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change file headers to MIT
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‎examples/standalone/epochtest/COPYING

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This file was deleted.

‎examples/standalone/epochtest/LICENSE

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MIT License
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Copyright (c) 2021 Phylogenetic Likelihood Working Group
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎java/beagle/Beagle.java

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*
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* This file is part of BEAGLE.
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*
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* BEAGLE is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Lesser General Public License as
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* published by the Free Software Foundation, either version 3 of
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* the License, or (at your option) any later version.
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*
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* BEAGLE is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public
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* License along with BEAGLE. If not, see
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* <http://www.gnu.org/licenses/>.
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* Use of this source code is governed by an MIT-style
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* license that can be found in the LICENSE file or at
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* https://opensource.org/licenses/MIT.
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*
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* @brief This file documents the API as well as header for the
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* Broad-platform Evolutionary Analysis General Likelihood Evaluator

‎libhmsbeagle/BeagleImpl.h

+32-42
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@@ -6,20 +6,10 @@
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*
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* This file is part of BEAGLE.
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*
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* BEAGLE is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Lesser General Public License as
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* published by the Free Software Foundation, either version 3 of
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* the License, or (at your option) any later version.
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* Use of this source code is governed by an MIT-style
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* license that can be found in the LICENSE file or at
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* https://opensource.org/licenses/MIT.
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*
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* BEAGLE is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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*
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* You should have received a copy of the GNU Lesser General Public
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* License along with BEAGLE. If not, see
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* <http://www.gnu.org/licenses/>.
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*
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* @author Andrew Rambaut
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* @author Marc Suchard
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* @author Daniel Ayres
@@ -42,31 +32,31 @@ class BeagleImpl
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{
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public:
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virtual ~BeagleImpl(){}
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virtual int createInstance(int tipCount,
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int partialsBufferCount,
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int compactBufferCount,
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int stateCount,
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int patternCount,
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int eigenBufferCount,
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int matrixBufferCount,
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int matrixBufferCount,
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int categoryCount,
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int scaleBufferCount,
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int resourceNumber,
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int pluginResourceNumber,
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long preferenceFlags,
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long requirementFlags) = 0;
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virtual int getInstanceDetails(BeagleInstanceDetails* returnInfo) = 0;
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virtual int setCPUThreadCount(int threadCount) = 0;
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virtual int setTipStates(int tipIndex,
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const int* inStates) = 0;
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virtual int setTipPartials(int tipIndex,
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const double* inPartials) = 0;
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virtual int setPartials(int bufferIndex,
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const double* inPartials) = 0;
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@@ -77,28 +67,28 @@ class BeagleImpl
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virtual int getPartials(int bufferIndex,
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int scaleIndex,
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double* outPartials) = 0;
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virtual int setEigenDecomposition(int eigenIndex,
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const double* inEigenVectors,
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const double* inInverseEigenVectors,
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const double* inEigenValues) = 0;
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virtual int setStateFrequencies(int stateFrequenciesIndex,
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const double* inStateFrequencies) = 0;
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const double* inStateFrequencies) = 0;
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virtual int setCategoryWeights(int categoryWeightsIndex,
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const double* inCategoryWeights) = 0;
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virtual int setPatternWeights(const double* inPatternWeights) = 0;
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virtual int setPatternPartitions(int partitionCount,
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const int* inPatternPartitions) = 0;
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virtual int setCategoryRates(const double* inCategoryRates) = 0;
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virtual int setCategoryRatesWithIndex(int categoryRatesIndex,
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const double* inCategoryRates) = 0;
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virtual int setTransitionMatrix(int matrixIndex,
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const double* inMatrix,
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double paddedValue) = 0;
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virtual int setTransitionMatrices(const int* matrixIndices,
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const double* inMatrices,
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const double* paddedValues,
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int count) = 0;
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int count) = 0;
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virtual int getTransitionMatrix(int matrixIndex,
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double* outMatrix) = 0;
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const int* secondDerivativeIndices,
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const double* edgeLengths,
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int count) = 0;
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virtual int updatePartials(const int* operations,
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int operationCount,
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int cumulativeScalingIndex) = 0;
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virtual int waitForPartials(const int* destinationPartials,
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int destinationPartialsCount) = 0;
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virtual int accumulateScaleFactors(const int* scalingIndices,
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int count,
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int cumulativeScalingIndex) = 0;
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int count,
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int cumulativeScaleIndex,
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int partitionIndex) = 0;
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virtual int removeScaleFactors(const int* scalingIndices,
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int count,
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int cumulativeScalingIndex) = 0;
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int count,
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int cumulativeScaleIndex,
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int partitionIndex) = 0;
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virtual int resetScaleFactors(int cumulativeScalingIndex) = 0;
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virtual int resetScaleFactors(int cumulativeScalingIndex) = 0;
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virtual int resetScaleFactorsByPartition(int cumulativeScaleIndex,
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int partitionIndex) = 0;
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int partitionIndex) = 0;
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virtual int copyScaleFactors(int destScalingIndex,
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int srcScalingIndex) = 0;
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int srcScalingIndex) = 0;
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virtual int getScaleFactors(int srcScalingIndex,
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double* scaleFactors) = 0;
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double* scaleFactors) = 0;
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virtual int calculateRootLogLikelihoods(const int* bufferIndices,
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const int* categoryWeightsIndices,
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const int* stateFrequenciesIndices,
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double* outSumFirstDerivative,
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double* outSumSecondDerivativeByPartition,
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double* outSumSecondDerivative) = 0;
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virtual int getLogLikelihood(double* outSumLogLikelihood) = 0;
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virtual int getDerivatives(double* outSumFirstDerivative,
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double* outSumSecondDerivative) = 0;
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virtual int getSiteLogLikelihoods(double* outLogLikelihoods) = 0;
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virtual int getSiteDerivatives(double* outFirstDerivatives,
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double* outSecondDerivatives) = 0;
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//protected:
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long preferenceFlags,
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long requirementFlags,
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int* errorCode) = 0; // pure virtual
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virtual const char* getName() = 0; // pure virtual
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virtual const long getFlags() = 0; // pure virtual
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};
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‎libhmsbeagle/CPU/AVXDefinitions.h

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*
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* This file is part of BEAGLE.
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*
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* BEAGLE is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Lesser General Public License as
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* published by the Free Software Foundation, either version 3 of
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* the License, or (at your option) any later version.
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*
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* BEAGLE is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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*
19-
* You should have received a copy of the GNU Lesser General Public
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* License along with BEAGLE. If not, see
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* <http://www.gnu.org/licenses/>.
9+
* Use of this source code is governed by an MIT-style
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* license that can be found in the LICENSE file or at
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* https://opensource.org/licenses/MIT.
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*
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* @author Marc Suchard
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*/

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