@Override public String getFeatureName(int i) { return delegate.getFeatureName(i); }
@Override public void mapFeatures(BaseInformationRecords.BaseInformationOrBuilder record, INDArray inputs, int indexOfRecord) { delegate.mapFeatures(record, inputs, indexOfRecord); }
@Override public int numberOfFeatures() { return delegate.numberOfFeatures(); }
new NamingConcatFeatureMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), // different new InverseNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(targetAlignedLengthMappers), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(queryAlignedLengthMappers), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(queryPositions), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(distancesToReadVariations), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(bamFlagMappers) // different );
new NamingConcatFeatureMapper<>( new MaxNormalizationMapper( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new InverseNormalizationMapper( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new MaxNormalizationMapper( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new InverseNormalizationMapper( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), new DensityMapper("numVariationsInRead", 20, sbiProperties, baseInformationOrBuilder -> numFeatures = delegate.numberOfFeatures();
@Override public float produceFeature(BaseInformationRecords.BaseInformationOrBuilder record, int featureIndex) { return delegate.produceFeature(record, featureIndex); }
@Override public void prepareToNormalize(BaseInformationRecords.BaseInformationOrBuilder record, int indexOfRecord) { delegate.prepareToNormalize(record, indexOfRecord); }
new NamingConcatFeatureMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), // different new CeilingNormalizationMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers),30), new InverseNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(targetAlignedLengthMappers), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(queryAlignedLengthMappers), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(queryPositions), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(distancesToReadVariations), // different new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(bamFlagMappers) // different );
new NamingConcatFeatureMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(matchesRefMappers), new MaxNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new MaxNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), new DensityMapper("numVariationsInRead", 20, sbiProperties, baseInformationOrBuilder -> numFeatures = delegate.numberOfFeatures();
@Override public float produceFeature(BaseInformationRecords.BaseInformationOrBuilder record, int featureIndex) { return delegate.produceFeature(record, featureIndex); } }
@Override public void prepareToNormalize(BaseInformationRecords.BaseInformationOrBuilder record, int indexOfRecord) { delegate.prepareToNormalize(record, indexOfRecord); }
new CountReorderingMapper(sampleIndex, new NamingConcatFeatureMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(matchesRefMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(originalGobyCountIndexMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(firstBaseMappers), new InverseNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new InverseNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(targetAlignedLengthMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(queryAlignedLengthMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(queryPositions), CountInfoOrBuilder::getNumVariationsInReadsList)), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(distancesToReadVariations), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(numVariationsInReadMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readMappingQualityMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(baseQualityMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(bamFlagMappers) ));
new NamingConcatFeatureMapper<>( new MeanNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new MeanNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), new DensityMapper("numVariationsInRead", 20, sbiProperties, baseInformationOrBuilder -> numFeatures = delegate.numberOfFeatures();
@Override public String getFeatureName(int i) { return delegate.getFeatureName(i); }
@Override public float produceFeature(BaseInformationRecords.BaseInformationOrBuilder record, int featureIndex) { return delegate.produceFeature(record, featureIndex); } /**
@Override public void prepareToNormalize(BaseInformationRecords.BaseInformationOrBuilder record, int indexOfRecord) { delegate.prepareToNormalize(record, indexOfRecord); }
@Override public void mapFeatures(BaseInformationRecords.BaseInformationOrBuilder record, INDArray inputs, int indexOfRecord) { delegate.mapFeatures(record, inputs, indexOfRecord); }
@Override public int numberOfFeatures() { return delegate.numberOfFeatures(); }
new CountReorderingMapper(sampleIndex,new NamingConcatFeatureMapper<>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(firstBaseMappers), new InverseNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(countMappers)), new InverseNormalizationMapper<BaseInformationRecords.BaseInformationOrBuilder>( new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readIndexMappers)), new GenomicContextMapper(sbiProperties), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(matchesRefMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(numVariationsInReadMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(readMappingQualityMappers), new NamingConcatFeatureMapper<BaseInformationRecords.BaseInformationOrBuilder>(baseQualityMappers) ));
@Override public String getFeatureName(int i) { return delegate.getFeatureName(i); }