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topsframework / tops

ToPS Framework: http://topsframework.github.io/tops/doc/api/
GNU General Public License v2.0
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Close #23 (Exceptions) #62

Closed ademar111190 closed 8 years ago

ademar111190 commented 8 years ago

I accidentally accepted the previous push, I believe that I have reverted the mistake made. This pull request is the correct one.

In this new pull request, I think that I have did all the suggestions, if you see that someone is still wrong or if you see someone new feel free to tell me.

ademar111190 commented 8 years ago

One more thing. I don't know why the CI fails, the test on my machine are correctly:

$ make test
[OK] Generating C++ library artifact build/model/GeneralizedHiddenMarkovModel.o 
[OK] Generating C++ library artifact build/model/InhomogeneousMarkovChain.o 
[OK] Generating C++ shared library lib/libmodel.so 
[OK] Generating C++ artifact build/exception/Exception.o 
[OK] Generating C++ artifact build/exception/InvalidModelDefinition.o 
[OK] Generating C++ artifact build/exception/NotYetImplemented.o 
[OK] Generating C++ artifact build/exception/OutOfRange.o 
[OK] Generating C++ artifact build/test/exception/NotYetImplementedTest.o 
[OK] Generating C++ artifact build/test/model/GeneralizedHiddenMarkovModelTest.o 
[OK] Generating C++ artifact build/test/model/InhomogeneousMarkovChainTest.o 
[OK] Generating C++ executable bin/test/test 
Running test bin/test/test ... 
######################################################################################################################################################
[==========] Running 80 tests from 20 test cases.
[----------] Global test environment set-up.
[----------] 1 test from NotYetImplemented
[ RUN      ] NotYetImplemented.ShouldThrowAMessage
[       OK ] NotYetImplemented.ShouldThrowAMessage (0 ms)
[----------] 1 test from NotYetImplemented (0 ms total)

[----------] 8 tests from DiscreteIIDModel
[ RUN      ] DiscreteIIDModel.ShouldBeTrainedUsingMLAlgorithm
[       OK ] DiscreteIIDModel.ShouldBeTrainedUsingMLAlgorithm (0 ms)
[ RUN      ] DiscreteIIDModel.ShouldBeTrainedUsingSmoothedHistogramBurgeAlgorithm
[       OK ] DiscreteIIDModel.ShouldBeTrainedUsingSmoothedHistogramBurgeAlgorithm (23 ms)
[ RUN      ] DiscreteIIDModel.ShouldBeTrainedUsingSmoothedHistogramStankeAlgorithm
[       OK ] DiscreteIIDModel.ShouldBeTrainedUsingSmoothedHistogramStankeAlgorithm (1229 ms)
[ RUN      ] DiscreteIIDModel.ShouldBeTrainedUsingSmoothedHistogramKernelDensityAlgorithm
[       OK ] DiscreteIIDModel.ShouldBeTrainedUsingSmoothedHistogramKernelDensityAlgorithm (228 ms)
[ RUN      ] DiscreteIIDModel.ShouldBeTrainedUsingMLAlgorithmWithEmptyDataSet
[       OK ] DiscreteIIDModel.ShouldBeTrainedUsingMLAlgorithmWithEmptyDataSet (0 ms)
[ RUN      ] DiscreteIIDModel.ShouldBeTrainedUsingSmoothedHistogramBurgeAlgorithmWithEmptyDataSet
[       OK ] DiscreteIIDModel.ShouldBeTrainedUsingSmoothedHistogramBurgeAlgorithmWithEmptyDataSet (0 ms)
[ RUN      ] DiscreteIIDModel.ShouldBeTrainedUsingSmoothedHistogramStankeAlgorithmWithAnEmptyDataSet
[       OK ] DiscreteIIDModel.ShouldBeTrainedUsingSmoothedHistogramStankeAlgorithmWithAnEmptyDataSet (0 ms)
[ RUN      ] DiscreteIIDModel.ShouldBeTrainedUsingSmoothedHistogramKernelDensityAlgorithmWithAnEmptyDataSet
[       OK ] DiscreteIIDModel.ShouldBeTrainedUsingSmoothedHistogramKernelDensityAlgorithmWithAnEmptyDataSet (0 ms)
[----------] 8 tests from DiscreteIIDModel (1480 ms total)

[----------] 7 tests from ADiscreteIIDModel
[ RUN      ] ADiscreteIIDModel.ShouldHaveAnAlphabetSize
[       OK ] ADiscreteIIDModel.ShouldHaveAnAlphabetSize (0 ms)
[ RUN      ] ADiscreteIIDModel.ShouldEvaluateASingleSymbol
[       OK ] ADiscreteIIDModel.ShouldEvaluateASingleSymbol (0 ms)
[ RUN      ] ADiscreteIIDModel.ShouldHaveEvaluateASequence
[       OK ] ADiscreteIIDModel.ShouldHaveEvaluateASequence (0 ms)
[ RUN      ] ADiscreteIIDModel.ShouldEvaluateASequencePosition
[       OK ] ADiscreteIIDModel.ShouldEvaluateASequencePosition (0 ms)
[ RUN      ] ADiscreteIIDModel.ShouldEvaluateASequenceWithPrefixSumArray
[       OK ] ADiscreteIIDModel.ShouldEvaluateASequenceWithPrefixSumArray (92 ms)
[ RUN      ] ADiscreteIIDModel.ShouldDrawSequenceWithDefaultSeed
[       OK ] ADiscreteIIDModel.ShouldDrawSequenceWithDefaultSeed (0 ms)
[ RUN      ] ADiscreteIIDModel.ShouldBeSExprSerialized
[       OK ] ADiscreteIIDModel.ShouldBeSExprSerialized (0 ms)
[----------] 7 tests from ADiscreteIIDModel (92 ms total)

[----------] 2 tests from ADiscreteIIDModelWithFixedSequenceAtPosition
[ RUN      ] ADiscreteIIDModelWithFixedSequenceAtPosition.ShouldEvaluateSequence
[       OK ] ADiscreteIIDModelWithFixedSequenceAtPosition.ShouldEvaluateSequence (0 ms)
[ RUN      ] ADiscreteIIDModelWithFixedSequenceAtPosition.ShouldDrawSequenceWithDefaultSeed
[       OK ] ADiscreteIIDModelWithFixedSequenceAtPosition.ShouldDrawSequenceWithDefaultSeed (0 ms)
[----------] 2 tests from ADiscreteIIDModelWithFixedSequenceAtPosition (0 ms total)

[----------] 10 tests from AGHMM
[ RUN      ] AGHMM.ShouldBeSExprSerialized
[       OK ] AGHMM.ShouldBeSExprSerialized (1 ms)
[ RUN      ] AGHMM.ShouldEvaluateSequence
[       OK ] AGHMM.ShouldEvaluateSequence (0 ms)
[ RUN      ] AGHMM.ShouldThrowAnNotYetImplementedInEvaluateSequence
[       OK ] AGHMM.ShouldThrowAnNotYetImplementedInEvaluateSequence (0 ms)
[ RUN      ] AGHMM.ShouldThrowAnNotYetImplementedInEvaluateSymbol
[       OK ] AGHMM.ShouldThrowAnNotYetImplementedInEvaluateSymbol (0 ms)
[ RUN      ] AGHMM.ShouldFindBestPathUsingViterbiDecodingWithoutCache
[       OK ] AGHMM.ShouldFindBestPathUsingViterbiDecodingWithoutCache (0 ms)
[ RUN      ] AGHMM.ShouldFindBestPathUsingViterbiDecodingWithCache
[       OK ] AGHMM.ShouldFindBestPathUsingViterbiDecodingWithCache (0 ms)
[ RUN      ] AGHMM.ShouldFindBestPathUsingPosteriorDecodingWithoutCache
[       OK ] AGHMM.ShouldFindBestPathUsingPosteriorDecodingWithoutCache (0 ms)
[ RUN      ] AGHMM.ShouldFindBestPathUsingPosteriorDecodingWithCache
[       OK ] AGHMM.ShouldFindBestPathUsingPosteriorDecodingWithCache (1 ms)
[ RUN      ] AGHMM.ShouldReturnTheSameValueForTheForwardAndBackwardAlgorithms
[       OK ] AGHMM.ShouldReturnTheSameValueForTheForwardAndBackwardAlgorithms (1 ms)
[ RUN      ] AGHMM.ReturnsTheSameValueForTheForwardAndBackwardAlgorithmsWithCache
[       OK ] AGHMM.ReturnsTheSameValueForTheForwardAndBackwardAlgorithmsWithCache (1 ms)
[----------] 10 tests from AGHMM (5 ms total)

[----------] 1 test from HiddenMarkovModel
[ RUN      ] HiddenMarkovModel.ShouldBeTrainedUsingMLAlgorithm
[       OK ] HiddenMarkovModel.ShouldBeTrainedUsingMLAlgorithm (0 ms)
[----------] 1 test from HiddenMarkovModel (0 ms total)

[----------] 13 tests from AHiddenMarkovModel
[ RUN      ] AHiddenMarkovModel.ShouldEvaluateTheJointProbability
[       OK ] AHiddenMarkovModel.ShouldEvaluateTheJointProbability (0 ms)
[ RUN      ] AHiddenMarkovModel.ShouldEvaluateTheJointProbabilityWithCache
[       OK ] AHiddenMarkovModel.ShouldEvaluateTheJointProbabilityWithCache (0 ms)
[ RUN      ] AHiddenMarkovModel.FindsTheBestPath
[       OK ] AHiddenMarkovModel.FindsTheBestPath (0 ms)
[ RUN      ] AHiddenMarkovModel.FindsTheBestPathWithCache
[       OK ] AHiddenMarkovModel.FindsTheBestPathWithCache (1 ms)
[ RUN      ] AHiddenMarkovModel.CalculatesProbabilityOfObservations
[       OK ] AHiddenMarkovModel.CalculatesProbabilityOfObservations (0 ms)
[ RUN      ] AHiddenMarkovModel.DecodesASequenceOfObservationsUsingThePosteriorProbability
[       OK ] AHiddenMarkovModel.DecodesASequenceOfObservationsUsingThePosteriorProbability (0 ms)
[ RUN      ] AHiddenMarkovModel.DecodesASequenceOfObservationsUsingThePosteriorProbabilityWithCache
[       OK ] AHiddenMarkovModel.DecodesASequenceOfObservationsUsingThePosteriorProbabilityWithCache (0 ms)
[ RUN      ] AHiddenMarkovModel.CalculatesForwardAndBackwardProbabilities
[       OK ] AHiddenMarkovModel.CalculatesForwardAndBackwardProbabilities (0 ms)
[ RUN      ] AHiddenMarkovModel.CalculatesForwardAndBackwardProbabilitiesWithCache
[       OK ] AHiddenMarkovModel.CalculatesForwardAndBackwardProbabilitiesWithCache (0 ms)
[ RUN      ] AHiddenMarkovModel.ShouldBeTrainedUsingBaumWelchAlgorithm
[       OK ] AHiddenMarkovModel.ShouldBeTrainedUsingBaumWelchAlgorithm (1 ms)
[ RUN      ] AHiddenMarkovModel.ShouldBeSExprSerialized
[       OK ] AHiddenMarkovModel.ShouldBeSExprSerialized (0 ms)
[ RUN      ] AHiddenMarkovModel.ShouldChooseSequenceWithDefaultSeed
[       OK ] AHiddenMarkovModel.ShouldChooseSequenceWithDefaultSeed (0 ms)
[ RUN      ] AHiddenMarkovModel.ShouldChooseLabelingWithSeed42
[       OK ] AHiddenMarkovModel.ShouldChooseLabelingWithSeed42 (0 ms)
[----------] 13 tests from AHiddenMarkovModel (2 ms total)

[----------] 5 tests from AnInhomogeneousMarkovChain
[ RUN      ] AnInhomogeneousMarkovChain.ShouldEvaluateASequence
[       OK ] AnInhomogeneousMarkovChain.ShouldEvaluateASequence (0 ms)
[ RUN      ] AnInhomogeneousMarkovChain.ShouldEvaluateASequenceWithPrefixSumArray
[       OK ] AnInhomogeneousMarkovChain.ShouldEvaluateASequenceWithPrefixSumArray (107 ms)
[ RUN      ] AnInhomogeneousMarkovChain.CanBeDecorated
[       OK ] AnInhomogeneousMarkovChain.CanBeDecorated (0 ms)
[ RUN      ] AnInhomogeneousMarkovChain.ShouldChooseSequenceWithDefaultSeed
[       OK ] AnInhomogeneousMarkovChain.ShouldChooseSequenceWithDefaultSeed (0 ms)
[ RUN      ] AnInhomogeneousMarkovChain.ShouldThrowAnOutOfRangeInDrawSymbol
[       OK ] AnInhomogeneousMarkovChain.ShouldThrowAnOutOfRangeInDrawSymbol (0 ms)
[----------] 5 tests from AnInhomogeneousMarkovChain (107 ms total)

[----------] 1 test from MDD
[ RUN      ] MDD.ShouldBeTrained
[       OK ] MDD.ShouldBeTrained (1 ms)
[----------] 1 test from MDD (1 ms total)

[----------] 4 tests from AMDD
[ RUN      ] AMDD.ShouldEvaluateASymbol
[       OK ] AMDD.ShouldEvaluateASymbol (0 ms)
[ RUN      ] AMDD.ShouldEvaluateASequence
[       OK ] AMDD.ShouldEvaluateASequence (0 ms)
[ RUN      ] AMDD.ShouldEvaluateASequenceWithPrefixSumArray
[       OK ] AMDD.ShouldEvaluateASequenceWithPrefixSumArray (0 ms)
[ RUN      ] AMDD.ShouldChooseSequenceWithDefaultSeed
[       OK ] AMDD.ShouldChooseSequenceWithDefaultSeed (0 ms)
[----------] 4 tests from AMDD (1 ms total)

[----------] 3 tests from AMultipleSequentialModel
[ RUN      ] AMultipleSequentialModel.ShouldEvaluateASequence
[       OK ] AMultipleSequentialModel.ShouldEvaluateASequence (0 ms)
[ RUN      ] AMultipleSequentialModel.ShouldEvaluateASequenceWithPrefixSumArray
[       OK ] AMultipleSequentialModel.ShouldEvaluateASequenceWithPrefixSumArray (0 ms)
[ RUN      ] AMultipleSequentialModel.ShouldChooseSequenceWithDefaultSeed
[       OK ] AMultipleSequentialModel.ShouldChooseSequenceWithDefaultSeed (0 ms)
[----------] 3 tests from AMultipleSequentialModel (0 ms total)

[----------] 1 test from PhasedInhomogeneousMarkovChain
[ RUN      ] PhasedInhomogeneousMarkovChain.ShouldBeTrained
[       OK ] PhasedInhomogeneousMarkovChain.ShouldBeTrained (0 ms)
[----------] 1 test from PhasedInhomogeneousMarkovChain (0 ms total)

[----------] 4 tests from APhasedInhomogeneousMarkovChain
[ RUN      ] APhasedInhomogeneousMarkovChain.ShouldEvaluateASequence
[       OK ] APhasedInhomogeneousMarkovChain.ShouldEvaluateASequence (0 ms)
[ RUN      ] APhasedInhomogeneousMarkovChain.ShouldEvaluateASequenceWithPrefixSumArray
[       OK ] APhasedInhomogeneousMarkovChain.ShouldEvaluateASequenceWithPrefixSumArray (1992 ms)
[ RUN      ] APhasedInhomogeneousMarkovChain.CanBeDecorated
[       OK ] APhasedInhomogeneousMarkovChain.CanBeDecorated (0 ms)
[ RUN      ] APhasedInhomogeneousMarkovChain.ShouldChooseSequenceWithDefaultSeed
[       OK ] APhasedInhomogeneousMarkovChain.ShouldChooseSequenceWithDefaultSeed (0 ms)
[----------] 4 tests from APhasedInhomogeneousMarkovChain (1992 ms total)

[----------] 3 tests from APhasedRunLengthDistribution
[ RUN      ] APhasedRunLengthDistribution.ShouldHaveAnAlphabetSize
[       OK ] APhasedRunLengthDistribution.ShouldHaveAnAlphabetSize (23 ms)
[ RUN      ] APhasedRunLengthDistribution.ShouldEvaluateASingleSymbol
[       OK ] APhasedRunLengthDistribution.ShouldEvaluateASingleSymbol (21 ms)
[ RUN      ] APhasedRunLengthDistribution.ShouldDrawSequenceWithDefaultSeed
[       OK ] APhasedRunLengthDistribution.ShouldDrawSequenceWithDefaultSeed (24 ms)
[----------] 3 tests from APhasedRunLengthDistribution (68 ms total)

[----------] 1 test from ASegment
[ RUN      ] ASegment.ShouldBeGeneratedBySequences
[       OK ] ASegment.ShouldBeGeneratedBySequences (0 ms)
[----------] 1 test from ASegment (0 ms total)

[----------] 1 test from SBSW
[ RUN      ] SBSW.ShouldBeTrained
[       OK ] SBSW.ShouldBeTrained (1 ms)
[----------] 1 test from SBSW (1 ms total)

[----------] 3 tests from ASBSW
[ RUN      ] ASBSW.ShouldEvaluateASequence
[       OK ] ASBSW.ShouldEvaluateASequence (0 ms)
[ RUN      ] ASBSW.ShouldEvaluateASequenceWithPrefixSumArray
[       OK ] ASBSW.ShouldEvaluateASequenceWithPrefixSumArray (0 ms)
[ RUN      ] ASBSW.ShouldChooseSequenceWithDefaultSeed
[       OK ] ASBSW.ShouldChooseSequenceWithDefaultSeed (0 ms)
[----------] 3 tests from ASBSW (0 ms total)

[----------] 5 tests from ATargetModel
[ RUN      ] ATargetModel.ShouldHaveAnAlphabetSize
[       OK ] ATargetModel.ShouldHaveAnAlphabetSize (0 ms)
[ RUN      ] ATargetModel.ShouldEvaluateASingleSymbol
[       OK ] ATargetModel.ShouldEvaluateASingleSymbol (0 ms)
[ RUN      ] ATargetModel.ShouldHaveEvaluateASequence
[       OK ] ATargetModel.ShouldHaveEvaluateASequence (0 ms)
[ RUN      ] ATargetModel.ShouldEvaluateASequenceWithPrefixSumArray
[       OK ] ATargetModel.ShouldEvaluateASequenceWithPrefixSumArray (0 ms)
[ RUN      ] ATargetModel.ShouldDrawSequenceWithDefaultSeed
[       OK ] ATargetModel.ShouldDrawSequenceWithDefaultSeed (0 ms)
[----------] 5 tests from ATargetModel (0 ms total)

[----------] 3 tests from VLMC
[ RUN      ] VLMC.ShouldBeTrainedUsingContextAlgorithm
[       OK ] VLMC.ShouldBeTrainedUsingContextAlgorithm (0 ms)
[ RUN      ] VLMC.ShouldBeTrainedUsingFixedLengthMarkovChainAlgorithm
[       OK ] VLMC.ShouldBeTrainedUsingFixedLengthMarkovChainAlgorithm (0 ms)
[ RUN      ] VLMC.ShouldBeTrainedUsingInterpolatedMarkovChainAlgorithm
[       OK ] VLMC.ShouldBeTrainedUsingInterpolatedMarkovChainAlgorithm (0 ms)
[----------] 3 tests from VLMC (0 ms total)

[----------] 4 tests from AVLMC
[ RUN      ] AVLMC.ShouldEvaluateAPosition
[       OK ] AVLMC.ShouldEvaluateAPosition (0 ms)
[ RUN      ] AVLMC.ShouldEvaluateASequence
[       OK ] AVLMC.ShouldEvaluateASequence (0 ms)
[ RUN      ] AVLMC.ShouldEvaluateASequenceWithPrefixSumArray
[       OK ] AVLMC.ShouldEvaluateASequenceWithPrefixSumArray (845 ms)
[ RUN      ] AVLMC.ShouldChooseSequenceWithDefaultSeed
[       OK ] AVLMC.ShouldChooseSequenceWithDefaultSeed (0 ms)
[----------] 4 tests from AVLMC (845 ms total)

[----------] Global test environment tear-down
[==========] 80 tests from 20 test cases ran. (4597 ms total)
[  PASSED  ] 80 tests.
######################################################################################################################################################
[OK] Running test bin/test/test 
[OK] All tests passed successfully
renatocf commented 8 years ago

I believe this is a problem with Travis. I'll try to investigate before accepting the pull request.

renatocf commented 8 years ago

@igorbonadio,

I fixed the remaining problems that were avoiding the compilation of ToPS exceptions. I believe we can merge it. Thanks @ademar111190 for the contribution!