../UnitTest++.h" 2 | #include "../TestReporterStdout.h" 3 | 4 | 5 | int main(int, char const *[]) 6 | { 7 | return UnitTest::RunAllTests(); 8 | } 9 | -------------------------------------------------------------------------------- /doc/html/search/files_2.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['genomiclocation_2eh',['GenomicLocation.h',['../_genomic_location_8h.html',1,'']]], 4 | ['genomicrange_2eh',['GenomicRange.h',['../_genomic_range_8h.html',1,'']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/search/files_67.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['genomiclocation_2eh',['GenomicLocation.h',['../_genomic_location_8h.html',1,'']]], 4 | ['genomicrange_2eh',['GenomicRange.h',['../_genomic_range_8h.html',1,'']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/files.js: -------------------------------------------------------------------------------- 1 | var files = 2 | [ 3 | [ "src", "dir_68267d1309a1af8e8297ef4c3efbcdba.html", "dir_68267d1309a1af8e8297ef4c3efbcdba" ], 4 | [ "utils", "dir_cbdb8362360e11eafe2fa3bc74cf0ffd.html", "dir_cbdb8362360e11eafe2fa3bc74cf0ffd" ] 5 | ]; -------------------------------------------------------------------------------- /doc/html/_archivable_8h.js: -------------------------------------------------------------------------------- 1 | var _archivable_8h = 2 | [ 3 | [ "Archivable", "class_subclone_seeker_1_1_archivable.html", "class_subclone_seeker_1_1_archivable" ], 4 | [ "DBObjectID_vec", "_archivable_8h.html#af64a595b2e279f680b0d1f755fcf4b8d", null ] 5 | ]; -------------------------------------------------------------------------------- /vendor/UnitTest++/src/ReportAssert.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_ASSERT_H 2 | #define UNITTEST_ASSERT_H 3 | 4 | namespace UnitTest { 5 | 6 | void ReportAssert(char const* description, char const* filename, int lineNumber); 7 | 8 | } 9 | 10 | #endif 11 | -------------------------------------------------------------------------------- /doc/html/search/classes_2.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['edgeprinttraverser',['EdgePrintTraverser',['../class_edge_print_traverser.html',1,'']]], 4 | ['eventcluster',['EventCluster',['../class_subclone_seeker_1_1_event_cluster.html',1,'SubcloneSeeker']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/TestSuite.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TESTSUITE_H 2 | #define UNITTEST_TESTSUITE_H 3 | 4 | namespace UnitTestSuite 5 | { 6 | inline char const* GetSuiteName () 7 | { 8 | return "DefaultSuite"; 9 | } 10 | } 11 | 12 | #endif 13 | -------------------------------------------------------------------------------- /doc/html/search/classes_65.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['edgeprinttraverser',['EdgePrintTraverser',['../class_edge_print_traverser.html',1,'']]], 4 | ['eventcluster',['EventCluster',['../class_subclone_explorer_1_1_event_cluster.html',1,'SubcloneExplorer']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/ReportAssert.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_ASSERT_H 2 | #define UNITTEST_ASSERT_H 3 | 4 | namespace UnitTest { 5 | 6 | void ReportAssert(char const* description, char const* filename, int lineNumber); 7 | 8 | } 9 | 10 | #endif 11 | -------------------------------------------------------------------------------- /doc/html/_event_cluster_8h.js: -------------------------------------------------------------------------------- 1 | var _event_cluster_8h = 2 | [ 3 | [ "EventCluster", "class_subclone_seeker_1_1_event_cluster.html", "class_subclone_seeker_1_1_event_cluster" ], 4 | [ "EventClusterPtr_vec", "_event_cluster_8h.html#ac9b56f33b2d4c610591c0c051e4b59fc", null ] 5 | ]; -------------------------------------------------------------------------------- /doc/html/_somatic_event_8h.js: -------------------------------------------------------------------------------- 1 | var _somatic_event_8h = 2 | [ 3 | [ "SomaticEvent", "class_subclone_seeker_1_1_somatic_event.html", "class_subclone_seeker_1_1_somatic_event" ], 4 | [ "SomaticEventPtr_vec", "_somatic_event_8h.html#a5381f45316c93237b73bb9602780aced", null ] 5 | ]; -------------------------------------------------------------------------------- /doc/html/navtreeindex1.js: -------------------------------------------------------------------------------- 1 | var NAVTREEINDEX1 = 2 | { 3 | "treeprint_8cc.html#adf764cbdea00d65edcd07bb9953ad2b7ab722558c98092963d783fea389da0000":[3,0,1,3,6], 4 | "treeprint_8cc.html#adf764cbdea00d65edcd07bb9953ad2b7ad5ee5a70ca23e53c2e3142980a35d196":[3,0,1,3,5], 5 | "utils.html":[1] 6 | }; 7 | -------------------------------------------------------------------------------- /doc/html/search/classes_3.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['genomiclocation',['GenomicLocation',['../class_subclone_seeker_1_1_genomic_location.html',1,'SubcloneSeeker']]], 4 | ['genomicrange',['GenomicRange',['../class_subclone_seeker_1_1_genomic_range.html',1,'SubcloneSeeker']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/TestSuite.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TESTSUITE_H 2 | #define UNITTEST_TESTSUITE_H 3 | 4 | namespace UnitTestSuite 5 | { 6 | inline char const* GetSuiteName () 7 | { 8 | return "DefaultSuite"; 9 | } 10 | } 11 | 12 | #endif 13 | -------------------------------------------------------------------------------- /doc/html/search/classes_67.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['genomiclocation',['GenomicLocation',['../class_subclone_explorer_1_1_genomic_location.html',1,'SubcloneExplorer']]], 4 | ['genomicrange',['GenomicRange',['../class_subclone_explorer_1_1_genomic_range.html',1,'SubcloneExplorer']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/class_subclone_seeker_1_1_c_n_v.js: -------------------------------------------------------------------------------- 1 | var class_subclone_seeker_1_1_c_n_v = 2 | [ 3 | [ "getTableName", "class_subclone_seeker_1_1_c_n_v.html#a3c72e962269177f7513ce312aef1ef18", null ], 4 | [ "isEqualTo", "class_subclone_seeker_1_1_c_n_v.html#af5e4b26f65b277b44ec922d33102c127", null ] 5 | ]; -------------------------------------------------------------------------------- /doc/html/class_subclone_explorer_1_1_c_n_v.js: -------------------------------------------------------------------------------- 1 | var class_subclone_explorer_1_1_c_n_v = 2 | [ 3 | [ "getTableName", "class_subclone_explorer_1_1_c_n_v.html#a3c72e962269177f7513ce312aef1ef18", null ], 4 | [ "isEqualTo", "class_subclone_explorer_1_1_c_n_v.html#af5e4b26f65b277b44ec922d33102c127", null ] 5 | ]; -------------------------------------------------------------------------------- /vendor/UnitTest++/docs/.svn/all-wcprops: -------------------------------------------------------------------------------- 1 | K 25 2 | svn:wc:ra_dav:version-url 3 | V 50 4 | /svnroot/unittest-cpp/!svn/ver/207/UnitTest++/docs 5 | END 6 | UnitTest++.html 7 | K 25 8 | svn:wc:ra_dav:version-url 9 | V 66 10 | /svnroot/unittest-cpp/!svn/ver/207/UnitTest++/docs/UnitTest++.html 11 | END 12 | -------------------------------------------------------------------------------- /doc/html/search/functions_8.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['main',['main',['../treeprint_8cc.html#a0ddf1224851353fc92bfbff6f499fa97',1,'treeprint.cc']]], 4 | ['members',['members',['../class_subclone_seeker_1_1_event_cluster.html#a8157a1b07cb86faa4f3db5256e493a61',1,'SubcloneSeeker::EventCluster']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/search/functions_6d.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['main',['main',['../treeprint_8cc.html#a0ddf1224851353fc92bfbff6f499fa97',1,'treeprint.cc']]], 4 | ['members',['members',['../class_subclone_explorer_1_1_event_cluster.html#a1e8c05740c7406dad982675d738ba5da',1,'SubcloneExplorer::EventCluster']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/ReportAssert.cpp: -------------------------------------------------------------------------------- 1 | #include "ReportAssert.h" 2 | #include "AssertException.h" 3 | 4 | namespace UnitTest { 5 | 6 | void ReportAssert(char const* description, char const* filename, int lineNumber) 7 | { 8 | throw AssertException(description, filename, lineNumber); 9 | } 10 | 11 | } 12 | -------------------------------------------------------------------------------- /doc/html/search/variables_4.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['length',['length',['../class_subclone_seeker_1_1_genomic_range.html#a667113ce76e665a988707cb3c0af0a96',1,'SubcloneSeeker::GenomicRange']]], 4 | ['location',['location',['../class_subclone_seeker_1_1_s_n_p.html#a75f6f776c0a95ccb97011566e8fe2660',1,'SubcloneSeeker::SNP']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/ReportAssert.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "ReportAssert.h" 2 | #include "AssertException.h" 3 | 4 | namespace UnitTest { 5 | 6 | void ReportAssert(char const* description, char const* filename, int lineNumber) 7 | { 8 | throw AssertException(description, filename, lineNumber); 9 | } 10 | 11 | } 12 | -------------------------------------------------------------------------------- /doc/html/search/all_5.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['fraction',['fraction',['../class_subclone_seeker_1_1_subclone.html#ad250d3e7338d579a98e9b0a1cb66d1ea',1,'SubcloneSeeker::Subclone']]], 4 | ['frequency',['frequency',['../class_subclone_seeker_1_1_somatic_event.html#aef56c53d7eb294a6063b4a5043a0ed87',1,'SubcloneSeeker::SomaticEvent']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/search/variables_3.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['id',['id',['../class_subclone_seeker_1_1_archivable.html#aec0d9a77bfec71a1dff3b07ca67e3cf1',1,'SubcloneSeeker::Archivable']]], 4 | ['iscompatible',['isCompatible',['../class_tree_merge_traverse_secondary.html#a5823ea751966c751e32ae1be4a810780',1,'TreeMergeTraverseSecondary']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/search/variables_1.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['children',['children',['../class_subclone_seeker_1_1_tree_node.html#a9c0c9e40b7e6f9c08d2722d4a67a4d36',1,'SubcloneSeeker::TreeNode']]], 4 | ['chrom',['chrom',['../class_subclone_seeker_1_1_genomic_location.html#a0ff41c7947d2170f87712f54dce73b8e',1,'SubcloneSeeker::GenomicLocation']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/search/variables_69.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['id',['id',['../class_subclone_explorer_1_1_archivable.html#a7e67ca95e2bab5ae71b8bef359758806',1,'SubcloneExplorer::Archivable']]], 4 | ['iscompatible',['isCompatible',['../class_tree_merge_traverse_secondary.html#a5823ea751966c751e32ae1be4a810780',1,'TreeMergeTraverseSecondary']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/search/variables_6c.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['length',['length',['../class_subclone_explorer_1_1_genomic_range.html#a2d79990de739173b7c87aabc3886c24c',1,'SubcloneExplorer::GenomicRange']]], 4 | ['location',['location',['../class_subclone_explorer_1_1_s_n_p.html#aacf3436a54ca0b4fe8b1843962a96204',1,'SubcloneExplorer::SNP']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/search/all_66.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['fraction',['fraction',['../class_subclone_explorer_1_1_subclone.html#ade2f888fe51eac039f7cc0de2930dc97',1,'SubcloneExplorer::Subclone']]], 4 | ['frequency',['frequency',['../class_subclone_explorer_1_1_somatic_event.html#a42f108dc0bc7bc0119bb6e0da2af32f3',1,'SubcloneExplorer::SomaticEvent']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/search/files_74.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['treemerge_5fp_2ecc',['treemerge_p.cc',['../treemerge__p_8cc.html',1,'']]], 4 | ['treemerge_5fp_2eh',['treemerge_p.h',['../treemerge__p_8h.html',1,'']]], 5 | ['treenode_2eh',['TreeNode.h',['../_tree_node_8h.html',1,'']]], 6 | ['treeprint_2ecc',['treeprint.cc',['../treeprint_8cc.html',1,'']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /doc/html/search/variables_63.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['children',['children',['../class_subclone_explorer_1_1_tree_node.html#ab2c661d0958e9176e57d9eb8dd3f58ea',1,'SubcloneExplorer::TreeNode']]], 4 | ['chrom',['chrom',['../class_subclone_explorer_1_1_genomic_location.html#a77351193107676decdc864b0b6acef51',1,'SubcloneExplorer::GenomicLocation']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/CurrentTest.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_CURRENTTESTRESULTS_H 2 | #define UNITTEST_CURRENTTESTRESULTS_H 3 | 4 | namespace UnitTest { 5 | 6 | class TestResults; 7 | class TestDetails; 8 | 9 | namespace CurrentTest 10 | { 11 | TestResults*& Results(); 12 | const TestDetails*& Details(); 13 | } 14 | 15 | } 16 | 17 | #endif 18 | -------------------------------------------------------------------------------- /doc/html/search/variables_5.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['ofclusterid',['ofClusterID',['../class_subclone_seeker_1_1_somatic_event.html#acdf2c80463f11c2e5debc5fc0ecc12ad',1,'SubcloneSeeker::SomaticEvent']]], 4 | ['ofsubcloneid',['ofSubcloneID',['../class_subclone_seeker_1_1_event_cluster.html#a903b39fdf82cb4c19f6aa2bce626b7d2',1,'SubcloneSeeker::EventCluster']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/dir_cbdb8362360e11eafe2fa3bc74cf0ffd.js: -------------------------------------------------------------------------------- 1 | var dir_cbdb8362360e11eafe2fa3bc74cf0ffd = 2 | [ 3 | [ "CoexistanceTable.h", "_coexistance_table_8h_source.html", null ], 4 | [ "treemerge_p.cc", "treemerge__p_8cc.html", "treemerge__p_8cc" ], 5 | [ "treemerge_p.h", "treemerge__p_8h.html", "treemerge__p_8h" ], 6 | [ "treeprint.cc", "treeprint_8cc.html", "treeprint_8cc" ] 7 | ]; -------------------------------------------------------------------------------- /doc/html/search/variables_6f.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['ofclusterid',['ofClusterID',['../class_subclone_explorer_1_1_somatic_event.html#ad84d19bfa348564a913f642248dc2ec1',1,'SubcloneExplorer::SomaticEvent']]], 4 | ['ofsubcloneid',['ofSubcloneID',['../class_subclone_explorer_1_1_event_cluster.html#ab54733136e96c5d63cf2bd454242ab79',1,'SubcloneExplorer::EventCluster']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/CurrentTest.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_CURRENTTESTRESULTS_H 2 | #define UNITTEST_CURRENTTESTRESULTS_H 3 | 4 | namespace UnitTest { 5 | 6 | class TestResults; 7 | class TestDetails; 8 | 9 | namespace CurrentTest 10 | { 11 | TestResults*& Results(); 12 | const TestDetails*& Details(); 13 | } 14 | 15 | } 16 | 17 | #endif 18 | -------------------------------------------------------------------------------- /doc/html/_tree_node_8h.js: -------------------------------------------------------------------------------- 1 | var _tree_node_8h = 2 | [ 3 | [ "TreeTraverseDelegate", "class_subclone_seeker_1_1_tree_traverse_delegate.html", "class_subclone_seeker_1_1_tree_traverse_delegate" ], 4 | [ "TreeNode", "class_subclone_seeker_1_1_tree_node.html", "class_subclone_seeker_1_1_tree_node" ], 5 | [ "TreeNodeVec_t", "_tree_node_8h.html#ad91cd3a2bfcb006efdfbcdfada6a31d5", null ] 6 | ]; -------------------------------------------------------------------------------- /doc/html/search/all_13.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['_7etreenode',['~TreeNode',['../class_subclone_seeker_1_1_tree_node.html#aee92fbe0c35f3552690400ac76105fa8',1,'SubcloneSeeker::TreeNode']]], 4 | ['_7etreetraversedelegate',['~TreeTraverseDelegate',['../class_subclone_seeker_1_1_tree_traverse_delegate.html#aaaa5ba3f2351546d402c890e4fde6147',1,'SubcloneSeeker::TreeTraverseDelegate']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/search/functions_12.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['_7etreenode',['~TreeNode',['../class_subclone_seeker_1_1_tree_node.html#aee92fbe0c35f3552690400ac76105fa8',1,'SubcloneSeeker::TreeNode']]], 4 | ['_7etreetraversedelegate',['~TreeTraverseDelegate',['../class_subclone_seeker_1_1_tree_traverse_delegate.html#aaaa5ba3f2351546d402c890e4fde6147',1,'SubcloneSeeker::TreeTraverseDelegate']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/tests/TestTestSuite.cpp: -------------------------------------------------------------------------------- 1 | #include "../UnitTest++.h" 2 | 3 | // We're really testing if it's possible to use the same suite in two files 4 | // to compile and link successfuly (TestTestSuite.cpp has suite with the same name) 5 | // Note: we are outside of the anonymous namespace 6 | SUITE(SameTestSuite) 7 | { 8 | TEST(DummyTest2) 9 | { 10 | } 11 | } 12 | 13 | -------------------------------------------------------------------------------- /doc/html/search/all_7e.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['_7etreenode',['~TreeNode',['../class_subclone_explorer_1_1_tree_node.html#aa39f8208d51c2c07b2d465a8d81ddf0a',1,'SubcloneExplorer::TreeNode']]], 4 | ['_7etreetraversedelegate',['~TreeTraverseDelegate',['../class_subclone_explorer_1_1_tree_traverse_delegate.html#a96b550503dc883a3512aea284630ae11',1,'SubcloneExplorer::TreeTraverseDelegate']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /doc/html/search/functions_7e.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['_7etreenode',['~TreeNode',['../class_subclone_explorer_1_1_tree_node.html#aa39f8208d51c2c07b2d465a8d81ddf0a',1,'SubcloneExplorer::TreeNode']]], 4 | ['_7etreetraversedelegate',['~TreeTraverseDelegate',['../class_subclone_explorer_1_1_tree_traverse_delegate.html#a96b550503dc883a3512aea284630ae11',1,'SubcloneExplorer::TreeTraverseDelegate']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/UnitTest++.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTESTCPP_H 2 | #define UNITTESTCPP_H 3 | 4 | //lint -esym(1509,*Fixture) 5 | 6 | #include "Config.h" 7 | #include "Test.h" 8 | #include "TestList.h" 9 | #include "TestSuite.h" 10 | #include "TestResults.h" 11 | 12 | #include "TestMacros.h" 13 | 14 | #include "CheckMacros.h" 15 | #include "TestRunner.h" 16 | #include "TimeConstraint.h" 17 | 18 | #endif 19 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/tests/.svn/text-base/TestTestSuite.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "../UnitTest++.h" 2 | 3 | // We're really testing if it's possible to use the same suite in two files 4 | // to compile and link successfuly (TestTestSuite.cpp has suite with the same name) 5 | // Note: we are outside of the anonymous namespace 6 | SUITE(SameTestSuite) 7 | { 8 | TEST(DummyTest2) 9 | { 10 | } 11 | } 12 | 13 | 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['treenode_2ecc',['TreeNode.cc',['../_tree_node_8cc.html',1,'']]], 6 | ['treenode_2eh',['TreeNode.h',['../_tree_node_8h.html',1,'']]], 7 | ['treeprint_2ecc',['treeprint.cc',['../treeprint_8cc.html',1,'']]] 8 | ]; 9 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/CurrentTest.cpp: -------------------------------------------------------------------------------- 1 | #include "CurrentTest.h" 2 | #include 3 | 4 | namespace UnitTest { 5 | 6 | TestResults*& CurrentTest::Results() 7 | { 8 | static TestResults* testResults = NULL; 9 | return testResults; 10 | } 11 | 12 | const TestDetails*& CurrentTest::Details() 13 | { 14 | static const TestDetails* testDetails = NULL; 15 | return testDetails; 16 | } 17 | 18 | } 19 | -------------------------------------------------------------------------------- /doc/html/class_coexistance_traverse_delegate.js: -------------------------------------------------------------------------------- 1 | var class_coexistance_traverse_delegate = 2 | [ 3 | [ "postprocessNode", "class_coexistance_traverse_delegate.html#a72de7175ef7d904d64083e0f8140b2db", null ], 4 | [ "preprocessNode", "class_coexistance_traverse_delegate.html#aec3d767c91054010b05a0593b460032f", null ], 5 | [ "processNode", "class_coexistance_traverse_delegate.html#aa3d80848e6da455ef4594def83c71eb1", null ] 6 | ]; -------------------------------------------------------------------------------- /doc/html/search/all_9.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['main',['main',['../treeprint_8cc.html#a0ddf1224851353fc92bfbff6f499fa97',1,'treeprint.cc']]], 4 | ['members',['members',['../class_subclone_seeker_1_1_event_cluster.html#a8157a1b07cb86faa4f3db5256e493a61',1,'SubcloneSeeker::EventCluster']]], 5 | ['min_5fclone_5ffrac',['MIN_CLONE_FRAC',['../treemerge__p_8cc.html#a83c5ed1b565344d61820946b9ad203ce',1,'treemerge_p.cc']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/UnitTest++.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTESTCPP_H 2 | #define UNITTESTCPP_H 3 | 4 | //lint -esym(1509,*Fixture) 5 | 6 | #include "Config.h" 7 | #include "Test.h" 8 | #include "TestList.h" 9 | #include "TestSuite.h" 10 | #include "TestResults.h" 11 | 12 | #include "TestMacros.h" 13 | 14 | #include "CheckMacros.h" 15 | #include "TestRunner.h" 16 | #include "TimeConstraint.h" 17 | 18 | #endif 19 | -------------------------------------------------------------------------------- /doc/html/search/all_6d.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['main',['main',['../treeprint_8cc.html#a0ddf1224851353fc92bfbff6f499fa97',1,'treeprint.cc']]], 4 | ['members',['members',['../class_subclone_explorer_1_1_event_cluster.html#a1e8c05740c7406dad982675d738ba5da',1,'SubcloneExplorer::EventCluster']]], 5 | ['min_5fclone_5ffrac',['MIN_CLONE_FRAC',['../treemerge__p_8cc.html#a83c5ed1b565344d61820946b9ad203ce',1,'treemerge_p.cc']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/CurrentTest.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "CurrentTest.h" 2 | #include 3 | 4 | namespace UnitTest { 5 | 6 | TestResults*& CurrentTest::Results() 7 | { 8 | static TestResults* testResults = NULL; 9 | return testResults; 10 | } 11 | 12 | const TestDetails*& CurrentTest::Details() 13 | { 14 | static const TestDetails* testDetails = NULL; 15 | return testDetails; 16 | } 17 | 18 | } 19 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/Win32/.svn/all-wcprops: -------------------------------------------------------------------------------- 1 | K 25 2 | svn:wc:ra_dav:version-url 3 | V 55 4 | /svnroot/unittest-cpp/!svn/ver/205/UnitTest++/src/Win32 5 | END 6 | TimeHelpers.cpp 7 | K 25 8 | svn:wc:ra_dav:version-url 9 | V 71 10 | /svnroot/unittest-cpp/!svn/ver/205/UnitTest++/src/Win32/TimeHelpers.cpp 11 | END 12 | TimeHelpers.h 13 | K 25 14 | svn:wc:ra_dav:version-url 15 | V 69 16 | /svnroot/unittest-cpp/!svn/ver/205/UnitTest++/src/Win32/TimeHelpers.h 17 | END 18 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/Posix/TimeHelpers.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TIMEHELPERS_H 2 | #define UNITTEST_TIMEHELPERS_H 3 | 4 | #include 5 | 6 | namespace UnitTest { 7 | 8 | class Timer 9 | { 10 | public: 11 | Timer(); 12 | void Start(); 13 | double GetTimeInMs() const; 14 | 15 | private: 16 | struct timeval m_startTime; 17 | }; 18 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No Matches
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8 | -------------------------------------------------------------------------------- /doc/html/search/all_12.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['vec_5fchromids',['vec_chromIDs',['../class_ref_genome.html#a3af6b0834e4413483dca48c5fa9dca02',1,'RefGenome']]], 4 | ['vec_5fchroms',['vec_chroms',['../class_ref_genome.html#a7fdee345aaa8e5f4fdfc0b71b1181d56',1,'RefGenome']]], 5 | ['vecallobjectsid',['vecAllObjectsID',['../class_subclone_seeker_1_1_archivable.html#a01d776ff965993518becc1b56d933dc2',1,'SubcloneSeeker::Archivable']]], 6 | ['veceventcluster',['vecEventCluster',['../class_subclone_seeker_1_1_subclone.html#a863bbbe0475a7e358a399fa92c5fe7bd',1,'SubcloneSeeker::Subclone']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /doc/html/search/functions_11.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['vec_5fchromids',['vec_chromIDs',['../class_ref_genome.html#a3af6b0834e4413483dca48c5fa9dca02',1,'RefGenome']]], 4 | ['vec_5fchroms',['vec_chroms',['../class_ref_genome.html#a7fdee345aaa8e5f4fdfc0b71b1181d56',1,'RefGenome']]], 5 | ['vecallobjectsid',['vecAllObjectsID',['../class_subclone_seeker_1_1_archivable.html#a01d776ff965993518becc1b56d933dc2',1,'SubcloneSeeker::Archivable']]], 6 | ['veceventcluster',['vecEventCluster',['../class_subclone_seeker_1_1_subclone.html#a863bbbe0475a7e358a399fa92c5fe7bd',1,'SubcloneSeeker::Subclone']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /doc/html/search/all_76.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['vec_5fchromids',['vec_chromIDs',['../class_ref_genome.html#a3af6b0834e4413483dca48c5fa9dca02',1,'RefGenome']]], 4 | ['vec_5fchroms',['vec_chroms',['../class_ref_genome.html#a7fdee345aaa8e5f4fdfc0b71b1181d56',1,'RefGenome']]], 5 | ['vecallobjectsid',['vecAllObjectsID',['../class_subclone_explorer_1_1_archivable.html#a01d776ff965993518becc1b56d933dc2',1,'SubcloneExplorer::Archivable']]], 6 | ['veceventcluster',['vecEventCluster',['../class_subclone_explorer_1_1_subclone.html#ad7f66e17d19c8672be96f6d1777cc846',1,'SubcloneExplorer::Subclone']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /doc/html/search/functions_76.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['vec_5fchromids',['vec_chromIDs',['../class_ref_genome.html#a3af6b0834e4413483dca48c5fa9dca02',1,'RefGenome']]], 4 | ['vec_5fchroms',['vec_chroms',['../class_ref_genome.html#a7fdee345aaa8e5f4fdfc0b71b1181d56',1,'RefGenome']]], 5 | ['vecallobjectsid',['vecAllObjectsID',['../class_subclone_explorer_1_1_archivable.html#a01d776ff965993518becc1b56d933dc2',1,'SubcloneExplorer::Archivable']]], 6 | ['veceventcluster',['vecEventCluster',['../class_subclone_explorer_1_1_subclone.html#ad7f66e17d19c8672be96f6d1777cc846',1,'SubcloneExplorer::Subclone']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/DeferredTestResult.cpp: -------------------------------------------------------------------------------- 1 | #include "DeferredTestResult.h" 2 | #include "Config.h" 3 | 4 | namespace UnitTest 5 | { 6 | 7 | DeferredTestResult::DeferredTestResult() 8 | : suiteName("") 9 | , testName("") 10 | , failureFile("") 11 | , timeElapsed(0.0f) 12 | , failed(false) 13 | { 14 | } 15 | 16 | DeferredTestResult::DeferredTestResult(char const* suite, char const* test) 17 | : suiteName(suite) 18 | , testName(test) 19 | , failureFile("") 20 | , timeElapsed(0.0f) 21 | , failed(false) 22 | { 23 | } 24 | 25 | DeferredTestResult::~DeferredTestResult() 26 | { 27 | } 28 | 29 | } 30 | -------------------------------------------------------------------------------- /doc/html/search/all_a.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['nodeeventslist',['nodeEventsList',['../treemerge__p_8cc.html#a7fd00f1249526144d7d3afb0cb6b5bb1',1,'nodeEventsList(Subclone *node): treemerge_p.cc'],['../treemerge__p_8h.html#a7fd00f1249526144d7d3afb0cb6b5bb1',1,'nodeEventsList(Subclone *node): treemerge_p.cc']]], 4 | ['nodeprinttraverser',['NodePrintTraverser',['../class_node_print_traverser.html',1,'']]], 5 | ['nodesofparentid',['nodesOfParentID',['../class_subclone_seeker_1_1_subclone_load_tree_traverser.html#a9019d57fdf3e77e9bb0efcd74a0b9f96',1,'SubcloneSeeker::SubcloneLoadTreeTraverser']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/TestDetails.cpp: -------------------------------------------------------------------------------- 1 | #include "TestDetails.h" 2 | 3 | namespace UnitTest { 4 | 5 | TestDetails::TestDetails(char const* testName_, char const* suiteName_, char const* filename_, int lineNumber_) 6 | : suiteName(suiteName_) 7 | , testName(testName_) 8 | , filename(filename_) 9 | , lineNumber(lineNumber_) 10 | { 11 | } 12 | 13 | TestDetails::TestDetails(const TestDetails& details, int lineNumber_) 14 | : suiteName(details.suiteName) 15 | , testName(details.testName) 16 | , filename(details.filename) 17 | , lineNumber(lineNumber_) 18 | { 19 | } 20 | 21 | 22 | } 23 | -------------------------------------------------------------------------------- /doc/html/search/all_6e.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['nodeeventslist',['nodeEventsList',['../treemerge__p_8cc.html#a7fd00f1249526144d7d3afb0cb6b5bb1',1,'nodeEventsList(Subclone *node): treemerge_p.cc'],['../treemerge__p_8h.html#a7fd00f1249526144d7d3afb0cb6b5bb1',1,'nodeEventsList(Subclone *node): treemerge_p.cc']]], 4 | ['nodeprinttraverser',['NodePrintTraverser',['../class_node_print_traverser.html',1,'']]], 5 | ['nodesofparentid',['nodesOfParentID',['../class_subclone_explorer_1_1_subclone_load_tree_traverser.html#a9019d57fdf3e77e9bb0efcd74a0b9f96',1,'SubcloneExplorer::SubcloneLoadTreeTraverser']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/DeferredTestResult.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "DeferredTestResult.h" 2 | #include "Config.h" 3 | 4 | namespace UnitTest 5 | { 6 | 7 | DeferredTestResult::DeferredTestResult() 8 | : suiteName("") 9 | , testName("") 10 | , failureFile("") 11 | , timeElapsed(0.0f) 12 | , failed(false) 13 | { 14 | } 15 | 16 | DeferredTestResult::DeferredTestResult(char const* suite, char const* test) 17 | : suiteName(suite) 18 | , testName(test) 19 | , failureFile("") 20 | , timeElapsed(0.0f) 21 | , failed(false) 22 | { 23 | } 24 | 25 | DeferredTestResult::~DeferredTestResult() 26 | { 27 | } 28 | 29 | } 30 | -------------------------------------------------------------------------------- /doc/html/search/functions_3.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['eventcluster',['EventCluster',['../class_subclone_seeker_1_1_event_cluster.html#a3189b072719d59e76b98942186883f5f',1,'SubcloneSeeker::EventCluster']]], 4 | ['eventsetcontains',['eventSetContains',['../treemerge__p_8cc.html#a36790025b1a9580a7089bbabf0b5b0f2',1,'eventSetContains(const SomaticEventPtr_vec &v_container, const SomaticEventPtr_vec &v_containee): treemerge_p.cc'],['../treemerge__p_8h.html#a36790025b1a9580a7089bbabf0b5b0f2',1,'eventSetContains(const SomaticEventPtr_vec &v_container, const SomaticEventPtr_vec &v_containee): treemerge_p.cc']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/TestDetails.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "TestDetails.h" 2 | 3 | namespace UnitTest { 4 | 5 | TestDetails::TestDetails(char const* testName_, char const* suiteName_, char const* filename_, int lineNumber_) 6 | : suiteName(suiteName_) 7 | , testName(testName_) 8 | , filename(filename_) 9 | , lineNumber(lineNumber_) 10 | { 11 | } 12 | 13 | TestDetails::TestDetails(const TestDetails& details, int lineNumber_) 14 | : suiteName(details.suiteName) 15 | , testName(details.testName) 16 | , filename(details.filename) 17 | , lineNumber(lineNumber_) 18 | { 19 | } 20 | 21 | 22 | } 23 | -------------------------------------------------------------------------------- /doc/html/search/functions_65.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['eventcluster',['EventCluster',['../class_subclone_explorer_1_1_event_cluster.html#ac7167e2e601fd1ff86648cc6227c1ab2',1,'SubcloneExplorer::EventCluster']]], 4 | ['eventsetcontains',['eventSetContains',['../treemerge__p_8cc.html#a36790025b1a9580a7089bbabf0b5b0f2',1,'eventSetContains(const SomaticEventPtr_vec &v_container, const SomaticEventPtr_vec &v_containee): treemerge_p.cc'],['../treemerge__p_8h.html#a36790025b1a9580a7089bbabf0b5b0f2',1,'eventSetContains(const SomaticEventPtr_vec &v_container, const SomaticEventPtr_vec &v_containee): treemerge_p.cc']]] 5 | ]; 6 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/TestReporter.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TESTREPORTER_H 2 | #define UNITTEST_TESTREPORTER_H 3 | 4 | namespace UnitTest { 5 | 6 | class TestDetails; 7 | 8 | class TestReporter 9 | { 10 | public: 11 | virtual ~TestReporter(); 12 | 13 | virtual void ReportTestStart(TestDetails const& test) = 0; 14 | virtual void ReportFailure(TestDetails const& test, char const* failure) = 0; 15 | virtual void ReportTestFinish(TestDetails const& test, float secondsElapsed) = 0; 16 | virtual void ReportSummary(int totalTestCount, int failedTestCount, int failureCount, float secondsElapsed) = 0; 17 | }; 18 | 19 | } 20 | #endif 21 | -------------------------------------------------------------------------------- /doc/html/class_subclone_seeker_1_1_subclone_save_tree_traverser.js: -------------------------------------------------------------------------------- 1 | var class_subclone_seeker_1_1_subclone_save_tree_traverser = 2 | [ 3 | [ "SubcloneSaveTreeTraverser", "class_subclone_seeker_1_1_subclone_save_tree_traverser.html#a15df8b8e8e402f55eeca660ad819717c", null ], 4 | [ "preprocessNode", "class_subclone_seeker_1_1_subclone_save_tree_traverser.html#a692c3e5f4da6bbfe1289a27897d05af2", null ], 5 | [ "processNode", "class_subclone_seeker_1_1_subclone_save_tree_traverser.html#a870dba44b5383681499c97aa15324434", null ], 6 | [ "_database", "class_subclone_seeker_1_1_subclone_save_tree_traverser.html#acb674bf7fe6b39ecc3c56afc77e1c4cd", null ] 7 | ]; -------------------------------------------------------------------------------- /vendor/UnitTest++/src/TestReporterStdout.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TESTREPORTERSTDOUT_H 2 | #define UNITTEST_TESTREPORTERSTDOUT_H 3 | 4 | #include "TestReporter.h" 5 | 6 | namespace UnitTest { 7 | 8 | class TestReporterStdout : public TestReporter 9 | { 10 | private: 11 | virtual void ReportTestStart(TestDetails const& test); 12 | virtual void ReportFailure(TestDetails const& test, char const* failure); 13 | virtual void ReportTestFinish(TestDetails const& test, float secondsElapsed); 14 | virtual void ReportSummary(int totalTestCount, int failedTestCount, int failureCount, float secondsElapsed); 15 | }; 16 | 17 | } 18 | 19 | #endif 20 | -------------------------------------------------------------------------------- /doc/html/search/classes_1.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['clusternotfounderror',['ClusterNotFoundError',['../class_coexistance_table_1_1_cluster_not_found_error.html',1,'CoexistanceTable']]], 4 | ['clusterpairalreadyobservederror',['ClusterPairAlreadyObservedError',['../class_coexistance_table_1_1_cluster_pair_already_observed_error.html',1,'CoexistanceTable']]], 5 | ['cnv',['CNV',['../class_subclone_seeker_1_1_c_n_v.html',1,'SubcloneSeeker']]], 6 | ['coexistancetable',['CoexistanceTable',['../class_coexistance_table.html',1,'']]], 7 | ['coexistancetraversedelegate',['CoexistanceTraverseDelegate',['../class_coexistance_traverse_delegate.html',1,'']]] 8 | ]; 9 | -------------------------------------------------------------------------------- /doc/html/class_subclone_explorer_1_1_subclone_save_tree_traverser.js: -------------------------------------------------------------------------------- 1 | var class_subclone_explorer_1_1_subclone_save_tree_traverser = 2 | [ 3 | [ "SubcloneSaveTreeTraverser", "class_subclone_explorer_1_1_subclone_save_tree_traverser.html#ade4a98f31676ea9901540186b9bf1f9e", null ], 4 | [ "preprocessNode", "class_subclone_explorer_1_1_subclone_save_tree_traverser.html#a692c3e5f4da6bbfe1289a27897d05af2", null ], 5 | [ "processNode", "class_subclone_explorer_1_1_subclone_save_tree_traverser.html#a870dba44b5383681499c97aa15324434", null ], 6 | [ "_database", "class_subclone_explorer_1_1_subclone_save_tree_traverser.html#ae8fc35cf05f52b583b7b06700fdefcee", null ] 7 | ]; -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/TestReporter.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TESTREPORTER_H 2 | #define UNITTEST_TESTREPORTER_H 3 | 4 | namespace UnitTest { 5 | 6 | class TestDetails; 7 | 8 | class TestReporter 9 | { 10 | public: 11 | virtual ~TestReporter(); 12 | 13 | virtual void ReportTestStart(TestDetails const& test) = 0; 14 | virtual void ReportFailure(TestDetails const& test, char const* failure) = 0; 15 | virtual void ReportTestFinish(TestDetails const& test, float secondsElapsed) = 0; 16 | virtual void ReportSummary(int totalTestCount, int failedTestCount, int failureCount, float secondsElapsed) = 0; 17 | }; 18 | 19 | } 20 | #endif 21 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/AssertException.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_ASSERTEXCEPTION_H 2 | #define UNITTEST_ASSERTEXCEPTION_H 3 | 4 | #include 5 | 6 | 7 | namespace UnitTest { 8 | 9 | class AssertException : public std::exception 10 | { 11 | public: 12 | AssertException(char const* description, char const* filename, int lineNumber); 13 | virtual ~AssertException() throw(); 14 | 15 | virtual char const* what() const throw(); 16 | 17 | char const* Filename() const; 18 | int LineNumber() const; 19 | 20 | private: 21 | char m_description[512]; 22 | char m_filename[256]; 23 | int m_lineNumber; 24 | }; 25 | 26 | } 27 | 28 | #endif 29 | -------------------------------------------------------------------------------- /doc/html/search/files_4.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['segmentalmutation_2ecc',['SegmentalMutation.cc',['../_segmental_mutation_8cc.html',1,'']]], 4 | ['segmentalmutation_2eh',['SegmentalMutation.h',['../_segmental_mutation_8h.html',1,'']]], 5 | ['snp_2ecc',['SNP.cc',['../_s_n_p_8cc.html',1,'']]], 6 | ['snp_2eh',['SNP.h',['../_s_n_p_8h.html',1,'']]], 7 | ['somaticevent_2ecc',['SomaticEvent.cc',['../_somatic_event_8cc.html',1,'']]], 8 | ['somaticevent_2eh',['SomaticEvent.h',['../_somatic_event_8h.html',1,'']]], 9 | ['subclone_2ecc',['Subclone.cc',['../_subclone_8cc.html',1,'']]], 10 | ['subclone_2eh',['Subclone.h',['../_subclone_8h.html',1,'']]] 11 | ]; 12 | -------------------------------------------------------------------------------- /doc/html/search/files_73.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['segmentalmutation_2ecc',['SegmentalMutation.cc',['../_segmental_mutation_8cc.html',1,'']]], 4 | ['segmentalmutation_2eh',['SegmentalMutation.h',['../_segmental_mutation_8h.html',1,'']]], 5 | ['snp_2ecc',['SNP.cc',['../_s_n_p_8cc.html',1,'']]], 6 | ['snp_2eh',['SNP.h',['../_s_n_p_8h.html',1,'']]], 7 | ['somaticevent_2ecc',['SomaticEvent.cc',['../_somatic_event_8cc.html',1,'']]], 8 | ['somaticevent_2eh',['SomaticEvent.h',['../_somatic_event_8h.html',1,'']]], 9 | ['subclone_2ecc',['Subclone.cc',['../_subclone_8cc.html',1,'']]], 10 | ['subclone_2eh',['Subclone.h',['../_subclone_8h.html',1,'']]] 11 | ]; 12 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/TestReporterStdout.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TESTREPORTERSTDOUT_H 2 | #define UNITTEST_TESTREPORTERSTDOUT_H 3 | 4 | #include "TestReporter.h" 5 | 6 | namespace UnitTest { 7 | 8 | class TestReporterStdout : public TestReporter 9 | { 10 | private: 11 | virtual void ReportTestStart(TestDetails const& test); 12 | virtual void ReportFailure(TestDetails const& test, char const* failure); 13 | virtual void ReportTestFinish(TestDetails const& test, float secondsElapsed); 14 | virtual void ReportSummary(int totalTestCount, int failedTestCount, int failureCount, float secondsElapsed); 15 | }; 16 | 17 | } 18 | 19 | #endif 20 | -------------------------------------------------------------------------------- /doc/html/class_subclone_seeker_1_1_genomic_location.js: -------------------------------------------------------------------------------- 1 | var class_subclone_seeker_1_1_genomic_location = 2 | [ 3 | [ "GenomicLocation", "class_subclone_seeker_1_1_genomic_location.html#a166d1c98f3d4d0631287127eb7d653cd", null ], 4 | [ "operator<", "class_subclone_seeker_1_1_genomic_location.html#a55aa0c08f503bcfec3b9867dd3242034", null ], 5 | [ "operator>", "class_subclone_seeker_1_1_genomic_location.html#a8b2470c0842e9b11d3c0e57d7b8cd803", null ], 6 | [ "chrom", "class_subclone_seeker_1_1_genomic_location.html#a0ff41c7947d2170f87712f54dce73b8e", null ], 7 | [ "position", "class_subclone_seeker_1_1_genomic_location.html#abfa364692e03c89b920ce74888956d29", null ] 8 | ]; -------------------------------------------------------------------------------- /doc/html/class_tree_print_traverser.js: -------------------------------------------------------------------------------- 1 | var class_tree_print_traverser = 2 | [ 3 | [ "postprocessNode", "class_tree_print_traverser.html#aebd7ac61ef639b769e0d7de4597e3202", null ], 4 | [ "postprocessNode", "class_tree_print_traverser.html#aebd7ac61ef639b769e0d7de4597e3202", null ], 5 | [ "preprocessNode", "class_tree_print_traverser.html#a1a430034a5f0637b3eda13bc54f779a3", null ], 6 | [ "preprocessNode", "class_tree_print_traverser.html#a1a430034a5f0637b3eda13bc54f779a3", null ], 7 | [ "processNode", "class_tree_print_traverser.html#a826b9309cf08e779dcc52d3ed0414167", null ], 8 | [ "processNode", "class_tree_print_traverser.html#a826b9309cf08e779dcc52d3ed0414167", null ] 9 | ]; -------------------------------------------------------------------------------- /doc/html/class_subclone_explorer_1_1_genomic_location.js: -------------------------------------------------------------------------------- 1 | var class_subclone_explorer_1_1_genomic_location = 2 | [ 3 | [ "GenomicLocation", "class_subclone_explorer_1_1_genomic_location.html#a29ccb8457031c7874243d378e0d34721", null ], 4 | [ "operator<", "class_subclone_explorer_1_1_genomic_location.html#a1622b4d20a2f93748a1c3e1640c72462", null ], 5 | [ "operator>", "class_subclone_explorer_1_1_genomic_location.html#a5754531f89dcb2c878ae984c4c6e8e62", null ], 6 | [ "chrom", "class_subclone_explorer_1_1_genomic_location.html#a77351193107676decdc864b0b6acef51", null ], 7 | [ "position", "class_subclone_explorer_1_1_genomic_location.html#af60520d5a86de5a9b64e8a60a813d231", null ] 8 | ]; -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/AssertException.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_ASSERTEXCEPTION_H 2 | #define UNITTEST_ASSERTEXCEPTION_H 3 | 4 | #include 5 | 6 | 7 | namespace UnitTest { 8 | 9 | class AssertException : public std::exception 10 | { 11 | public: 12 | AssertException(char const* description, char const* filename, int lineNumber); 13 | virtual ~AssertException() throw(); 14 | 15 | virtual char const* what() const throw(); 16 | 17 | char const* Filename() const; 18 | int LineNumber() const; 19 | 20 | private: 21 | char m_description[512]; 22 | char m_filename[256]; 23 | int m_lineNumber; 24 | }; 25 | 26 | } 27 | 28 | #endif 29 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/TestList.cpp: -------------------------------------------------------------------------------- 1 | #include "TestList.h" 2 | #include "Test.h" 3 | 4 | #include 5 | 6 | namespace UnitTest { 7 | 8 | TestList::TestList() 9 | : m_head(0) 10 | , m_tail(0) 11 | { 12 | } 13 | 14 | void TestList::Add(Test* test) 15 | { 16 | if (m_tail == 0) 17 | { 18 | assert(m_head == 0); 19 | m_head = test; 20 | m_tail = test; 21 | } 22 | else 23 | { 24 | m_tail->next = test; 25 | m_tail = test; 26 | } 27 | } 28 | 29 | Test* TestList::GetHead() const 30 | { 31 | return m_head; 32 | } 33 | 34 | ListAdder::ListAdder(TestList& list, Test* test) 35 | { 36 | list.Add(test); 37 | } 38 | 39 | } 40 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/TestDetails.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TESTDETAILS_H 2 | #define UNITTEST_TESTDETAILS_H 3 | 4 | namespace UnitTest { 5 | 6 | class TestDetails 7 | { 8 | public: 9 | TestDetails(char const* testName, char const* suiteName, char const* filename, int lineNumber); 10 | TestDetails(const TestDetails& details, int lineNumber); 11 | 12 | char const* const suiteName; 13 | char const* const testName; 14 | char const* const filename; 15 | int const lineNumber; 16 | 17 | TestDetails(TestDetails const&); // Why is it public? --> http://gcc.gnu.org/bugs.html#cxx_rvalbind 18 | private: 19 | TestDetails& operator=(TestDetails const&); 20 | }; 21 | 22 | } 23 | 24 | #endif 25 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | all: libss utils 2 | 3 | libss: 4 | make -C src 5 | 6 | utils: libss 7 | make -C utils 8 | 9 | doc: DOXYGEN-exists doc/source/mainpage.md 10 | doxygen doc/Doxyfile 11 | 12 | DOXYGEN-exists: ; @which doxygen > /dev/null 2>&1 13 | 14 | doc/source/mainpage.md: README.md doc/extra/mainpage_header.md doc/extra/mainpage_additional.md 15 | cat doc/extra/mainpage_header.md $< doc/extra/mainpage_additional.md > $@ 16 | 17 | check: libss utils 18 | make -C vendor/UnitTest++ 19 | make -C test check 20 | make -C utils check 21 | 22 | clean: 23 | make -C vendor/UnitTest++ clean 24 | make -C src clean 25 | make -C utils clean 26 | make -C test clean 27 | 28 | .PHONY: all libss utils check clean doc 29 | -------------------------------------------------------------------------------- /doc/html/treemerge__p_8h.js: -------------------------------------------------------------------------------- 1 | var treemerge__p_8h = 2 | [ 3 | [ "BOUNDRY_RESOLUTION", "treemerge__p_8h.html#a63777350dacef4ba0869630657870963", null ], 4 | [ "checkPlacement", "treemerge__p_8h.html#a65b4cce7423497687bb0d27f026d1a53", null ], 5 | [ "eventSetContains", "treemerge__p_8h.html#a36790025b1a9580a7089bbabf0b5b0f2", null ], 6 | [ "nodeEventsList", "treemerge__p_8h.html#a7fd00f1249526144d7d3afb0cb6b5bb1", null ], 7 | [ "resultSetComparator", "treemerge__p_8h.html#a545793e62441d9f1bff284749b7069df", null ], 8 | [ "SomaticEventDifference", "treemerge__p_8h.html#a079749a809b7e71b2ae3d75a134f5eee", null ], 9 | [ "TreeMerge", "treemerge__p_8h.html#a85bc0ada4190a2a82a56527fc31aa98e", null ] 10 | ]; -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/TestList.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "TestList.h" 2 | #include "Test.h" 3 | 4 | #include 5 | 6 | namespace UnitTest { 7 | 8 | TestList::TestList() 9 | : m_head(0) 10 | , m_tail(0) 11 | { 12 | } 13 | 14 | void TestList::Add(Test* test) 15 | { 16 | if (m_tail == 0) 17 | { 18 | assert(m_head == 0); 19 | m_head = test; 20 | m_tail = test; 21 | } 22 | else 23 | { 24 | m_tail->next = test; 25 | m_tail = test; 26 | } 27 | } 28 | 29 | Test* TestList::GetHead() const 30 | { 31 | return m_head; 32 | } 33 | 34 | ListAdder::ListAdder(TestList& list, Test* test) 35 | { 36 | list.Add(test); 37 | } 38 | 39 | } 40 | -------------------------------------------------------------------------------- /vendor/UnitTest++/docs/.svn/entries: -------------------------------------------------------------------------------- 1 | 10 2 | 3 | dir 4 | 207 5 | https://unittest-cpp.svn.sourceforge.net/svnroot/unittest-cpp/UnitTest++/docs 6 | https://unittest-cpp.svn.sourceforge.net/svnroot/unittest-cpp 7 | 8 | 9 | 10 | 2009-04-27T00:51:43.411738Z 11 | 207 12 | llopis 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | feadf2a4-a60d-0410-a25d-8df00a7d1702 28 | 29 | UnitTest++.html 30 | file 31 | 32 | 33 | 34 | 35 | 2013-07-17T06:11:37.000000Z 36 | ac11e11e79cffa411d27c4b1bc4b72f8 37 | 2009-04-27T00:51:43.411738Z 38 | 207 39 | llopis 40 | has-props 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 12332 62 | 63 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/TestDetails.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TESTDETAILS_H 2 | #define UNITTEST_TESTDETAILS_H 3 | 4 | namespace UnitTest { 5 | 6 | class TestDetails 7 | { 8 | public: 9 | TestDetails(char const* testName, char const* suiteName, char const* filename, int lineNumber); 10 | TestDetails(const TestDetails& details, int lineNumber); 11 | 12 | char const* const suiteName; 13 | char const* const testName; 14 | char const* const filename; 15 | int const lineNumber; 16 | 17 | TestDetails(TestDetails const&); // Why is it public? --> http://gcc.gnu.org/bugs.html#cxx_rvalbind 18 | private: 19 | TestDetails& operator=(TestDetails const&); 20 | }; 21 | 22 | } 23 | 24 | #endif 25 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/Posix/TimeHelpers.cpp: -------------------------------------------------------------------------------- 1 | #include "TimeHelpers.h" 2 | #include 3 | 4 | namespace UnitTest { 5 | 6 | Timer::Timer() 7 | { 8 | m_startTime.tv_sec = 0; 9 | m_startTime.tv_usec = 0; 10 | } 11 | 12 | void Timer::Start() 13 | { 14 | gettimeofday(&m_startTime, 0); 15 | } 16 | 17 | double Timer::GetTimeInMs() const 18 | { 19 | struct timeval currentTime; 20 | gettimeofday(¤tTime, 0); 21 | 22 | double const dsecs = currentTime.tv_sec - m_startTime.tv_sec; 23 | double const dus = currentTime.tv_usec - m_startTime.tv_usec; 24 | 25 | return (dsecs * 1000.0) + (dus / 1000.0); 26 | } 27 | 28 | void TimeHelpers::SleepMs(int ms) 29 | { 30 | usleep(ms * 1000); 31 | } 32 | 33 | } 34 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/Test.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TEST_H 2 | #define UNITTEST_TEST_H 3 | 4 | #include "TestDetails.h" 5 | 6 | namespace UnitTest { 7 | 8 | class TestResults; 9 | class TestList; 10 | 11 | class Test 12 | { 13 | public: 14 | explicit Test(char const* testName, char const* suiteName = "DefaultSuite", char const* filename = "", int lineNumber = 0); 15 | virtual ~Test(); 16 | void Run(); 17 | 18 | TestDetails const m_details; 19 | Test* next; 20 | mutable bool m_timeConstraintExempt; 21 | 22 | static TestList& GetTestList(); 23 | 24 | virtual void RunImpl() const; 25 | 26 | private: 27 | Test(Test const&); 28 | Test& operator =(Test const&); 29 | }; 30 | 31 | 32 | } 33 | 34 | #endif 35 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/Posix/.svn/text-base/TimeHelpers.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "TimeHelpers.h" 2 | #include 3 | 4 | namespace UnitTest { 5 | 6 | Timer::Timer() 7 | { 8 | m_startTime.tv_sec = 0; 9 | m_startTime.tv_usec = 0; 10 | } 11 | 12 | void Timer::Start() 13 | { 14 | gettimeofday(&m_startTime, 0); 15 | } 16 | 17 | double Timer::GetTimeInMs() const 18 | { 19 | struct timeval currentTime; 20 | gettimeofday(¤tTime, 0); 21 | 22 | double const dsecs = currentTime.tv_sec - m_startTime.tv_sec; 23 | double const dus = currentTime.tv_usec - m_startTime.tv_usec; 24 | 25 | return (dsecs * 1000.0) + (dus / 1000.0); 26 | } 27 | 28 | void TimeHelpers::SleepMs(int ms) 29 | { 30 | usleep(ms * 1000); 31 | } 32 | 33 | } 34 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/Test.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TEST_H 2 | #define UNITTEST_TEST_H 3 | 4 | #include "TestDetails.h" 5 | 6 | namespace UnitTest { 7 | 8 | class TestResults; 9 | class TestList; 10 | 11 | class Test 12 | { 13 | public: 14 | explicit Test(char const* testName, char const* suiteName = "DefaultSuite", char const* filename = "", int lineNumber = 0); 15 | virtual ~Test(); 16 | void Run(); 17 | 18 | TestDetails const m_details; 19 | Test* next; 20 | mutable bool m_timeConstraintExempt; 21 | 22 | static TestList& GetTestList(); 23 | 24 | virtual void RunImpl() const; 25 | 26 | private: 27 | Test(Test const&); 28 | Test& operator =(Test const&); 29 | }; 30 | 31 | 32 | } 33 | 34 | #endif 35 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/AssertException.cpp: -------------------------------------------------------------------------------- 1 | #include "AssertException.h" 2 | #include 3 | 4 | namespace UnitTest { 5 | 6 | AssertException::AssertException(char const* description, char const* filename, int lineNumber) 7 | : m_lineNumber(lineNumber) 8 | { 9 | using namespace std; 10 | 11 | strcpy(m_description, description); 12 | strcpy(m_filename, filename); 13 | } 14 | 15 | AssertException::~AssertException() throw() 16 | { 17 | } 18 | 19 | char const* AssertException::what() const throw() 20 | { 21 | return m_description; 22 | } 23 | 24 | char const* AssertException::Filename() const 25 | { 26 | return m_filename; 27 | } 28 | 29 | int AssertException::LineNumber() const 30 | { 31 | return m_lineNumber; 32 | } 33 | 34 | } 35 | -------------------------------------------------------------------------------- /doc/html/search/classes_7.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['segmentalmutation',['SegmentalMutation',['../class_subclone_seeker_1_1_segmental_mutation.html',1,'SubcloneSeeker']]], 4 | ['snp',['SNP',['../class_subclone_seeker_1_1_s_n_p.html',1,'SubcloneSeeker']]], 5 | ['somaticevent',['SomaticEvent',['../class_subclone_seeker_1_1_somatic_event.html',1,'SubcloneSeeker']]], 6 | ['subclone',['Subclone',['../class_subclone_seeker_1_1_subclone.html',1,'SubcloneSeeker']]], 7 | ['subcloneloadtreetraverser',['SubcloneLoadTreeTraverser',['../class_subclone_seeker_1_1_subclone_load_tree_traverser.html',1,'SubcloneSeeker']]], 8 | ['subclonesavetreetraverser',['SubcloneSaveTreeTraverser',['../class_subclone_seeker_1_1_subclone_save_tree_traverser.html',1,'SubcloneSeeker']]] 9 | ]; 10 | -------------------------------------------------------------------------------- /doc/html/search/functions_6.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['isequalto',['isEqualTo',['../class_subclone_seeker_1_1_c_n_v.html#af5e4b26f65b277b44ec922d33102c127',1,'SubcloneSeeker::CNV::isEqualTo()'],['../class_subclone_seeker_1_1_somatic_event.html#a7989de2aceeed60d97799ca79c0709fb',1,'SubcloneSeeker::SomaticEvent::isEqualTo()']]], 4 | ['isleaf',['isLeaf',['../class_subclone_seeker_1_1_tree_node.html#a57299570ae1145599c8aa23012843104',1,'SubcloneSeeker::TreeNode']]], 5 | ['isroot',['isRoot',['../class_subclone_seeker_1_1_tree_node.html#a848b75450733d8f5bceb807aa9d27092',1,'SubcloneSeeker::TreeNode']]], 6 | ['isterminated',['isTerminated',['../class_subclone_seeker_1_1_tree_traverse_delegate.html#a3e15793559ecc1949fa04ca17ab656f6',1,'SubcloneSeeker::TreeTraverseDelegate']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /src/Makefile: -------------------------------------------------------------------------------- 1 | # 2 | # Makefile for SubcloneSeeker 3 | # 4 | 5 | CC=gcc 6 | CXX=g++ 7 | AR=ar 8 | 9 | CFLAGS=-I../vendor 10 | 11 | SOURCES=Archivable.cc \ 12 | EventCluster.cc \ 13 | RefGenome.cc \ 14 | SNP.cc \ 15 | SegmentalMutation.cc \ 16 | SomaticEvent.cc \ 17 | Subclone.cc \ 18 | TreeNode.cc 19 | 20 | SQLITE3_SOURCES=../vendor/sqlite3/sqlite3.c 21 | 22 | OBJECTS=$(SOURCES:.cc=.o) 23 | EXTRA_OBJECTS=$(SQLITE3_SOURCES:.c=.o) 24 | 25 | TARGET=libss.a 26 | 27 | .cc.o: 28 | $(CXX) $(CFLAGS) -c -o $@ $< 29 | 30 | .c.o: 31 | $(CC) $(CFLAGS) -c -o $@ $< 32 | 33 | all: $(TARGET) 34 | 35 | $(TARGET): $(OBJECTS) $(EXTRA_OBJECTS) 36 | ar rcs $(TARGET) $(OBJECTS) $(EXTRA_OBJECTS) 37 | 38 | clean: 39 | rm -rf $(OBJECTS) $(TARGET) 40 | 41 | .PHONY: all clean 42 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/DeferredTestResult.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_DEFERREDTESTRESULT_H 2 | #define UNITTEST_DEFERREDTESTRESULT_H 3 | 4 | #include "Config.h" 5 | 6 | #include 7 | #include 8 | 9 | namespace UnitTest 10 | { 11 | 12 | struct DeferredTestResult 13 | { 14 | DeferredTestResult(); 15 | DeferredTestResult(char const* suite, char const* test); 16 | ~DeferredTestResult(); 17 | 18 | std::string suiteName; 19 | std::string testName; 20 | std::string failureFile; 21 | 22 | typedef std::pair< int, std::string > Failure; 23 | typedef std::vector< Failure > FailureVec; 24 | FailureVec failures; 25 | 26 | float timeElapsed; 27 | bool failed; 28 | }; 29 | 30 | } 31 | 32 | #endif //UNITTEST_DEFERREDTESTRESULT_H 33 | -------------------------------------------------------------------------------- /doc/html/search/functions_d.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['removechild',['removeChild',['../class_subclone_seeker_1_1_tree_node.html#aec9f17f221002078c4abb69bfda33d54',1,'SubcloneSeeker::TreeNode']]], 4 | ['resultsetcomparator',['resultSetComparator',['../treemerge__p_8cc.html#a545793e62441d9f1bff284749b7069df',1,'resultSetComparator(const SomaticEventPtr_vec &v1, const SomaticEventPtr_vec &v2): treemerge_p.cc'],['../treemerge__p_8h.html#a545793e62441d9f1bff284749b7069df',1,'resultSetComparator(const SomaticEventPtr_vec &v1, const SomaticEventPtr_vec &v2): treemerge_p.cc']]], 5 | ['rootnodes',['rootNodes',['../class_subclone_seeker_1_1_subclone_load_tree_traverser.html#aab73727e9ec645ccfa2c2f41c00f1d35',1,'SubcloneSeeker::SubcloneLoadTreeTraverser']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /doc/html/search/functions_72.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['removechild',['removeChild',['../class_subclone_explorer_1_1_tree_node.html#aec9f17f221002078c4abb69bfda33d54',1,'SubcloneExplorer::TreeNode']]], 4 | ['resultsetcomparator',['resultSetComparator',['../treemerge__p_8cc.html#a545793e62441d9f1bff284749b7069df',1,'resultSetComparator(const SomaticEventPtr_vec &v1, const SomaticEventPtr_vec &v2): treemerge_p.cc'],['../treemerge__p_8h.html#a545793e62441d9f1bff284749b7069df',1,'resultSetComparator(const SomaticEventPtr_vec &v1, const SomaticEventPtr_vec &v2): treemerge_p.cc']]], 5 | ['rootnodes',['rootNodes',['../class_subclone_explorer_1_1_subclone_load_tree_traverser.html#aab73727e9ec645ccfa2c2f41c00f1d35',1,'SubcloneExplorer::SubcloneLoadTreeTraverser']]] 6 | ]; 7 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/AssertException.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "AssertException.h" 2 | #include 3 | 4 | namespace UnitTest { 5 | 6 | AssertException::AssertException(char const* description, char const* filename, int lineNumber) 7 | : m_lineNumber(lineNumber) 8 | { 9 | using namespace std; 10 | 11 | strcpy(m_description, description); 12 | strcpy(m_filename, filename); 13 | } 14 | 15 | AssertException::~AssertException() throw() 16 | { 17 | } 18 | 19 | char const* AssertException::what() const throw() 20 | { 21 | return m_description; 22 | } 23 | 24 | char const* AssertException::Filename() const 25 | { 26 | return m_filename; 27 | } 28 | 29 | int AssertException::LineNumber() const 30 | { 31 | return m_lineNumber; 32 | } 33 | 34 | } 35 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/Posix/.svn/all-wcprops: -------------------------------------------------------------------------------- 1 | K 25 2 | svn:wc:ra_dav:version-url 3 | V 55 4 | /svnroot/unittest-cpp/!svn/ver/205/UnitTest++/src/Posix 5 | END 6 | TimeHelpers.cpp 7 | K 25 8 | svn:wc:ra_dav:version-url 9 | V 71 10 | /svnroot/unittest-cpp/!svn/ver/205/UnitTest++/src/Posix/TimeHelpers.cpp 11 | END 12 | TimeHelpers.h 13 | K 25 14 | svn:wc:ra_dav:version-url 15 | V 69 16 | /svnroot/unittest-cpp/!svn/ver/205/UnitTest++/src/Posix/TimeHelpers.h 17 | END 18 | SignalTranslator.cpp 19 | K 25 20 | svn:wc:ra_dav:version-url 21 | V 76 22 | /svnroot/unittest-cpp/!svn/ver/187/UnitTest++/src/Posix/SignalTranslator.cpp 23 | END 24 | SignalTranslator.h 25 | K 25 26 | svn:wc:ra_dav:version-url 27 | V 74 28 | /svnroot/unittest-cpp/!svn/ver/187/UnitTest++/src/Posix/SignalTranslator.h 29 | END 30 | -------------------------------------------------------------------------------- /doc/html/search/functions_1.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['bindobjecttostatement',['bindObjectToStatement',['../class_subclone_seeker_1_1_archivable.html#a21dc93130360b090a2245531c76529a6',1,'SubcloneSeeker::Archivable::bindObjectToStatement()'],['../class_subclone_seeker_1_1_event_cluster.html#aea4cf3701d316f11599df0b150b7c5e9',1,'SubcloneSeeker::EventCluster::bindObjectToStatement()'],['../class_subclone_seeker_1_1_segmental_mutation.html#a3874bfdb9f685984653e278938ef2435',1,'SubcloneSeeker::SegmentalMutation::bindObjectToStatement()'],['../class_subclone_seeker_1_1_s_n_p.html#aad61d75a0a6a56bdb999086db35c2c3e',1,'SubcloneSeeker::SNP::bindObjectToStatement()'],['../class_subclone_seeker_1_1_subclone.html#a264d4cceb61601c761a3fca36efababf',1,'SubcloneSeeker::Subclone::bindObjectToStatement()']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /doc/html/search/functions_69.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['isequalto',['isEqualTo',['../class_subclone_explorer_1_1_c_n_v.html#af5e4b26f65b277b44ec922d33102c127',1,'SubcloneExplorer::CNV::isEqualTo()'],['../class_subclone_explorer_1_1_somatic_event.html#aafe477834c6930c141591cfe488fd606',1,'SubcloneExplorer::SomaticEvent::isEqualTo()']]], 4 | ['isleaf',['isLeaf',['../class_subclone_explorer_1_1_tree_node.html#a9d0017ad33ed7d5351c01e1e3b88815d',1,'SubcloneExplorer::TreeNode']]], 5 | ['isroot',['isRoot',['../class_subclone_explorer_1_1_tree_node.html#a61764447c6c95c7d7ddf98feffcd2943',1,'SubcloneExplorer::TreeNode']]], 6 | ['isterminated',['isTerminated',['../class_subclone_explorer_1_1_tree_traverse_delegate.html#aa85b12536ab25909e228d4698145da51',1,'SubcloneExplorer::TreeTraverseDelegate']]] 7 | ]; 8 | -------------------------------------------------------------------------------- /doc/html/search/classes_73.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['segmentalmutation',['SegmentalMutation',['../class_subclone_explorer_1_1_segmental_mutation.html',1,'SubcloneExplorer']]], 4 | ['snp',['SNP',['../class_subclone_explorer_1_1_s_n_p.html',1,'SubcloneExplorer']]], 5 | ['somaticevent',['SomaticEvent',['../class_subclone_explorer_1_1_somatic_event.html',1,'SubcloneExplorer']]], 6 | ['subclone',['Subclone',['../class_subclone_explorer_1_1_subclone.html',1,'SubcloneExplorer']]], 7 | ['subcloneloadtreetraverser',['SubcloneLoadTreeTraverser',['../class_subclone_explorer_1_1_subclone_load_tree_traverser.html',1,'SubcloneExplorer']]], 8 | ['subclonesavetreetraverser',['SubcloneSaveTreeTraverser',['../class_subclone_explorer_1_1_subclone_save_tree_traverser.html',1,'SubcloneExplorer']]] 9 | ]; 10 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/DeferredTestResult.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_DEFERREDTESTRESULT_H 2 | #define UNITTEST_DEFERREDTESTRESULT_H 3 | 4 | #include "Config.h" 5 | 6 | #include 7 | #include 8 | 9 | namespace UnitTest 10 | { 11 | 12 | struct DeferredTestResult 13 | { 14 | DeferredTestResult(); 15 | DeferredTestResult(char const* suite, char const* test); 16 | ~DeferredTestResult(); 17 | 18 | std::string suiteName; 19 | std::string testName; 20 | std::string failureFile; 21 | 22 | typedef std::pair< int, std::string > Failure; 23 | typedef std::vector< Failure > FailureVec; 24 | FailureVec failures; 25 | 26 | float timeElapsed; 27 | bool failed; 28 | }; 29 | 30 | } 31 | 32 | #endif //UNITTEST_DEFERREDTESTRESULT_H 33 | -------------------------------------------------------------------------------- /doc/html/search/functions_62.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['bindobjecttostatement',['bindObjectToStatement',['../class_subclone_explorer_1_1_archivable.html#a9ed3c4d32672bbb8c04ec2bd3caef725',1,'SubcloneExplorer::Archivable::bindObjectToStatement()'],['../class_subclone_explorer_1_1_event_cluster.html#aea4cf3701d316f11599df0b150b7c5e9',1,'SubcloneExplorer::EventCluster::bindObjectToStatement()'],['../class_subclone_explorer_1_1_segmental_mutation.html#a3874bfdb9f685984653e278938ef2435',1,'SubcloneExplorer::SegmentalMutation::bindObjectToStatement()'],['../class_subclone_explorer_1_1_s_n_p.html#aad61d75a0a6a56bdb999086db35c2c3e',1,'SubcloneExplorer::SNP::bindObjectToStatement()'],['../class_subclone_explorer_1_1_subclone.html#a264d4cceb61601c761a3fca36efababf',1,'SubcloneExplorer::Subclone::bindObjectToStatement()']]] 4 | ]; 5 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/DeferredTestReporter.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_DEFERREDTESTREPORTER_H 2 | #define UNITTEST_DEFERREDTESTREPORTER_H 3 | 4 | #include "TestReporter.h" 5 | #include "DeferredTestResult.h" 6 | #include "Config.h" 7 | 8 | #include 9 | 10 | namespace UnitTest 11 | { 12 | 13 | class DeferredTestReporter : public TestReporter 14 | { 15 | public: 16 | virtual void ReportTestStart(TestDetails const& details); 17 | virtual void ReportFailure(TestDetails const& details, char const* failure); 18 | virtual void ReportTestFinish(TestDetails const& details, float secondsElapsed); 19 | 20 | typedef std::vector< DeferredTestResult > DeferredTestResultList; 21 | DeferredTestResultList& GetResults(); 22 | 23 | private: 24 | DeferredTestResultList m_results; 25 | }; 26 | 27 | } 28 | 29 | #endif 30 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/TimeConstraint.cpp: -------------------------------------------------------------------------------- 1 | #include "TimeConstraint.h" 2 | #include "TestResults.h" 3 | #include "MemoryOutStream.h" 4 | #include "CurrentTest.h" 5 | 6 | namespace UnitTest { 7 | 8 | 9 | TimeConstraint::TimeConstraint(int ms, TestDetails const& details) 10 | : m_details(details) 11 | , m_maxMs(ms) 12 | { 13 | m_timer.Start(); 14 | } 15 | 16 | TimeConstraint::~TimeConstraint() 17 | { 18 | double const totalTimeInMs = m_timer.GetTimeInMs(); 19 | if (totalTimeInMs > m_maxMs) 20 | { 21 | MemoryOutStream stream; 22 | stream << "Time constraint failed. Expected to run test under " << m_maxMs << 23 | "ms but took " << totalTimeInMs << "ms."; 24 | 25 | UnitTest::CurrentTest::Results()->OnTestFailure(m_details, stream.GetText()); 26 | } 27 | } 28 | 29 | } 30 | -------------------------------------------------------------------------------- /utils/CoexistanceTable.h: -------------------------------------------------------------------------------- 1 | #ifndef COEXISTANCETABLE_H 2 | #define COEXISTANCETABLE_H 3 | 4 | #include "EventCluster.h" 5 | #include 6 | 7 | using SubcloneSeeker::EventCluster; 8 | 9 | class CoexistanceTable { 10 | 11 | typedef std::map clusterIndexMapT; 12 | 13 | protected: 14 | clusterIndexMapT clusterIndexMap; 15 | unsigned long **clusterCoexistanceMap; 16 | bool **clusterCoexistanceOnceMap; 17 | unsigned long caseCount; 18 | size_t clusterCount; 19 | 20 | public: 21 | CoexistanceTable(const std::vector& clusters); 22 | ~CoexistanceTable(); 23 | 24 | void NewCase(); 25 | void ObserveCoexistance(const EventCluster& cluster1, const EventCluster& cluster2); 26 | 27 | class ClusterNotFoundError {}; 28 | class ClusterPairAlreadyObservedError {}; 29 | }; 30 | 31 | #endif 32 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/Win32/TimeHelpers.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TIMEHELPERS_H 2 | #define UNITTEST_TIMEHELPERS_H 3 | 4 | #include "../Config.h" 5 | 6 | 7 | #ifdef UNITTEST_MINGW 8 | #ifndef __int64 9 | #define __int64 long long 10 | #endif 11 | #endif 12 | 13 | namespace UnitTest { 14 | 15 | class Timer 16 | { 17 | public: 18 | Timer(); 19 | void Start(); 20 | double GetTimeInMs() const; 21 | 22 | private: 23 | __int64 GetTime() const; 24 | 25 | void* m_threadHandle; 26 | 27 | #if defined(_WIN64) 28 | unsigned __int64 m_processAffinityMask; 29 | #else 30 | unsigned long m_processAffinityMask; 31 | #endif 32 | 33 | __int64 m_startTime; 34 | __int64 m_frequency; 35 | }; 36 | 37 | 38 | namespace TimeHelpers 39 | { 40 | void SleepMs (int ms); 41 | } 42 | 43 | 44 | } 45 | 46 | 47 | 48 | #endif 49 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/DeferredTestReporter.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_DEFERREDTESTREPORTER_H 2 | #define UNITTEST_DEFERREDTESTREPORTER_H 3 | 4 | #include "TestReporter.h" 5 | #include "DeferredTestResult.h" 6 | #include "Config.h" 7 | 8 | #include 9 | 10 | namespace UnitTest 11 | { 12 | 13 | class DeferredTestReporter : public TestReporter 14 | { 15 | public: 16 | virtual void ReportTestStart(TestDetails const& details); 17 | virtual void ReportFailure(TestDetails const& details, char const* failure); 18 | virtual void ReportTestFinish(TestDetails const& details, float secondsElapsed); 19 | 20 | typedef std::vector< DeferredTestResult > DeferredTestResultList; 21 | DeferredTestResultList& GetResults(); 22 | 23 | private: 24 | DeferredTestResultList m_results; 25 | }; 26 | 27 | } 28 | 29 | #endif 30 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/TimeConstraint.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "TimeConstraint.h" 2 | #include "TestResults.h" 3 | #include "MemoryOutStream.h" 4 | #include "CurrentTest.h" 5 | 6 | namespace UnitTest { 7 | 8 | 9 | TimeConstraint::TimeConstraint(int ms, TestDetails const& details) 10 | : m_details(details) 11 | , m_maxMs(ms) 12 | { 13 | m_timer.Start(); 14 | } 15 | 16 | TimeConstraint::~TimeConstraint() 17 | { 18 | double const totalTimeInMs = m_timer.GetTimeInMs(); 19 | if (totalTimeInMs > m_maxMs) 20 | { 21 | MemoryOutStream stream; 22 | stream << "Time constraint failed. Expected to run test under " << m_maxMs << 23 | "ms but took " << totalTimeInMs << "ms."; 24 | 25 | UnitTest::CurrentTest::Results()->OnTestFailure(m_details, stream.GetText()); 26 | } 27 | } 28 | 29 | } 30 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/TimeConstraint.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TIMECONSTRAINT_H 2 | #define UNITTEST_TIMECONSTRAINT_H 3 | 4 | #include "TimeHelpers.h" 5 | 6 | namespace UnitTest { 7 | 8 | class TestResults; 9 | class TestDetails; 10 | 11 | class TimeConstraint 12 | { 13 | public: 14 | TimeConstraint(int ms, TestDetails const& details); 15 | ~TimeConstraint(); 16 | 17 | private: 18 | void operator=(TimeConstraint const&); 19 | TimeConstraint(TimeConstraint const&); 20 | 21 | Timer m_timer; 22 | TestDetails const& m_details; 23 | int const m_maxMs; 24 | }; 25 | 26 | #define UNITTEST_TIME_CONSTRAINT(ms) \ 27 | UnitTest::TimeConstraint unitTest__timeConstraint__(ms, UnitTest::TestDetails(m_details, __LINE__)) 28 | 29 | #define UNITTEST_TIME_CONSTRAINT_EXEMPT() do { m_timeConstraintExempt = true; } while (0) 30 | 31 | } 32 | 33 | #endif 34 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/Win32/.svn/text-base/TimeHelpers.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TIMEHELPERS_H 2 | #define UNITTEST_TIMEHELPERS_H 3 | 4 | #include "../Config.h" 5 | 6 | 7 | #ifdef UNITTEST_MINGW 8 | #ifndef __int64 9 | #define __int64 long long 10 | #endif 11 | #endif 12 | 13 | namespace UnitTest { 14 | 15 | class Timer 16 | { 17 | public: 18 | Timer(); 19 | void Start(); 20 | double GetTimeInMs() const; 21 | 22 | private: 23 | __int64 GetTime() const; 24 | 25 | void* m_threadHandle; 26 | 27 | #if defined(_WIN64) 28 | unsigned __int64 m_processAffinityMask; 29 | #else 30 | unsigned long m_processAffinityMask; 31 | #endif 32 | 33 | __int64 m_startTime; 34 | __int64 m_frequency; 35 | }; 36 | 37 | 38 | namespace TimeHelpers 39 | { 40 | void SleepMs (int ms); 41 | } 42 | 43 | 44 | } 45 | 46 | 47 | 48 | #endif 49 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/Test.cpp: -------------------------------------------------------------------------------- 1 | #include "Config.h" 2 | #include "Test.h" 3 | #include "TestList.h" 4 | #include "TestResults.h" 5 | #include "AssertException.h" 6 | #include "MemoryOutStream.h" 7 | #include "ExecuteTest.h" 8 | 9 | #ifdef UNITTEST_POSIX 10 | #include "Posix/SignalTranslator.h" 11 | #endif 12 | 13 | namespace UnitTest { 14 | 15 | TestList& Test::GetTestList() 16 | { 17 | static TestList s_list; 18 | return s_list; 19 | } 20 | 21 | Test::Test(char const* testName, char const* suiteName, char const* filename, int lineNumber) 22 | : m_details(testName, suiteName, filename, lineNumber) 23 | , next(0) 24 | , m_timeConstraintExempt(false) 25 | { 26 | } 27 | 28 | Test::~Test() 29 | { 30 | } 31 | 32 | void Test::Run() 33 | { 34 | ExecuteTest(*this, m_details); 35 | } 36 | 37 | void Test::RunImpl() const 38 | { 39 | } 40 | 41 | } 42 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/TimeConstraint.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TIMECONSTRAINT_H 2 | #define UNITTEST_TIMECONSTRAINT_H 3 | 4 | #include "TimeHelpers.h" 5 | 6 | namespace UnitTest { 7 | 8 | class TestResults; 9 | class TestDetails; 10 | 11 | class TimeConstraint 12 | { 13 | public: 14 | TimeConstraint(int ms, TestDetails const& details); 15 | ~TimeConstraint(); 16 | 17 | private: 18 | void operator=(TimeConstraint const&); 19 | TimeConstraint(TimeConstraint const&); 20 | 21 | Timer m_timer; 22 | TestDetails const& m_details; 23 | int const m_maxMs; 24 | }; 25 | 26 | #define UNITTEST_TIME_CONSTRAINT(ms) \ 27 | UnitTest::TimeConstraint unitTest__timeConstraint__(ms, UnitTest::TestDetails(m_details, __LINE__)) 28 | 29 | #define UNITTEST_TIME_CONSTRAINT_EXEMPT() do { m_timeConstraintExempt = true; } while (0) 30 | 31 | } 32 | 33 | #endif 34 | -------------------------------------------------------------------------------- /doc/html/class_subclone_seeker_1_1_s_n_p.js: -------------------------------------------------------------------------------- 1 | var class_subclone_seeker_1_1_s_n_p = 2 | [ 3 | [ "bindObjectToStatement", "class_subclone_seeker_1_1_s_n_p.html#aad61d75a0a6a56bdb999086db35c2c3e", null ], 4 | [ "createObjectStatementStr", "class_subclone_seeker_1_1_s_n_p.html#a14ed98f3914a61d0f1a1a8879c2e62c8", null ], 5 | [ "getTableName", "class_subclone_seeker_1_1_s_n_p.html#a7f0fcf54763c4c1835c941cee04d5a2b", null ], 6 | [ "selectObjectColumnListStr", "class_subclone_seeker_1_1_s_n_p.html#a76395cde38b99f48f7236e9d066664b1", null ], 7 | [ "updateObjectFromStatement", "class_subclone_seeker_1_1_s_n_p.html#a070b05399a6af8fd328e0647ca5502aa", null ], 8 | [ "updateObjectStatementStr", "class_subclone_seeker_1_1_s_n_p.html#a9032bc6e9eaaf8fa100926d801d913ae", null ], 9 | [ "location", "class_subclone_seeker_1_1_s_n_p.html#a75f6f776c0a95ccb97011566e8fe2660", null ] 10 | ]; -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/Test.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "Config.h" 2 | #include "Test.h" 3 | #include "TestList.h" 4 | #include "TestResults.h" 5 | #include "AssertException.h" 6 | #include "MemoryOutStream.h" 7 | #include "ExecuteTest.h" 8 | 9 | #ifdef UNITTEST_POSIX 10 | #include "Posix/SignalTranslator.h" 11 | #endif 12 | 13 | namespace UnitTest { 14 | 15 | TestList& Test::GetTestList() 16 | { 17 | static TestList s_list; 18 | return s_list; 19 | } 20 | 21 | Test::Test(char const* testName, char const* suiteName, char const* filename, int lineNumber) 22 | : m_details(testName, suiteName, filename, lineNumber) 23 | , next(0) 24 | , m_timeConstraintExempt(false) 25 | { 26 | } 27 | 28 | Test::~Test() 29 | { 30 | } 31 | 32 | void Test::Run() 33 | { 34 | ExecuteTest(*this, m_details); 35 | } 36 | 37 | void Test::RunImpl() const 38 | { 39 | } 40 | 41 | } 42 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/tests/TestCurrentTest.cpp: -------------------------------------------------------------------------------- 1 | #include "../UnitTest++.h" 2 | #include "../CurrentTest.h" 3 | #include "ScopedCurrentTest.h" 4 | 5 | namespace 6 | { 7 | 8 | TEST(CanSetandGetDetails) 9 | { 10 | bool ok = false; 11 | { 12 | ScopedCurrentTest scopedTest; 13 | 14 | const UnitTest::TestDetails* details = reinterpret_cast< const UnitTest::TestDetails* >(12345); 15 | UnitTest::CurrentTest::Details() = details; 16 | 17 | ok = (UnitTest::CurrentTest::Details() == details); 18 | } 19 | 20 | CHECK(ok); 21 | } 22 | 23 | TEST(CanSetAndGetResults) 24 | { 25 | bool ok = false; 26 | { 27 | ScopedCurrentTest scopedTest; 28 | 29 | UnitTest::TestResults results; 30 | UnitTest::CurrentTest::Results() = &results; 31 | 32 | ok = (UnitTest::CurrentTest::Results() == &results); 33 | } 34 | 35 | CHECK(ok); 36 | } 37 | 38 | } 39 | -------------------------------------------------------------------------------- /doc/html/class_subclone_explorer_1_1_s_n_p.js: -------------------------------------------------------------------------------- 1 | var class_subclone_explorer_1_1_s_n_p = 2 | [ 3 | [ "bindObjectToStatement", "class_subclone_explorer_1_1_s_n_p.html#aad61d75a0a6a56bdb999086db35c2c3e", null ], 4 | [ "createObjectStatementStr", "class_subclone_explorer_1_1_s_n_p.html#a14ed98f3914a61d0f1a1a8879c2e62c8", null ], 5 | [ "getTableName", "class_subclone_explorer_1_1_s_n_p.html#a7f0fcf54763c4c1835c941cee04d5a2b", null ], 6 | [ "selectObjectColumnListStr", "class_subclone_explorer_1_1_s_n_p.html#a76395cde38b99f48f7236e9d066664b1", null ], 7 | [ "updateObjectFromStatement", "class_subclone_explorer_1_1_s_n_p.html#a070b05399a6af8fd328e0647ca5502aa", null ], 8 | [ "updateObjectStatementStr", "class_subclone_explorer_1_1_s_n_p.html#a9032bc6e9eaaf8fa100926d801d913ae", null ], 9 | [ "location", "class_subclone_explorer_1_1_s_n_p.html#aacf3436a54ca0b4fe8b1843962a96204", null ] 10 | ]; -------------------------------------------------------------------------------- /test/Makefile: -------------------------------------------------------------------------------- 1 | # 2 | # Makefile for SubcloneSeeker 3 | # 4 | 5 | CC=gcc 6 | CXX=g++ 7 | AR=ar 8 | 9 | CFLAGS=-I../vendor -I../src 10 | CXXFLAGS=$(CFLAGS) 11 | TEST_FLAGS=-I../vendor/UnitTest++ 12 | LDFLAGS=-L../src 13 | LDADDS=../src/libss.a -lpthread -ldl 14 | LDADDS_TEST=../vendor/UnitTest++/libUnitTest++.a 15 | 16 | TEST_SOURCES=TestEventCluster.cc \ 17 | TestGenomicLocation.cc \ 18 | TestGenomicRange.cc \ 19 | TestSomaticEvent.cc \ 20 | TestSubclone.cc \ 21 | TestTreeNode.cc 22 | 23 | TESTS=$(TEST_SOURCES:.cc=.test) 24 | TEST_STUBS=$(TESTS:.test=.stub) 25 | 26 | .SUFFIXES: .test .stub 27 | 28 | .cc.test: 29 | $(CXX) $(CXXFLAGS) $(TEST_FLAGS) -o $@ $< $(LDADDS) $(LDADDS_TEST) 30 | 31 | %.stub: %.test 32 | @echo "Running $(<:.test=)..." 33 | @./$< 34 | 35 | all: check 36 | 37 | check: $(TEST_STUBS) 38 | 39 | clean: 40 | rm -rf $(TESTS) 41 | 42 | .PHONY: all clean check 43 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/tests/.svn/text-base/TestCurrentTest.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "../UnitTest++.h" 2 | #include "../CurrentTest.h" 3 | #include "ScopedCurrentTest.h" 4 | 5 | namespace 6 | { 7 | 8 | TEST(CanSetandGetDetails) 9 | { 10 | bool ok = false; 11 | { 12 | ScopedCurrentTest scopedTest; 13 | 14 | const UnitTest::TestDetails* details = reinterpret_cast< const UnitTest::TestDetails* >(12345); 15 | UnitTest::CurrentTest::Details() = details; 16 | 17 | ok = (UnitTest::CurrentTest::Details() == details); 18 | } 19 | 20 | CHECK(ok); 21 | } 22 | 23 | TEST(CanSetAndGetResults) 24 | { 25 | bool ok = false; 26 | { 27 | ScopedCurrentTest scopedTest; 28 | 29 | UnitTest::TestResults results; 30 | UnitTest::CurrentTest::Results() = &results; 31 | 32 | ok = (UnitTest::CurrentTest::Results() == &results); 33 | } 34 | 35 | CHECK(ok); 36 | } 37 | 38 | } 39 | -------------------------------------------------------------------------------- /doc/html/search/all_2.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['bindobjecttostatement',['bindObjectToStatement',['../class_subclone_seeker_1_1_archivable.html#a21dc93130360b090a2245531c76529a6',1,'SubcloneSeeker::Archivable::bindObjectToStatement()'],['../class_subclone_seeker_1_1_event_cluster.html#aea4cf3701d316f11599df0b150b7c5e9',1,'SubcloneSeeker::EventCluster::bindObjectToStatement()'],['../class_subclone_seeker_1_1_segmental_mutation.html#a3874bfdb9f685984653e278938ef2435',1,'SubcloneSeeker::SegmentalMutation::bindObjectToStatement()'],['../class_subclone_seeker_1_1_s_n_p.html#aad61d75a0a6a56bdb999086db35c2c3e',1,'SubcloneSeeker::SNP::bindObjectToStatement()'],['../class_subclone_seeker_1_1_subclone.html#a264d4cceb61601c761a3fca36efababf',1,'SubcloneSeeker::Subclone::bindObjectToStatement()']]], 4 | ['boundry_5fresolution',['BOUNDRY_RESOLUTION',['../treemerge__p_8h.html#a63777350dacef4ba0869630657870963',1,'treemerge_p.h']]] 5 | ]; 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6 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/TestResults.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TESTRESULTS_H 2 | #define UNITTEST_TESTRESULTS_H 3 | 4 | namespace UnitTest { 5 | 6 | class TestReporter; 7 | class TestDetails; 8 | 9 | class TestResults 10 | { 11 | public: 12 | explicit TestResults(TestReporter* reporter = 0); 13 | 14 | void OnTestStart(TestDetails const& test); 15 | void OnTestFailure(TestDetails const& test, char const* failure); 16 | void OnTestFinish(TestDetails const& test, float secondsElapsed); 17 | 18 | int GetTotalTestCount() const; 19 | int GetFailedTestCount() const; 20 | int GetFailureCount() const; 21 | 22 | private: 23 | TestReporter* m_testReporter; 24 | int m_totalTestCount; 25 | int m_failedTestCount; 26 | int m_failureCount; 27 | 28 | bool m_currentTestFailed; 29 | 30 | TestResults(TestResults const&); 31 | TestResults& operator =(TestResults const&); 32 | }; 33 | 34 | } 35 | 36 | #endif 37 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/TestResults.h.svn-base: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_TESTRESULTS_H 2 | #define UNITTEST_TESTRESULTS_H 3 | 4 | namespace UnitTest { 5 | 6 | class TestReporter; 7 | class TestDetails; 8 | 9 | class TestResults 10 | { 11 | public: 12 | explicit TestResults(TestReporter* reporter = 0); 13 | 14 | void OnTestStart(TestDetails const& test); 15 | void OnTestFailure(TestDetails const& test, char const* failure); 16 | void OnTestFinish(TestDetails const& test, float secondsElapsed); 17 | 18 | int GetTotalTestCount() const; 19 | int GetFailedTestCount() const; 20 | int GetFailureCount() const; 21 | 22 | private: 23 | TestReporter* m_testReporter; 24 | int m_totalTestCount; 25 | int m_failedTestCount; 26 | int m_failureCount; 27 | 28 | bool m_currentTestFailed; 29 | 30 | TestResults(TestResults const&); 31 | TestResults& operator =(TestResults const&); 32 | }; 33 | 34 | } 35 | 36 | #endif 37 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/DeferredTestReporter.cpp: -------------------------------------------------------------------------------- 1 | #include "DeferredTestReporter.h" 2 | #include "TestDetails.h" 3 | 4 | using namespace UnitTest; 5 | 6 | void DeferredTestReporter::ReportTestStart(TestDetails const& details) 7 | { 8 | m_results.push_back(DeferredTestResult(details.suiteName, details.testName)); 9 | } 10 | 11 | void DeferredTestReporter::ReportFailure(TestDetails const& details, char const* failure) 12 | { 13 | DeferredTestResult& r = m_results.back(); 14 | r.failed = true; 15 | r.failures.push_back(DeferredTestResult::Failure(details.lineNumber, failure)); 16 | r.failureFile = details.filename; 17 | } 18 | 19 | void DeferredTestReporter::ReportTestFinish(TestDetails const&, float secondsElapsed) 20 | { 21 | DeferredTestResult& r = m_results.back(); 22 | r.timeElapsed = secondsElapsed; 23 | } 24 | 25 | DeferredTestReporter::DeferredTestResultList& DeferredTestReporter::GetResults() 26 | { 27 | return m_results; 28 | } 29 | -------------------------------------------------------------------------------- /doc/html/search/functions_a.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['operator_3c',['operator<',['../class_subclone_seeker_1_1_event_cluster.html#abbd9dc836385e1d36ddb72e8b48aad8b',1,'SubcloneSeeker::EventCluster::operator<()'],['../class_subclone_seeker_1_1_genomic_location.html#a55aa0c08f503bcfec3b9867dd3242034',1,'SubcloneSeeker::GenomicLocation::operator<()']]], 4 | ['operator_3d_3d',['operator==',['../class_subclone_seeker_1_1_genomic_range.html#a11a4d97d1fa8c091dded531e76056973',1,'SubcloneSeeker::GenomicRange']]], 5 | ['operator_3e',['operator>',['../class_subclone_seeker_1_1_event_cluster.html#a4285019e9949515a834d65b227735853',1,'SubcloneSeeker::EventCluster::operator>()'],['../class_subclone_seeker_1_1_genomic_location.html#a8b2470c0842e9b11d3c0e57d7b8cd803',1,'SubcloneSeeker::GenomicLocation::operator>()']]], 6 | ['overlaps',['overlaps',['../class_subclone_seeker_1_1_genomic_range.html#ad40bf7d27b00fbdd3b5eeb84b41cd08a',1,'SubcloneSeeker::GenomicRange']]] 7 | ]; 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-------------------------------------------------------------------------------- /vendor/UnitTest++/src/.svn/text-base/DeferredTestReporter.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "DeferredTestReporter.h" 2 | #include "TestDetails.h" 3 | 4 | using namespace UnitTest; 5 | 6 | void DeferredTestReporter::ReportTestStart(TestDetails const& details) 7 | { 8 | m_results.push_back(DeferredTestResult(details.suiteName, details.testName)); 9 | } 10 | 11 | void DeferredTestReporter::ReportFailure(TestDetails const& details, char const* failure) 12 | { 13 | DeferredTestResult& r = m_results.back(); 14 | r.failed = true; 15 | r.failures.push_back(DeferredTestResult::Failure(details.lineNumber, failure)); 16 | r.failureFile = details.filename; 17 | } 18 | 19 | void DeferredTestReporter::ReportTestFinish(TestDetails const&, float secondsElapsed) 20 | { 21 | DeferredTestResult& r = m_results.back(); 22 | r.timeElapsed = secondsElapsed; 23 | } 24 | 25 | DeferredTestReporter::DeferredTestResultList& DeferredTestReporter::GetResults() 26 | { 27 | return m_results; 28 | } 29 | -------------------------------------------------------------------------------- /doc/html/class_subclone_seeker_1_1_segmental_mutation.js: -------------------------------------------------------------------------------- 1 | var class_subclone_seeker_1_1_segmental_mutation = 2 | [ 3 | [ "SegmentalMutation", "class_subclone_seeker_1_1_segmental_mutation.html#a6cb4611d13dba7d4b90e4d664f66a5fb", null ], 4 | [ "bindObjectToStatement", "class_subclone_seeker_1_1_segmental_mutation.html#a3874bfdb9f685984653e278938ef2435", null ], 5 | [ "createObjectStatementStr", "class_subclone_seeker_1_1_segmental_mutation.html#a1d66893b82e224e6348f5689c59583e1", null ], 6 | [ "selectObjectColumnListStr", "class_subclone_seeker_1_1_segmental_mutation.html#ab139ed14dd33b1374235577fb86eda2f", null ], 7 | [ "updateObjectFromStatement", "class_subclone_seeker_1_1_segmental_mutation.html#a8d9ab88cafed0831b4871bdff25754a9", null ], 8 | [ "updateObjectStatementStr", "class_subclone_seeker_1_1_segmental_mutation.html#a373b8aeb1f5d840f3b7de35ebaa53d1c", null ], 9 | [ "range", "class_subclone_seeker_1_1_segmental_mutation.html#a03db5155dd9091e8a142877df83cd7ce", null ] 10 | ]; 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10 | -------------------------------------------------------------------------------- /doc/html/class_subclone_explorer_1_1_segmental_mutation.js: -------------------------------------------------------------------------------- 1 | var class_subclone_explorer_1_1_segmental_mutation = 2 | [ 3 | [ "SegmentalMutation", "class_subclone_explorer_1_1_segmental_mutation.html#a32293640fdefd69f3734961b4219181a", null ], 4 | [ "bindObjectToStatement", "class_subclone_explorer_1_1_segmental_mutation.html#a3874bfdb9f685984653e278938ef2435", null ], 5 | [ "createObjectStatementStr", "class_subclone_explorer_1_1_segmental_mutation.html#a1d66893b82e224e6348f5689c59583e1", null ], 6 | [ "selectObjectColumnListStr", "class_subclone_explorer_1_1_segmental_mutation.html#ab139ed14dd33b1374235577fb86eda2f", null ], 7 | [ "updateObjectFromStatement", "class_subclone_explorer_1_1_segmental_mutation.html#a8d9ab88cafed0831b4871bdff25754a9", null ], 8 | [ "updateObjectStatementStr", "class_subclone_explorer_1_1_segmental_mutation.html#a373b8aeb1f5d840f3b7de35ebaa53d1c", null ], 9 | [ "range", "class_subclone_explorer_1_1_segmental_mutation.html#a126dc16608ec7cc57f5f890ec498a7dc", null ] 10 | ]; -------------------------------------------------------------------------------- /doc/html/class_subclone_seeker_1_1_somatic_event.js: -------------------------------------------------------------------------------- 1 | var class_subclone_seeker_1_1_somatic_event = 2 | [ 3 | [ "SomaticEvent", "class_subclone_seeker_1_1_somatic_event.html#aa463ef8688b9fc4eba6111bf2ab700d7", null ], 4 | [ "allObjectsOfCluster", "class_subclone_seeker_1_1_somatic_event.html#a0064ccd2c056e4e4a50f2a5c3e63c822", null ], 5 | [ "clusterID", "class_subclone_seeker_1_1_somatic_event.html#a6a53f11563de4a666e60890710c523a0", null ], 6 | [ "createTableStatementStr", "class_subclone_seeker_1_1_somatic_event.html#ac6ffe96eee9d590bf724ecb49a5d1e9f", null ], 7 | [ "isEqualTo", "class_subclone_seeker_1_1_somatic_event.html#a7989de2aceeed60d97799ca79c0709fb", null ], 8 | [ "setClusterID", "class_subclone_seeker_1_1_somatic_event.html#a1a0fe5df82bec5c37fecb1ae8f6d0234", null ], 9 | [ "frequency", "class_subclone_seeker_1_1_somatic_event.html#aef56c53d7eb294a6063b4a5043a0ed87", null ], 10 | [ "ofClusterID", "class_subclone_seeker_1_1_somatic_event.html#acdf2c80463f11c2e5debc5fc0ecc12ad", null ] 11 | ]; -------------------------------------------------------------------------------- /vendor/UnitTest++/src/tests/TestAssertHandler.cpp: -------------------------------------------------------------------------------- 1 | #include "../UnitTest++.h" 2 | #include "../AssertException.h" 3 | #include "../ReportAssert.h" 4 | 5 | using namespace UnitTest; 6 | 7 | namespace { 8 | 9 | TEST(ReportAssertThrowsAssertException) 10 | { 11 | bool caught = false; 12 | 13 | try 14 | { 15 | ReportAssert("", "", 0); 16 | } 17 | catch(AssertException const&) 18 | { 19 | caught = true; 20 | } 21 | 22 | CHECK (true == caught); 23 | } 24 | 25 | TEST(ReportAssertSetsCorrectInfoInException) 26 | { 27 | const int lineNumber = 12345; 28 | const char* description = "description"; 29 | const char* filename = "filename"; 30 | 31 | try 32 | { 33 | ReportAssert(description, filename, lineNumber); 34 | } 35 | catch(AssertException const& e) 36 | { 37 | CHECK_EQUAL(description, e.what()); 38 | CHECK_EQUAL(filename, e.Filename()); 39 | CHECK_EQUAL(lineNumber, e.LineNumber()); 40 | } 41 | } 42 | 43 | 44 | } 45 | -------------------------------------------------------------------------------- /doc/html/class_subclone_explorer_1_1_somatic_event.js: -------------------------------------------------------------------------------- 1 | var class_subclone_explorer_1_1_somatic_event = 2 | [ 3 | [ "SomaticEvent", "class_subclone_explorer_1_1_somatic_event.html#a36d8cb7db1e0098d41e26b6b1e48dab9", null ], 4 | [ "allObjectsOfCluster", "class_subclone_explorer_1_1_somatic_event.html#a0064ccd2c056e4e4a50f2a5c3e63c822", null ], 5 | [ "clusterID", "class_subclone_explorer_1_1_somatic_event.html#a74d3db2c5bdc791cfa5c14f9f6e8e8fe", null ], 6 | [ "createTableStatementStr", "class_subclone_explorer_1_1_somatic_event.html#ac6ffe96eee9d590bf724ecb49a5d1e9f", null ], 7 | [ "isEqualTo", "class_subclone_explorer_1_1_somatic_event.html#aafe477834c6930c141591cfe488fd606", null ], 8 | [ "setClusterID", "class_subclone_explorer_1_1_somatic_event.html#a52af3954dabb7b45b2d9b3bcef504f5e", null ], 9 | [ "frequency", "class_subclone_explorer_1_1_somatic_event.html#a42f108dc0bc7bc0119bb6e0da2af32f3", null ], 10 | [ "ofClusterID", "class_subclone_explorer_1_1_somatic_event.html#ad84d19bfa348564a913f642248dc2ec1", null ] 11 | ]; -------------------------------------------------------------------------------- /vendor/UnitTest++/src/tests/.svn/text-base/TestAssertHandler.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "../UnitTest++.h" 2 | #include "../AssertException.h" 3 | #include "../ReportAssert.h" 4 | 5 | using namespace UnitTest; 6 | 7 | namespace { 8 | 9 | TEST(ReportAssertThrowsAssertException) 10 | { 11 | bool caught = false; 12 | 13 | try 14 | { 15 | ReportAssert("", "", 0); 16 | } 17 | catch(AssertException const&) 18 | { 19 | caught = true; 20 | } 21 | 22 | CHECK (true == caught); 23 | } 24 | 25 | TEST(ReportAssertSetsCorrectInfoInException) 26 | { 27 | const int lineNumber = 12345; 28 | const char* description = "description"; 29 | const char* filename = "filename"; 30 | 31 | try 32 | { 33 | ReportAssert(description, filename, lineNumber); 34 | } 35 | catch(AssertException const& e) 36 | { 37 | CHECK_EQUAL(description, e.what()); 38 | CHECK_EQUAL(filename, e.Filename()); 39 | CHECK_EQUAL(lineNumber, e.LineNumber()); 40 | } 41 | } 42 | 43 | 44 | } 45 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/tests/TestTestList.cpp: -------------------------------------------------------------------------------- 1 | #include "../UnitTest++.h" 2 | #include "../TestList.h" 3 | 4 | using namespace UnitTest; 5 | 6 | namespace { 7 | 8 | 9 | TEST (TestListIsEmptyByDefault) 10 | { 11 | TestList list; 12 | CHECK (list.GetHead() == 0); 13 | } 14 | 15 | TEST (AddingTestSetsHeadToTest) 16 | { 17 | Test test("test"); 18 | TestList list; 19 | list.Add(&test); 20 | 21 | CHECK (list.GetHead() == &test); 22 | CHECK (test.next == 0); 23 | } 24 | 25 | TEST (AddingSecondTestAddsItToEndOfList) 26 | { 27 | Test test1("test1"); 28 | Test test2("test2"); 29 | 30 | TestList list; 31 | list.Add(&test1); 32 | list.Add(&test2); 33 | 34 | CHECK (list.GetHead() == &test1); 35 | CHECK (test1.next == &test2); 36 | CHECK (test2.next == 0); 37 | } 38 | 39 | TEST (ListAdderAddsTestToList) 40 | { 41 | TestList list; 42 | 43 | Test test(""); 44 | ListAdder adder(list, &test); 45 | 46 | CHECK (list.GetHead() == &test); 47 | CHECK (test.next == 0); 48 | } 49 | 50 | } 51 | -------------------------------------------------------------------------------- /doc/html/search/all_7.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['id',['id',['../class_subclone_seeker_1_1_archivable.html#aec0d9a77bfec71a1dff3b07ca67e3cf1',1,'SubcloneSeeker::Archivable']]], 4 | ['iscompatible',['isCompatible',['../class_tree_merge_traverse_secondary.html#a5823ea751966c751e32ae1be4a810780',1,'TreeMergeTraverseSecondary']]], 5 | ['isequalto',['isEqualTo',['../class_subclone_seeker_1_1_c_n_v.html#af5e4b26f65b277b44ec922d33102c127',1,'SubcloneSeeker::CNV::isEqualTo()'],['../class_subclone_seeker_1_1_somatic_event.html#a7989de2aceeed60d97799ca79c0709fb',1,'SubcloneSeeker::SomaticEvent::isEqualTo()']]], 6 | ['isleaf',['isLeaf',['../class_subclone_seeker_1_1_tree_node.html#a57299570ae1145599c8aa23012843104',1,'SubcloneSeeker::TreeNode']]], 7 | ['isroot',['isRoot',['../class_subclone_seeker_1_1_tree_node.html#a848b75450733d8f5bceb807aa9d27092',1,'SubcloneSeeker::TreeNode']]], 8 | ['isterminated',['isTerminated',['../class_subclone_seeker_1_1_tree_traverse_delegate.html#a3e15793559ecc1949fa04ca17ab656f6',1,'SubcloneSeeker::TreeTraverseDelegate']]] 9 | ]; 10 | -------------------------------------------------------------------------------- /doc/html/search/all_e.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['range',['range',['../class_subclone_seeker_1_1_segmental_mutation.html#a03db5155dd9091e8a142877df83cd7ce',1,'SubcloneSeeker::SegmentalMutation']]], 4 | ['refgenome',['RefGenome',['../class_ref_genome.html',1,'']]], 5 | ['refgenome_2eh',['RefGenome.h',['../_ref_genome_8h.html',1,'']]], 6 | ['removechild',['removeChild',['../class_subclone_seeker_1_1_tree_node.html#aec9f17f221002078c4abb69bfda33d54',1,'SubcloneSeeker::TreeNode']]], 7 | ['resultsetcomparator',['resultSetComparator',['../treemerge__p_8cc.html#a545793e62441d9f1bff284749b7069df',1,'resultSetComparator(const SomaticEventPtr_vec &v1, const SomaticEventPtr_vec &v2): treemerge_p.cc'],['../treemerge__p_8h.html#a545793e62441d9f1bff284749b7069df',1,'resultSetComparator(const SomaticEventPtr_vec &v1, const SomaticEventPtr_vec &v2): treemerge_p.cc']]], 8 | ['rootnodes',['rootNodes',['../class_subclone_seeker_1_1_subclone_load_tree_traverser.html#aab73727e9ec645ccfa2c2f41c00f1d35',1,'SubcloneSeeker::SubcloneLoadTreeTraverser']]] 9 | ]; 10 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/Win32/.svn/entries: -------------------------------------------------------------------------------- 1 | 10 2 | 3 | dir 4 | 207 5 | https://unittest-cpp.svn.sourceforge.net/svnroot/unittest-cpp/UnitTest++/src/Win32 6 | https://unittest-cpp.svn.sourceforge.net/svnroot/unittest-cpp 7 | 8 | 9 | 10 | 2009-02-02T04:50:16.945106Z 11 | 205 12 | cnicholson 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | feadf2a4-a60d-0410-a25d-8df00a7d1702 28 | 29 | TimeHelpers.cpp 30 | file 31 | 32 | 33 | 34 | 35 | 2013-07-17T06:11:37.000000Z 36 | 6c838740f3bb378bbdbd66efcdec989e 37 | 2009-02-02T04:50:16.945106Z 38 | 205 39 | cnicholson 40 | has-props 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 1094 62 | 63 | TimeHelpers.h 64 | file 65 | 66 | 67 | 68 | 69 | 2013-07-17T06:11:37.000000Z 70 | 2dafb4c49147ee5d68d1ef0413800fff 71 | 2009-02-02T04:50:16.945106Z 72 | 205 73 | cnicholson 74 | has-props 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 586 96 | 97 | -------------------------------------------------------------------------------- /vendor/UnitTest++/src/tests/.svn/text-base/TestTestList.cpp.svn-base: -------------------------------------------------------------------------------- 1 | #include "../UnitTest++.h" 2 | #include "../TestList.h" 3 | 4 | using namespace UnitTest; 5 | 6 | namespace { 7 | 8 | 9 | TEST (TestListIsEmptyByDefault) 10 | { 11 | TestList list; 12 | CHECK (list.GetHead() == 0); 13 | } 14 | 15 | TEST (AddingTestSetsHeadToTest) 16 | { 17 | Test test("test"); 18 | TestList list; 19 | list.Add(&test); 20 | 21 | CHECK (list.GetHead() == &test); 22 | CHECK (test.next == 0); 23 | } 24 | 25 | TEST (AddingSecondTestAddsItToEndOfList) 26 | { 27 | Test test1("test1"); 28 | Test test2("test2"); 29 | 30 | TestList list; 31 | list.Add(&test1); 32 | list.Add(&test2); 33 | 34 | CHECK (list.GetHead() == &test1); 35 | CHECK (test1.next == &test2); 36 | CHECK (test2.next == 0); 37 | } 38 | 39 | TEST (ListAdderAddsTestToList) 40 | { 41 | TestList list; 42 | 43 | Test test(""); 44 | ListAdder adder(list, &test); 45 | 46 | CHECK (list.GetHead() == &test); 47 | CHECK (test.next == 0); 48 | } 49 | 50 | } 51 | -------------------------------------------------------------------------------- /doc/html/search/all_69.js: -------------------------------------------------------------------------------- 1 | var searchData= 2 | [ 3 | ['id',['id',['../class_subclone_explorer_1_1_archivable.html#a7e67ca95e2bab5ae71b8bef359758806',1,'SubcloneExplorer::Archivable']]], 4 | ['iscompatible',['isCompatible',['../class_tree_merge_traverse_secondary.html#a5823ea751966c751e32ae1be4a810780',1,'TreeMergeTraverseSecondary']]], 5 | ['isequalto',['isEqualTo',['../class_subclone_explorer_1_1_c_n_v.html#af5e4b26f65b277b44ec922d33102c127',1,'SubcloneExplorer::CNV::isEqualTo()'],['../class_subclone_explorer_1_1_somatic_event.html#aafe477834c6930c141591cfe488fd606',1,'SubcloneExplorer::SomaticEvent::isEqualTo()']]], 6 | ['isleaf',['isLeaf',['../class_subclone_explorer_1_1_tree_node.html#a9d0017ad33ed7d5351c01e1e3b88815d',1,'SubcloneExplorer::TreeNode']]], 7 | ['isroot',['isRoot',['../class_subclone_explorer_1_1_tree_node.html#a61764447c6c95c7d7ddf98feffcd2943',1,'SubcloneExplorer::TreeNode']]], 8 | ['isterminated',['isTerminated',['../class_subclone_explorer_1_1_tree_traverse_delegate.html#aa85b12536ab25909e228d4698145da51',1,'SubcloneExplorer::TreeTraverseDelegate']]] 9 | ]; 10 | -------------------------------------------------------------------------------- /doc/html/class_subclone_seeker_1_1_tree_traverse_delegate.js: -------------------------------------------------------------------------------- 1 | var class_subclone_seeker_1_1_tree_traverse_delegate = 2 | [ 3 | [ "TreeTraverseDelegate", "class_subclone_seeker_1_1_tree_traverse_delegate.html#a640ce08a884fc2ae6e39298def2de8f3", null ], 4 | [ "~TreeTraverseDelegate", "class_subclone_seeker_1_1_tree_traverse_delegate.html#aaaa5ba3f2351546d402c890e4fde6147", null ], 5 | [ "isTerminated", "class_subclone_seeker_1_1_tree_traverse_delegate.html#a3e15793559ecc1949fa04ca17ab656f6", null ], 6 | [ "postprocessNode", "class_subclone_seeker_1_1_tree_traverse_delegate.html#a8ad5dc8fcaf603494e63582988d76093", null ], 7 | [ "preprocessNode", "class_subclone_seeker_1_1_tree_traverse_delegate.html#a42a135424c06cd01eb938376061ee949", null ], 8 | [ "processNode", "class_subclone_seeker_1_1_tree_traverse_delegate.html#a4bf2d3eda4c43103d2388dc41f6ff891", null ], 9 | [ "terminate", "class_subclone_seeker_1_1_tree_traverse_delegate.html#aec7c9f7f61234131af59b9ad80f9ae65", null ], 10 | [ "_isTerminated", "class_subclone_seeker_1_1_tree_traverse_delegate.html#a5515fc8591f48a1a90966cd3330c8bc3", null ] 11 | ]; -------------------------------------------------------------------------------- /vendor/UnitTest++/src/Config.h: -------------------------------------------------------------------------------- 1 | #ifndef UNITTEST_CONFIG_H 2 | #define UNITTEST_CONFIG_H 3 | 4 | // Standard defines documented here: http://predef.sourceforge.net 5 | 6 | #if defined(_MSC_VER) 7 | #pragma warning(disable:4127) // conditional expression is constant 8 | #pragma warning(disable:4702) // unreachable code 9 | #pragma warning(disable:4722) // destructor never returns, potential memory leak 10 | 11 | #if (_MSC_VER == 1200) // VC6 12 | #pragma warning(disable:4786) 13 | #pragma warning(disable:4290) 14 | #endif 15 | #endif 16 | 17 | #if defined(unix) || defined(__unix__) || defined(__unix) || defined(linux) || \ 18 | defined(__APPLE__) || defined(__NetBSD__) || defined(__OpenBSD__) || defined(__FreeBSD__) 19 | #define UNITTEST_POSIX 20 | #endif 21 | 22 | #if defined(__MINGW32__) 23 | #define UNITTEST_MINGW 24 | #endif 25 | 26 | // by default, MemoryOutStream is implemented in terms of std::ostringstream, which can be expensive. 27 | // uncomment this line to use the custom MemoryOutStream (no deps on std::ostringstream). 28 | 29 | //#define UNITTEST_USE_CUSTOM_STREAMS 30 | 31 | #endif 32 | -------------------------------------------------------------------------------- /doc/html/search/all_0.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
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