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1.40.0 #351
| @@ -0,0 +1,69 @@ | ||
| +// Copyright 2015, Google Inc. | ||
| +// All rights reserved. | ||
| +// | ||
| +// Redistribution and use in source and binary forms, with or without | ||
| +// modification, are permitted provided that the following conditions are | ||
| +// met: | ||
| +// | ||
| +// * Redistributions of source code must retain the above copyright | ||
| +// notice, this list of conditions and the following disclaimer. | ||
| +// * Redistributions in binary form must reproduce the above | ||
| +// copyright notice, this list of conditions and the following disclaimer | ||
| +// in the documentation and/or other materials provided with the | ||
| +// distribution. | ||
| +// * Neither the name of Google Inc. nor the names of its | ||
| +// contributors may be used to endorse or promote products derived from | ||
| +// this software without specific prior written permission. | ||
| +// | ||
| +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS | ||
| +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT | ||
| +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR | ||
| +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT | ||
| +// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, | ||
| +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT | ||
| +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, | ||
| +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY | ||
| +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT | ||
| +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | ||
| +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| +// | ||
| +// Injection point for custom user configurations. | ||
| +// The following macros can be defined: | ||
| +// | ||
| +// Flag related macros: | ||
| +// GTEST_FLAG(flag_name) | ||
| +// GTEST_USE_OWN_FLAGFILE_FLAG_ - Define to 0 when the system provides its | ||
| +// own flagfile flag parsing. | ||
| +// GTEST_DECLARE_bool_(name) | ||
| +// GTEST_DECLARE_int32_(name) | ||
| +// GTEST_DECLARE_string_(name) | ||
| +// GTEST_DEFINE_bool_(name, default_val, doc) | ||
| +// GTEST_DEFINE_int32_(name, default_val, doc) | ||
| +// GTEST_DEFINE_string_(name, default_val, doc) | ||
| +// | ||
| +// Test filtering: | ||
| +// GTEST_TEST_FILTER_ENV_VAR_ - The name of an environment variable that | ||
| +// will be used if --GTEST_FLAG(test_filter) | ||
| +// is not provided. | ||
| +// | ||
| +// Logging: | ||
| +// GTEST_LOG_(severity) | ||
| +// GTEST_CHECK_(condition) | ||
| +// Functions LogToStderr() and FlushInfoLog() have to be provided too. | ||
| +// | ||
| +// Threading: | ||
| +// GTEST_HAS_NOTIFICATION_ - Enabled if Notification is already provided. | ||
| +// GTEST_HAS_MUTEX_AND_THREAD_LOCAL_ - Enabled if Mutex and ThreadLocal are | ||
| +// already provided. | ||
| +// Must also provide GTEST_DECLARE_STATIC_MUTEX_(mutex) and | ||
| +// GTEST_DEFINE_STATIC_MUTEX_(mutex) | ||
| +// | ||
| +// GTEST_EXCLUSIVE_LOCK_REQUIRED_(locks) | ||
| +// GTEST_LOCK_EXCLUDED_(locks) | ||
| +// | ||
| +// ** Custom implementation starts here ** | ||
| + | ||
| +#ifndef GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_PORT_H_ | ||
| +#define GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_PORT_H_ | ||
| + | ||
| +#endif // GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_PORT_H_ |
| @@ -0,0 +1,42 @@ | ||
| +// Copyright 2015, Google Inc. | ||
| +// All rights reserved. | ||
| +// | ||
| +// Redistribution and use in source and binary forms, with or without | ||
| +// modification, are permitted provided that the following conditions are | ||
| +// met: | ||
| +// | ||
| +// * Redistributions of source code must retain the above copyright | ||
| +// notice, this list of conditions and the following disclaimer. | ||
| +// * Redistributions in binary form must reproduce the above | ||
| +// copyright notice, this list of conditions and the following disclaimer | ||
| +// in the documentation and/or other materials provided with the | ||
| +// distribution. | ||
| +// * Neither the name of Google Inc. nor the names of its | ||
| +// contributors may be used to endorse or promote products derived from | ||
| +// this software without specific prior written permission. | ||
| +// | ||
| +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS | ||
| +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT | ||
| +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR | ||
| +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT | ||
| +// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, | ||
| +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT | ||
| +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, | ||
| +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY | ||
| +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT | ||
| +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | ||
| +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| +// | ||
| +// This file provides an injection point for custom printers in a local | ||
| +// installation of gTest. | ||
| +// It will be included from gtest-printers.h and the overrides in this file | ||
| +// will be visible to everyone. | ||
| +// See documentation at gtest-printers.h for details on how to define a | ||
| +// custom printer. | ||
| +// | ||
| +// ** Custom implementation starts here ** | ||
| + | ||
| +#ifndef GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_PRINTERS_H_ | ||
| +#define GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_PRINTERS_H_ | ||
| + | ||
| +#endif // GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_PRINTERS_H_ |
| @@ -0,0 +1,41 @@ | ||
| +// Copyright 2015, Google Inc. | ||
| +// All rights reserved. | ||
| +// | ||
| +// Redistribution and use in source and binary forms, with or without | ||
| +// modification, are permitted provided that the following conditions are | ||
| +// met: | ||
| +// | ||
| +// * Redistributions of source code must retain the above copyright | ||
| +// notice, this list of conditions and the following disclaimer. | ||
| +// * Redistributions in binary form must reproduce the above | ||
| +// copyright notice, this list of conditions and the following disclaimer | ||
| +// in the documentation and/or other materials provided with the | ||
| +// distribution. | ||
| +// * Neither the name of Google Inc. nor the names of its | ||
| +// contributors may be used to endorse or promote products derived from | ||
| +// this software without specific prior written permission. | ||
| +// | ||
| +// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS | ||
| +// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT | ||
| +// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR | ||
| +// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT | ||
| +// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, | ||
| +// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT | ||
| +// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, | ||
| +// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY | ||
| +// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT | ||
| +// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE | ||
| +// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. | ||
| +// | ||
| +// Injection point for custom user configurations. | ||
| +// The following macros can be defined: | ||
| +// | ||
| +// GTEST_OS_STACK_TRACE_GETTER_ - The name of an implementation of | ||
| +// OsStackTraceGetterInterface. | ||
| +// | ||
| +// ** Custom implementation starts here ** | ||
| + | ||
| +#ifndef GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_H_ | ||
| +#define GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_H_ | ||
| + | ||
| +#endif // GTEST_INCLUDE_GTEST_INTERNAL_CUSTOM_GTEST_H_ |
| @@ -0,0 +1,28 @@ | ||
| +// | ||
| +// fakemcc.hpp | ||
| +// Mothur | ||
| +// | ||
| +// Created by Sarah Westcott on 4/18/17. | ||
| +// Copyright © 2017 Schloss Lab. All rights reserved. | ||
| +// | ||
| + | ||
| +#ifndef fakemcc_hpp | ||
| +#define fakemcc_hpp | ||
| + | ||
| +#include "mothurout.h" | ||
| + | ||
| + | ||
| +class FakeClusterCalcValues { | ||
| + | ||
| +public: | ||
| + | ||
| + FakeClusterCalcValues() { tp = 823; tn = 1944106; fp = 95; fn = 354; } | ||
| + ~FakeClusterCalcValues() {} | ||
| + | ||
| + long long tp, tn, fp, fn; | ||
| +}; | ||
| + | ||
| + | ||
| + | ||
| +#endif /* fakemcc_hpp */ | ||
| + |
| @@ -0,0 +1,54 @@ | ||
| +// | ||
| +// fakeoligos.h | ||
| +// Mothur | ||
| +// | ||
| +// Created by Sarah Westcott on 5/1/17. | ||
| +// Copyright © 2017 Schloss Lab. All rights reserved. | ||
| +// | ||
| + | ||
| +#ifndef fakeoligos_h | ||
| +#define fakeoligos_h | ||
| + | ||
| +#include "mothurout.h" | ||
| + | ||
| + | ||
| +class FakeOligos { | ||
| + | ||
| +public: | ||
| + | ||
| + FakeOligos() { | ||
| + bdiffs=1; pdiffs=2; rdiffs=0; ldiffs=0; sdiffs=0; | ||
| + | ||
| + //single | ||
| + primers["CCGTCAATTCMTTTRAGT"] = 0; | ||
| + barcodes["AATGGTAC"] = 0; //F003D000 | ||
| + barcodes["AACCTGGC"] = 1; //F003D002 | ||
| + barcodes["TTCGTGGC"] = 2; //F003D004 | ||
| + barcodes["TTCTTGAC"] = 3; //F003D006 | ||
| + barcodes["TTCGCGAC"] = 4; //F003D008 | ||
| + barcodes["TCCAGAAC"] = 5; //F003D142 | ||
| + barcodes["AAGGCCTC"] = 6; //F003D144 | ||
| + barcodes["TGACCGTC"] = 7; //F003D146 | ||
| + barcodes["AGGTTGTC"] = 8; //F003D148 | ||
| + barcodes["TGGTGAAC"] = 9; //F003D150 | ||
| + barcodes["AACCGTGTC"] = 10; //MOCK.GQY1XT001 | ||
| + | ||
| + | ||
| + } | ||
| + ~FakeOligos() {} | ||
| + | ||
| + int bdiffs, pdiffs, rdiffs, ldiffs, sdiffs; | ||
| + map<string, int> barcodes; | ||
| + map<string, int> primers; | ||
| + | ||
| + vector<string> revPrimer; | ||
| + vector<string> linker; | ||
| + vector<string> spacer; | ||
| + map<int, oligosPair> ipbarcodes; | ||
| + map<int, oligosPair> ipprimers; | ||
| + | ||
| +}; | ||
| + | ||
| + | ||
| + | ||
| +#endif /* fakeoligos_h */ |
| @@ -0,0 +1,42 @@ | ||
| +// | ||
| +// fakeoptimatrix.cpp | ||
| +// Mothur | ||
| +// | ||
| +// Created by Sarah Westcott on 4/20/17. | ||
| +// Copyright © 2017 Schloss Lab. All rights reserved. | ||
| +// | ||
| + | ||
| +#include "fakeoptimatrix.hpp" | ||
| + | ||
| +/***********************************************************************/ | ||
| +FakeOptiMatrix::FakeOptiMatrix() : OptiMatrix() { | ||
| + try { | ||
| + m = MothurOut::getInstance(); | ||
| + | ||
| + //create 10 singletons | ||
| + for (int i = 90; i < 100; i++) { singletons.push_back(toString(i)); } | ||
| + | ||
| + //create 90 non singletons | ||
| + for (int i = 0; i < 90; i++) { nameMap.push_back(toString(i)); } | ||
| + | ||
| + closeness.resize(90); | ||
| + int count = 0; | ||
| + for (int i = 0; i < 9; i++) { | ||
| + set<int> close; | ||
| + //create list of all sequences in this set | ||
| + for (int j = 0; j < 10; j++) { close.insert((j+count)); } | ||
| + | ||
| + for (set<int>::iterator it = close.begin(); it != close.end(); it++) { | ||
| + //add close sequences to each sequence in this set, do not include self | ||
| + for (int j = 0; j < 10; j++) { if ((j+count) != *it) { closeness[j+count].insert(*it); } } | ||
| + } | ||
| + count += 10; | ||
| + } | ||
| + } | ||
| + catch(exception& e) { | ||
| + m->errorOut(e, "FakeOptiMatrix", "FakeOptiMatrix"); | ||
| + exit(1); | ||
| + } | ||
| +} | ||
| +/***********************************************************************/ | ||
| + |
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