From ca4e2a6b8d255007d386acb3d18a0ea48d4cd900 Mon Sep 17 00:00:00 2001 From: mikesh Date: Mon, 16 Feb 2015 22:22:53 +0300 Subject: [PATCH] Rename project --- pom.xml | 8 ++-- .../model/classifier/TrainClassifier.groovy | 4 +- .../core/align/processor/AlignerFactory.java | 7 --- .../core/align/reference/KmerLibrary.java | 4 -- .../core/align/entity/PAlignmentResult.java | 4 +- .../core/align/entity/SAlignmentResult.java | 4 +- .../core/align/kmer/KMerFinder.java | 4 +- .../core/align/kmer/KMerFinderResult.java | 4 +- .../core/align/kmer/KmerMap.java | 2 +- .../core/align/kmer/KmerUtils.java | 6 +-- .../core/align/processor/Aligner.java | 8 ++-- .../core/align/processor/AlignerFactory.java | 7 +++ .../AlignerFactoryWithReference.java | 4 +- .../aligners/AlignmentEvaluator.java | 2 +- .../aligners/DummyAlignmentEvaluator.java | 2 +- .../aligners/ExtendedExomeAligner.java | 16 +++---- .../aligners/ExtendedExomeAlignerFactory.java | 6 +-- .../aligners/LocalAlignmentEvaluator.java | 3 +- .../aligners/SimpleExomeAligner.java | 12 ++--- .../aligners/SimpleExomeAlignerFactory.java | 6 +-- .../core/align/reference/KmerLibrary.java | 4 ++ .../core/align/reference/Reference.java | 2 +- .../align/reference/ReferenceLibrary.java | 4 +- .../core/assemble/entity/Consensus.java | 4 +- .../core/assemble/entity/PConsensus.java | 4 +- .../core/assemble/entity/SConsensus.java | 5 +-- .../core/assemble/misc/AssemblerFactory.java | 8 ++-- .../assemble/misc/AssemblerParameters.java | 4 +- .../core/assemble/misc/PAssemblerFactory.java | 10 ++--- .../core/assemble/misc/SAssemblerFactory.java | 8 ++-- .../core/assemble/processor/Assembler.java | 10 ++--- .../core/assemble/processor/PAssembler.java | 8 ++-- .../core/assemble/processor/SAssembler.java | 10 ++--- .../consalign/entity/AlignedConsensus.java | 6 +-- .../entity/AlignerReferenceLibrary.java | 15 +++---- .../misc/ConsensusAlignerFactory.java | 8 ++-- .../misc/ConsensusAlignerParameters.java | 4 +- .../misc/PConsensusAlignerFactory.java | 8 ++-- .../misc/SConsensusAlignerFactory.java | 8 ++-- .../mutations/MutationQualityPair.java | 2 +- .../mutations/MutationsAndCoverage.java | 12 ++--- .../mutations/MutationsExtractor.java | 10 ++--- .../mutations/NucleotideCoverage.java | 2 +- .../consalign/processor/ConsensusAligner.java | 14 +++--- .../processor/PConsensusAligner.java | 22 +++++----- .../processor/SConsensusAligner.java | 18 ++++---- .../core/correct/CorrectedConsensus.java | 12 ++--- .../core/correct/Corrector.java | 16 +++---- .../core/correct/CorrectorParameters.java | 6 +-- .../correct/CorrectorReferenceLibrary.java | 18 ++++---- .../core/correct/MutationFilter.java | 2 +- .../core/haplotype/Haplotype.java | 6 +-- .../core/haplotype/HaplotypeCounters.java | 2 +- .../core/haplotype/HaplotypeTree.java | 12 ++--- .../haplotype/HaplotypeTreeParameters.java | 4 +- .../core/io/entity/Mig.java | 2 +- .../core/io/entity/PMig.java | 2 +- .../core/io/entity/SMig.java | 2 +- .../core/io/misc/MigReaderParameters.java | 4 +- .../core/io/misc/ReadInfo.java | 4 +- .../core/io/misc/UmiHistogram.java | 2 +- .../core/io/misc/index/IndexingInfo.java | 4 +- .../core/io/misc/index/UmiIndexer.java | 10 ++--- .../core/io/readers/MigReader.java | 22 +++++----- .../core/io/readers/PMigReader.java | 21 +++++---- .../core/io/readers/SMigReader.java | 12 ++--- .../core/mutations/MigecMutation.java | 2 +- .../mutations/MigecMutationsCollection.java | 5 +-- .../core/mutations/MutationDifference.java | 6 +-- .../core/mutations/MutationsCollection.java | 2 +- .../mutations/wrappers/DeletionWrapper.java | 2 +- .../core/mutations/wrappers/IndelWrapper.java | 2 +- .../mutations/wrappers/InsertionWrapper.java | 2 +- .../mutations/wrappers/MutationWrapper.java | 2 +- .../wrappers/MutationWrapperCollection.java | 7 ++- .../wrappers/SubstitutionWrapper.java | 2 +- .../model/classifier/BaseInstanceFactory.java | 4 +- .../classifier/BaseVariantClassifier.java | 4 +- .../model/classifier/ClassifierResult.java | 2 +- .../model/classifier/InstanceFactory.java | 4 +- .../model/classifier/VariantClassifier.java | 4 +- .../model/variant/Variant.java | 4 +- .../model/variant/VariantContainer.java | 4 +- .../model/variant/VariantLibrary.java | 8 ++-- .../pipeline/ExomePipeline.java | 31 +++++++------ .../pipeline/MigecCli.java | 6 +-- .../pipeline/MigecParameterSet.java | 18 ++++---- .../pipeline/MigecPipeline.java | 44 +++++++++---------- .../pipeline/TestPipeline.java | 18 ++++---- .../demultiplex/barcode/BarcodeSearcher.java | 4 +- .../barcode/BarcodeSearcherResult.java | 2 +- .../demultiplex/config/BarcodeListParser.java | 10 ++--- .../demultiplex/entity/CheckoutResult.java | 4 +- .../entity/DemultiplexParameters.java | 6 +-- .../demultiplex/entity/PCheckoutResult.java | 4 +- .../demultiplex/entity/SCheckoutResult.java | 4 +- .../entity/SimpleCheckoutResult.java | 4 +- .../processor/CheckoutProcessor.java | 6 +-- .../demultiplex/processor/HeaderParser.java | 10 ++--- .../processor/PCheckoutProcessor.java | 8 ++-- .../processor/ReadPositionUmiExtractor.java | 10 ++--- .../processor/SCheckoutProcessor.java | 10 ++--- .../preproc/misc/ReadOverlapper.java | 2 +- .../{migec2 => oncomigec}/util/Basics.java | 2 +- .../util/ParameterSet.java | 2 +- .../util/ProcessorResultWrapper.java | 2 +- .../util/QualityHistogram.java | 2 +- .../{migec2 => oncomigec}/util/Util.java | 2 +- .../core/align/kmer/KMerFinderTest.java | 13 +++--- .../processor/aligners/AlignersTest.java | 16 +++---- .../assemble/processor/AssemblerTest.java | 18 ++++---- .../mutations/MutationsExtractorTest.java | 24 +++++----- .../processor/ConsensusAlignerTest.java | 36 +++++++-------- .../core/correct/CorrectorTest.java | 27 ++++++------ .../core/haplotype/HaplotypeTreeDataTest.java | 28 ++++++------ .../core/io/misc/UmiHistogramTest.java | 4 +- .../core/io/readers/PMigReaderTest.java | 15 +++---- .../core/io/readers/SMigReaderTest.java | 11 +++-- .../model/classifier/ClassifierTest.java | 2 +- .../pipeline/MigecParameterSetTest.java | 5 +-- .../barcode/BarcodeSearcherTest.java | 6 +-- .../processor/CheckoutProcessorTest.java | 9 ++-- .../preproc/misc/OverlapTest.java | 4 +- .../util/testing/DoubleRange.java | 2 +- .../util/testing/IntRange.java | 2 +- .../util/testing/PercentRange.java | 4 +- .../util/testing/TestResources.java | 2 +- .../generators/GeneratorMutationModel.java | 4 +- .../generators/RandomIndelGenerator.java | 4 +- .../generators/RandomMigGenerator.java | 8 ++-- .../generators/RandomReferenceGenerator.java | 8 ++-- 131 files changed, 499 insertions(+), 516 deletions(-) rename src/main/groovy/com/milaboratory/{migec2 => oncomigec}/model/classifier/TrainClassifier.groovy (97%) delete mode 100644 src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactory.java delete mode 100644 src/main/java/com/milaboratory/migec2/core/align/reference/KmerLibrary.java rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/entity/PAlignmentResult.java (95%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/entity/SAlignmentResult.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/kmer/KMerFinder.java (94%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/kmer/KMerFinderResult.java (77%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/kmer/KmerMap.java (99%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/kmer/KmerUtils.java (90%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/processor/Aligner.java (88%) create mode 100644 src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactory.java rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/processor/AlignerFactoryWithReference.java (78%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/processor/aligners/AlignmentEvaluator.java (92%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/processor/aligners/DummyAlignmentEvaluator.java (93%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/processor/aligners/ExtendedExomeAligner.java (83%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/processor/aligners/ExtendedExomeAlignerFactory.java (82%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/processor/aligners/LocalAlignmentEvaluator.java (95%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/processor/aligners/SimpleExomeAligner.java (89%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/processor/aligners/SimpleExomeAlignerFactory.java (85%) create mode 100644 src/main/java/com/milaboratory/oncomigec/core/align/reference/KmerLibrary.java rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/reference/Reference.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/align/reference/ReferenceLibrary.java (96%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/assemble/entity/Consensus.java (71%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/assemble/entity/PConsensus.java (95%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/assemble/entity/SConsensus.java (95%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/assemble/misc/AssemblerFactory.java (60%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/assemble/misc/AssemblerParameters.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/assemble/misc/PAssemblerFactory.java (56%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/assemble/misc/SAssemblerFactory.java (59%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/assemble/processor/Assembler.java (91%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/assemble/processor/PAssembler.java (88%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/assemble/processor/SAssembler.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/entity/AlignedConsensus.java (92%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/entity/AlignerReferenceLibrary.java (84%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/misc/ConsensusAlignerFactory.java (66%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/misc/ConsensusAlignerParameters.java (96%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/misc/PConsensusAlignerFactory.java (66%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/misc/SConsensusAlignerFactory.java (66%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/mutations/MutationQualityPair.java (86%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/mutations/MutationsAndCoverage.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/mutations/MutationsExtractor.java (96%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/mutations/NucleotideCoverage.java (98%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/processor/ConsensusAligner.java (79%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/processor/PConsensusAligner.java (87%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/processor/SConsensusAligner.java (78%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/correct/CorrectedConsensus.java (93%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/correct/Corrector.java (89%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/correct/CorrectorParameters.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/correct/CorrectorReferenceLibrary.java (96%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/correct/MutationFilter.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/haplotype/Haplotype.java (94%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/haplotype/HaplotypeCounters.java (95%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/haplotype/HaplotypeTree.java (96%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/haplotype/HaplotypeTreeParameters.java (96%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/io/entity/Mig.java (94%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/io/entity/PMig.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/io/entity/SMig.java (96%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/io/misc/MigReaderParameters.java (94%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/io/misc/ReadInfo.java (91%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/io/misc/UmiHistogram.java (99%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/io/misc/index/IndexingInfo.java (89%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/io/misc/index/UmiIndexer.java (81%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/io/readers/MigReader.java (90%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/io/readers/PMigReader.java (92%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/io/readers/SMigReader.java (90%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/mutations/MigecMutation.java (96%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/mutations/MigecMutationsCollection.java (95%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/mutations/MutationDifference.java (93%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/mutations/MutationsCollection.java (73%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/mutations/wrappers/DeletionWrapper.java (93%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/mutations/wrappers/IndelWrapper.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/mutations/wrappers/InsertionWrapper.java (92%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/mutations/wrappers/MutationWrapper.java (90%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/mutations/wrappers/MutationWrapperCollection.java (92%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/core/mutations/wrappers/SubstitutionWrapper.java (94%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/model/classifier/BaseInstanceFactory.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/model/classifier/BaseVariantClassifier.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/model/classifier/ClassifierResult.java (95%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/model/classifier/InstanceFactory.java (91%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/model/classifier/VariantClassifier.java (87%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/model/variant/Variant.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/model/variant/VariantContainer.java (98%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/model/variant/VariantLibrary.java (93%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/pipeline/ExomePipeline.java (81%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/pipeline/MigecCli.java (99%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/pipeline/MigecParameterSet.java (95%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/pipeline/MigecPipeline.java (86%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/pipeline/TestPipeline.java (70%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/barcode/BarcodeSearcher.java (98%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/barcode/BarcodeSearcherResult.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/config/BarcodeListParser.java (95%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/entity/CheckoutResult.java (92%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/entity/DemultiplexParameters.java (96%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/entity/PCheckoutResult.java (92%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/entity/SCheckoutResult.java (62%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/entity/SimpleCheckoutResult.java (72%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/processor/CheckoutProcessor.java (94%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/processor/HeaderParser.java (72%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/processor/PCheckoutProcessor.java (95%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/processor/ReadPositionUmiExtractor.java (81%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/processor/SCheckoutProcessor.java (85%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/preproc/misc/ReadOverlapper.java (99%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/util/Basics.java (99%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/util/ParameterSet.java (68%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/util/ProcessorResultWrapper.java (92%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/util/QualityHistogram.java (97%) rename src/main/java/com/milaboratory/{migec2 => oncomigec}/util/Util.java (99%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/core/align/kmer/KMerFinderTest.java (87%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/core/align/processor/aligners/AlignersTest.java (91%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/core/assemble/processor/AssemblerTest.java (92%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/mutations/MutationsExtractorTest.java (95%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/core/consalign/processor/ConsensusAlignerTest.java (85%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/core/correct/CorrectorTest.java (82%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/core/haplotype/HaplotypeTreeDataTest.java (85%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/core/io/misc/UmiHistogramTest.java (94%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/core/io/readers/PMigReaderTest.java (91%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/core/io/readers/SMigReaderTest.java (86%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/model/classifier/ClassifierTest.java (94%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/pipeline/MigecParameterSetTest.java (91%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/barcode/BarcodeSearcherTest.java (98%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/preproc/demultiplex/processor/CheckoutProcessorTest.java (87%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/preproc/misc/OverlapTest.java (98%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/util/testing/DoubleRange.java (97%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/util/testing/IntRange.java (97%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/util/testing/PercentRange.java (95%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/util/testing/TestResources.java (95%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/util/testing/generators/GeneratorMutationModel.java (95%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/util/testing/generators/RandomIndelGenerator.java (92%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/util/testing/generators/RandomMigGenerator.java (95%) rename src/test/java/com/milaboratory/{migec2 => oncomigec}/util/testing/generators/RandomReferenceGenerator.java (95%) diff --git a/pom.xml b/pom.xml index 2734743..04109a8 100644 --- a/pom.xml +++ b/pom.xml @@ -3,10 +3,10 @@ 4.0.0 com.milaboratory - migec2 + oncomigec 1.0-SNAPSHOT jar - MIGEC2 + OncoMIGEC @@ -167,7 +167,7 @@ - com.milaboratory.migec2.pipeline.MigecCli + com.milaboratory.oncomigec.pipeline.MigecCli true @@ -228,7 +228,7 @@ - com.milaboratory.migec2.pipeline.MigecCli + com.milaboratory.oncomigec.pipeline.MigecCli true diff --git a/src/main/groovy/com/milaboratory/migec2/model/classifier/TrainClassifier.groovy b/src/main/groovy/com/milaboratory/oncomigec/model/classifier/TrainClassifier.groovy similarity index 97% rename from src/main/groovy/com/milaboratory/migec2/model/classifier/TrainClassifier.groovy rename to src/main/groovy/com/milaboratory/oncomigec/model/classifier/TrainClassifier.groovy index ab6a9e8..86c39c8 100644 --- a/src/main/groovy/com/milaboratory/migec2/model/classifier/TrainClassifier.groovy +++ b/src/main/groovy/com/milaboratory/oncomigec/model/classifier/TrainClassifier.groovy @@ -16,10 +16,10 @@ * Last modified on 23.11.2014 by mikesh */ -package com.milaboratory.migec2.model.classifier +package com.milaboratory.oncomigec.model.classifier import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet -import com.milaboratory.migec2.model.variant.Variant +import com.milaboratory.oncomigec.model.variant.Variant import weka.core.Instance def cli = new CliBuilder(usage: "TrainClassifier [options] control_variants input_vardump output_prefix\n" + diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactory.java b/src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactory.java deleted file mode 100644 index 54ffaa6..0000000 --- a/src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactory.java +++ /dev/null @@ -1,7 +0,0 @@ -package com.milaboratory.migec2.core.align.processor; - -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; - -public interface AlignerFactory { - public T fromReferenceLibrary(ReferenceLibrary referenceLibrary); -} diff --git a/src/main/java/com/milaboratory/migec2/core/align/reference/KmerLibrary.java b/src/main/java/com/milaboratory/migec2/core/align/reference/KmerLibrary.java deleted file mode 100644 index de4acee..0000000 --- a/src/main/java/com/milaboratory/migec2/core/align/reference/KmerLibrary.java +++ /dev/null @@ -1,4 +0,0 @@ -package com.milaboratory.migec2.core.align.reference; - -public class KmerLibrary { -} diff --git a/src/main/java/com/milaboratory/migec2/core/align/entity/PAlignmentResult.java b/src/main/java/com/milaboratory/oncomigec/core/align/entity/PAlignmentResult.java similarity index 95% rename from src/main/java/com/milaboratory/migec2/core/align/entity/PAlignmentResult.java rename to src/main/java/com/milaboratory/oncomigec/core/align/entity/PAlignmentResult.java index 54bea2e..4212eb2 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/entity/PAlignmentResult.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/entity/PAlignmentResult.java @@ -13,10 +13,10 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.align.entity; +package com.milaboratory.oncomigec.core.align.entity; import com.milaboratory.core.sequence.Range; -import com.milaboratory.migec2.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.Reference; import java.util.List; diff --git a/src/main/java/com/milaboratory/migec2/core/align/entity/SAlignmentResult.java b/src/main/java/com/milaboratory/oncomigec/core/align/entity/SAlignmentResult.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/core/align/entity/SAlignmentResult.java rename to src/main/java/com/milaboratory/oncomigec/core/align/entity/SAlignmentResult.java index 958d838..389a427 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/entity/SAlignmentResult.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/entity/SAlignmentResult.java @@ -13,13 +13,13 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.align.entity; +package com.milaboratory.oncomigec.core.align.entity; import com.milaboratory.core.sequence.Range; import com.milaboratory.core.sequence.alignment.LocalAlignment; import com.milaboratory.core.sequence.mutations.Mutations; import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet; -import com.milaboratory.migec2.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.Reference; import java.util.ArrayList; import java.util.List; diff --git a/src/main/java/com/milaboratory/migec2/core/align/kmer/KMerFinder.java b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinder.java similarity index 94% rename from src/main/java/com/milaboratory/migec2/core/align/kmer/KMerFinder.java rename to src/main/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinder.java index f544be9..d8f5d59 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/kmer/KMerFinder.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinder.java @@ -1,7 +1,7 @@ -package com.milaboratory.migec2.core.align.kmer; +package com.milaboratory.oncomigec.core.align.kmer; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; import com.milaboratory.util.IntArrayList; public class KMerFinder { diff --git a/src/main/java/com/milaboratory/migec2/core/align/kmer/KMerFinderResult.java b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinderResult.java similarity index 77% rename from src/main/java/com/milaboratory/migec2/core/align/kmer/KMerFinderResult.java rename to src/main/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinderResult.java index 47b1b7c..e41ea44 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/kmer/KMerFinderResult.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinderResult.java @@ -1,6 +1,6 @@ -package com.milaboratory.migec2.core.align.kmer; +package com.milaboratory.oncomigec.core.align.kmer; -import com.milaboratory.migec2.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.Reference; public class KMerFinderResult { private final double information; diff --git a/src/main/java/com/milaboratory/migec2/core/align/kmer/KmerMap.java b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KmerMap.java similarity index 99% rename from src/main/java/com/milaboratory/migec2/core/align/kmer/KmerMap.java rename to src/main/java/com/milaboratory/oncomigec/core/align/kmer/KmerMap.java index 49dbcc2..2be8967 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/kmer/KmerMap.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KmerMap.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.core.align.kmer; +package com.milaboratory.oncomigec.core.align.kmer; // // Adapted from KAnalyze package, see diff --git a/src/main/java/com/milaboratory/migec2/core/align/kmer/KmerUtils.java b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KmerUtils.java similarity index 90% rename from src/main/java/com/milaboratory/migec2/core/align/kmer/KmerUtils.java rename to src/main/java/com/milaboratory/oncomigec/core/align/kmer/KmerUtils.java index 9f7fcb7..3056047 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/kmer/KmerUtils.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/kmer/KmerUtils.java @@ -1,8 +1,8 @@ -package com.milaboratory.migec2.core.align.kmer; +package com.milaboratory.oncomigec.core.align.kmer; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; public class KmerUtils { private final int k; diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/Aligner.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/Aligner.java similarity index 88% rename from src/main/java/com/milaboratory/migec2/core/align/processor/Aligner.java rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/Aligner.java index f9e9470..c8933a2 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/processor/Aligner.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/Aligner.java @@ -13,12 +13,12 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.align.processor; +package com.milaboratory.oncomigec.core.align.processor; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.core.align.entity.PAlignmentResult; -import com.milaboratory.migec2.core.align.entity.SAlignmentResult; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.align.entity.PAlignmentResult; +import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; public interface Aligner { /** diff --git a/src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactory.java new file mode 100644 index 0000000..eb53b37 --- /dev/null +++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactory.java @@ -0,0 +1,7 @@ +package com.milaboratory.oncomigec.core.align.processor; + +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; + +public interface AlignerFactory { + public T fromReferenceLibrary(ReferenceLibrary referenceLibrary); +} diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactoryWithReference.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactoryWithReference.java similarity index 78% rename from src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactoryWithReference.java rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactoryWithReference.java index 8df9e0b..4eb9e96 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/processor/AlignerFactoryWithReference.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/AlignerFactoryWithReference.java @@ -1,6 +1,6 @@ -package com.milaboratory.migec2.core.align.processor; +package com.milaboratory.oncomigec.core.align.processor; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; public class AlignerFactoryWithReference { private final ReferenceLibrary referenceLibrary; diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/AlignmentEvaluator.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/AlignmentEvaluator.java similarity index 92% rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/AlignmentEvaluator.java rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/AlignmentEvaluator.java index 1067045..ef7e3e8 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/AlignmentEvaluator.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/AlignmentEvaluator.java @@ -14,7 +14,7 @@ * limitations under the License. */ -package com.milaboratory.migec2.core.align.processor.aligners; +package com.milaboratory.oncomigec.core.align.processor.aligners; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/DummyAlignmentEvaluator.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/DummyAlignmentEvaluator.java similarity index 93% rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/DummyAlignmentEvaluator.java rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/DummyAlignmentEvaluator.java index 0cfa8cd..855e78d 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/DummyAlignmentEvaluator.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/DummyAlignmentEvaluator.java @@ -16,7 +16,7 @@ * Last modified on 19.11.2014 by mikesh */ -package com.milaboratory.migec2.core.align.processor.aligners; +package com.milaboratory.oncomigec.core.align.processor.aligners; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/ExtendedExomeAligner.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/ExtendedExomeAligner.java similarity index 83% rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/ExtendedExomeAligner.java rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/ExtendedExomeAligner.java index 3f203c4..e7bf15d 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/ExtendedExomeAligner.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/ExtendedExomeAligner.java @@ -1,17 +1,17 @@ -package com.milaboratory.migec2.core.align.processor.aligners; +package com.milaboratory.oncomigec.core.align.processor.aligners; import com.milaboratory.core.sequence.Range; import com.milaboratory.core.sequence.alignment.AffineGapAlignmentScoring; import com.milaboratory.core.sequence.alignment.LocalAligner; import com.milaboratory.core.sequence.alignment.LocalAlignment; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.core.align.entity.PAlignmentResult; -import com.milaboratory.migec2.core.align.entity.SAlignmentResult; -import com.milaboratory.migec2.core.align.kmer.KMerFinder; -import com.milaboratory.migec2.core.align.kmer.KMerFinderResult; -import com.milaboratory.migec2.core.align.processor.Aligner; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.align.entity.PAlignmentResult; +import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult; +import com.milaboratory.oncomigec.core.align.kmer.KMerFinder; +import com.milaboratory.oncomigec.core.align.kmer.KMerFinderResult; +import com.milaboratory.oncomigec.core.align.processor.Aligner; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; import java.util.ArrayList; import java.util.List; diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/ExtendedExomeAlignerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/ExtendedExomeAlignerFactory.java similarity index 82% rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/ExtendedExomeAlignerFactory.java rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/ExtendedExomeAlignerFactory.java index e81322d..ad439c1 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/ExtendedExomeAlignerFactory.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/ExtendedExomeAlignerFactory.java @@ -1,7 +1,7 @@ -package com.milaboratory.migec2.core.align.processor.aligners; +package com.milaboratory.oncomigec.core.align.processor.aligners; -import com.milaboratory.migec2.core.align.processor.AlignerFactory; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.align.processor.AlignerFactory; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; public class ExtendedExomeAlignerFactory implements AlignerFactory { private final int k; diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/LocalAlignmentEvaluator.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/LocalAlignmentEvaluator.java similarity index 95% rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/LocalAlignmentEvaluator.java rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/LocalAlignmentEvaluator.java index 959cc45..1a404e1 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/LocalAlignmentEvaluator.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/LocalAlignmentEvaluator.java @@ -14,10 +14,9 @@ * limitations under the License. */ -package com.milaboratory.migec2.core.align.processor.aligners; +package com.milaboratory.oncomigec.core.align.processor.aligners; import com.milaboratory.core.sequence.alignment.LocalAlignment; -import com.milaboratory.core.sequence.aminoacid.AminoAcidAlphabet; import com.milaboratory.core.sequence.mutations.Mutations; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/SimpleExomeAligner.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/SimpleExomeAligner.java similarity index 89% rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/SimpleExomeAligner.java rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/SimpleExomeAligner.java index c788663..2093566 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/SimpleExomeAligner.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/SimpleExomeAligner.java @@ -13,16 +13,16 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.align.processor.aligners; +package com.milaboratory.oncomigec.core.align.processor.aligners; import com.milaboratory.core.sequence.Range; import com.milaboratory.core.sequence.alignment.*; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.core.align.entity.PAlignmentResult; -import com.milaboratory.migec2.core.align.entity.SAlignmentResult; -import com.milaboratory.migec2.core.align.processor.Aligner; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.align.entity.PAlignmentResult; +import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult; +import com.milaboratory.oncomigec.core.align.processor.Aligner; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; import java.util.ArrayList; import java.util.List; diff --git a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/SimpleExomeAlignerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/SimpleExomeAlignerFactory.java similarity index 85% rename from src/main/java/com/milaboratory/migec2/core/align/processor/aligners/SimpleExomeAlignerFactory.java rename to src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/SimpleExomeAlignerFactory.java index 959d4f7..82a8d56 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/processor/aligners/SimpleExomeAlignerFactory.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/processor/aligners/SimpleExomeAlignerFactory.java @@ -1,8 +1,8 @@ -package com.milaboratory.migec2.core.align.processor.aligners; +package com.milaboratory.oncomigec.core.align.processor.aligners; import com.milaboratory.core.sequence.alignment.KAlignerParameters; -import com.milaboratory.migec2.core.align.processor.AlignerFactory; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.align.processor.AlignerFactory; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; public class SimpleExomeAlignerFactory implements AlignerFactory { private final KAlignerParameters parameters; diff --git a/src/main/java/com/milaboratory/oncomigec/core/align/reference/KmerLibrary.java b/src/main/java/com/milaboratory/oncomigec/core/align/reference/KmerLibrary.java new file mode 100644 index 0000000..d760d5d --- /dev/null +++ b/src/main/java/com/milaboratory/oncomigec/core/align/reference/KmerLibrary.java @@ -0,0 +1,4 @@ +package com.milaboratory.oncomigec.core.align.reference; + +public class KmerLibrary { +} diff --git a/src/main/java/com/milaboratory/migec2/core/align/reference/Reference.java b/src/main/java/com/milaboratory/oncomigec/core/align/reference/Reference.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/core/align/reference/Reference.java rename to src/main/java/com/milaboratory/oncomigec/core/align/reference/Reference.java index fe5cb91..510b127 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/reference/Reference.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/reference/Reference.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.align.reference; +package com.milaboratory.oncomigec.core.align.reference; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; diff --git a/src/main/java/com/milaboratory/migec2/core/align/reference/ReferenceLibrary.java b/src/main/java/com/milaboratory/oncomigec/core/align/reference/ReferenceLibrary.java similarity index 96% rename from src/main/java/com/milaboratory/migec2/core/align/reference/ReferenceLibrary.java rename to src/main/java/com/milaboratory/oncomigec/core/align/reference/ReferenceLibrary.java index f7f6553..72c37fe 100644 --- a/src/main/java/com/milaboratory/migec2/core/align/reference/ReferenceLibrary.java +++ b/src/main/java/com/milaboratory/oncomigec/core/align/reference/ReferenceLibrary.java @@ -13,11 +13,11 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.align.reference; +package com.milaboratory.oncomigec.core.align.reference; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; import com.milaboratory.core.sequencing.read.SSequencingRead; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.util.Util; import java.io.File; import java.io.IOException; diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/entity/Consensus.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/entity/Consensus.java similarity index 71% rename from src/main/java/com/milaboratory/migec2/core/assemble/entity/Consensus.java rename to src/main/java/com/milaboratory/oncomigec/core/assemble/entity/Consensus.java index e28f7bc..279939d 100644 --- a/src/main/java/com/milaboratory/migec2/core/assemble/entity/Consensus.java +++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/entity/Consensus.java @@ -1,7 +1,7 @@ -package com.milaboratory.migec2.core.assemble.entity; +package com.milaboratory.oncomigec.core.assemble.entity; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.util.QualityHistogram; +import com.milaboratory.oncomigec.util.QualityHistogram; public interface Consensus { public int size(); diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/entity/PConsensus.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/entity/PConsensus.java similarity index 95% rename from src/main/java/com/milaboratory/migec2/core/assemble/entity/PConsensus.java rename to src/main/java/com/milaboratory/oncomigec/core/assemble/entity/PConsensus.java index d9567ff..9497c89 100644 --- a/src/main/java/com/milaboratory/migec2/core/assemble/entity/PConsensus.java +++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/entity/PConsensus.java @@ -13,10 +13,10 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.assemble.entity; +package com.milaboratory.oncomigec.core.assemble.entity; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.util.QualityHistogram; +import com.milaboratory.oncomigec.util.QualityHistogram; public final class PConsensus implements Consensus { private final SConsensus consensus1, consensus2; diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/entity/SConsensus.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/entity/SConsensus.java similarity index 95% rename from src/main/java/com/milaboratory/migec2/core/assemble/entity/SConsensus.java rename to src/main/java/com/milaboratory/oncomigec/core/assemble/entity/SConsensus.java index 1b9d621..add5adf 100644 --- a/src/main/java/com/milaboratory/migec2/core/assemble/entity/SConsensus.java +++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/entity/SConsensus.java @@ -13,12 +13,11 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.assemble.entity; +package com.milaboratory.oncomigec.core.assemble.entity; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.util.QualityHistogram; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.util.QualityHistogram; import java.util.List; diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/misc/AssemblerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/AssemblerFactory.java similarity index 60% rename from src/main/java/com/milaboratory/migec2/core/assemble/misc/AssemblerFactory.java rename to src/main/java/com/milaboratory/oncomigec/core/assemble/misc/AssemblerFactory.java index 4bf5398..6360a73 100644 --- a/src/main/java/com/milaboratory/migec2/core/assemble/misc/AssemblerFactory.java +++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/AssemblerFactory.java @@ -1,8 +1,8 @@ -package com.milaboratory.migec2.core.assemble.misc; +package com.milaboratory.oncomigec.core.assemble.misc; -import com.milaboratory.migec2.core.assemble.entity.Consensus; -import com.milaboratory.migec2.core.assemble.processor.Assembler; -import com.milaboratory.migec2.core.io.entity.Mig; +import com.milaboratory.oncomigec.core.assemble.entity.Consensus; +import com.milaboratory.oncomigec.core.assemble.processor.Assembler; +import com.milaboratory.oncomigec.core.io.entity.Mig; public abstract class AssemblerFactory { protected final AssemblerParameters parameters; diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/misc/AssemblerParameters.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/AssemblerParameters.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/core/assemble/misc/AssemblerParameters.java rename to src/main/java/com/milaboratory/oncomigec/core/assemble/misc/AssemblerParameters.java index 997446d..b68a6bf 100644 --- a/src/main/java/com/milaboratory/migec2/core/assemble/misc/AssemblerParameters.java +++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/AssemblerParameters.java @@ -1,6 +1,6 @@ -package com.milaboratory.migec2.core.assemble.misc; +package com.milaboratory.oncomigec.core.assemble.misc; -import com.milaboratory.migec2.util.ParameterSet; +import com.milaboratory.oncomigec.util.ParameterSet; import org.jdom.Element; public final class AssemblerParameters implements ParameterSet { diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/misc/PAssemblerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/PAssemblerFactory.java similarity index 56% rename from src/main/java/com/milaboratory/migec2/core/assemble/misc/PAssemblerFactory.java rename to src/main/java/com/milaboratory/oncomigec/core/assemble/misc/PAssemblerFactory.java index c4d5261..ad15dde 100644 --- a/src/main/java/com/milaboratory/migec2/core/assemble/misc/PAssemblerFactory.java +++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/PAssemblerFactory.java @@ -1,9 +1,9 @@ -package com.milaboratory.migec2.core.assemble.misc; +package com.milaboratory.oncomigec.core.assemble.misc; -import com.milaboratory.migec2.core.assemble.entity.PConsensus; -import com.milaboratory.migec2.core.assemble.processor.PAssembler; -import com.milaboratory.migec2.core.assemble.processor.SAssembler; -import com.milaboratory.migec2.core.io.entity.PMig; +import com.milaboratory.oncomigec.core.assemble.entity.PConsensus; +import com.milaboratory.oncomigec.core.assemble.processor.PAssembler; +import com.milaboratory.oncomigec.core.assemble.processor.SAssembler; +import com.milaboratory.oncomigec.core.io.entity.PMig; public final class PAssemblerFactory extends AssemblerFactory { diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/misc/SAssemblerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/SAssemblerFactory.java similarity index 59% rename from src/main/java/com/milaboratory/migec2/core/assemble/misc/SAssemblerFactory.java rename to src/main/java/com/milaboratory/oncomigec/core/assemble/misc/SAssemblerFactory.java index bb0273d..7014407 100644 --- a/src/main/java/com/milaboratory/migec2/core/assemble/misc/SAssemblerFactory.java +++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/misc/SAssemblerFactory.java @@ -1,8 +1,8 @@ -package com.milaboratory.migec2.core.assemble.misc; +package com.milaboratory.oncomigec.core.assemble.misc; -import com.milaboratory.migec2.core.assemble.entity.SConsensus; -import com.milaboratory.migec2.core.assemble.processor.SAssembler; -import com.milaboratory.migec2.core.io.entity.SMig; +import com.milaboratory.oncomigec.core.assemble.entity.SConsensus; +import com.milaboratory.oncomigec.core.assemble.processor.SAssembler; +import com.milaboratory.oncomigec.core.io.entity.SMig; public final class SAssemblerFactory extends AssemblerFactory { diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/processor/Assembler.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/processor/Assembler.java similarity index 91% rename from src/main/java/com/milaboratory/migec2/core/assemble/processor/Assembler.java rename to src/main/java/com/milaboratory/oncomigec/core/assemble/processor/Assembler.java index 6c6c70a..a35ea44 100644 --- a/src/main/java/com/milaboratory/migec2/core/assemble/processor/Assembler.java +++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/processor/Assembler.java @@ -13,13 +13,13 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.assemble.processor; +package com.milaboratory.oncomigec.core.assemble.processor; import cc.redberry.pipe.Processor; -import com.milaboratory.migec2.core.assemble.entity.Consensus; -import com.milaboratory.migec2.core.io.entity.Mig; -import com.milaboratory.migec2.util.ProcessorResultWrapper; -import com.milaboratory.migec2.util.QualityHistogram; +import com.milaboratory.oncomigec.core.assemble.entity.Consensus; +import com.milaboratory.oncomigec.core.io.entity.Mig; +import com.milaboratory.oncomigec.util.ProcessorResultWrapper; +import com.milaboratory.oncomigec.util.QualityHistogram; import java.util.Collections; import java.util.LinkedList; diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/processor/PAssembler.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/processor/PAssembler.java similarity index 88% rename from src/main/java/com/milaboratory/migec2/core/assemble/processor/PAssembler.java rename to src/main/java/com/milaboratory/oncomigec/core/assemble/processor/PAssembler.java index dfaf41d..15d86ee 100644 --- a/src/main/java/com/milaboratory/migec2/core/assemble/processor/PAssembler.java +++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/processor/PAssembler.java @@ -1,8 +1,8 @@ -package com.milaboratory.migec2.core.assemble.processor; +package com.milaboratory.oncomigec.core.assemble.processor; -import com.milaboratory.migec2.core.assemble.entity.PConsensus; -import com.milaboratory.migec2.core.assemble.entity.SConsensus; -import com.milaboratory.migec2.core.io.entity.PMig; +import com.milaboratory.oncomigec.core.assemble.entity.PConsensus; +import com.milaboratory.oncomigec.core.assemble.entity.SConsensus; +import com.milaboratory.oncomigec.core.io.entity.PMig; public final class PAssembler extends Assembler { private final SAssembler assembler1, assembler2; diff --git a/src/main/java/com/milaboratory/migec2/core/assemble/processor/SAssembler.java b/src/main/java/com/milaboratory/oncomigec/core/assemble/processor/SAssembler.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/core/assemble/processor/SAssembler.java rename to src/main/java/com/milaboratory/oncomigec/core/assemble/processor/SAssembler.java index c327727..a9301c2 100644 --- a/src/main/java/com/milaboratory/migec2/core/assemble/processor/SAssembler.java +++ b/src/main/java/com/milaboratory/oncomigec/core/assemble/processor/SAssembler.java @@ -1,14 +1,14 @@ -package com.milaboratory.migec2.core.assemble.processor; +package com.milaboratory.oncomigec.core.assemble.processor; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; import com.milaboratory.core.sequence.nucleotide.NucleotideSequenceBuilder; import com.milaboratory.core.sequence.quality.SequenceQualityPhred; import com.milaboratory.core.sequencing.read.SSequencingRead; -import com.milaboratory.migec2.core.assemble.entity.SConsensus; -import com.milaboratory.migec2.core.assemble.misc.AssemblerParameters; -import com.milaboratory.migec2.core.io.entity.SMig; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.core.assemble.entity.SConsensus; +import com.milaboratory.oncomigec.core.assemble.misc.AssemblerParameters; +import com.milaboratory.oncomigec.core.io.entity.SMig; +import com.milaboratory.oncomigec.util.Util; import java.util.ArrayList; import java.util.HashMap; diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/entity/AlignedConsensus.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/entity/AlignedConsensus.java similarity index 92% rename from src/main/java/com/milaboratory/migec2/core/consalign/entity/AlignedConsensus.java rename to src/main/java/com/milaboratory/oncomigec/core/consalign/entity/AlignedConsensus.java index 3af8bc0..c3ea99d 100644 --- a/src/main/java/com/milaboratory/migec2/core/consalign/entity/AlignedConsensus.java +++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/entity/AlignedConsensus.java @@ -13,11 +13,11 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.consalign.entity; +package com.milaboratory.oncomigec.core.consalign.entity; import com.milaboratory.core.sequence.Range; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.mutations.MigecMutationsCollection; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection; import java.util.List; diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/entity/AlignerReferenceLibrary.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/entity/AlignerReferenceLibrary.java similarity index 84% rename from src/main/java/com/milaboratory/migec2/core/consalign/entity/AlignerReferenceLibrary.java rename to src/main/java/com/milaboratory/oncomigec/core/consalign/entity/AlignerReferenceLibrary.java index e96a744..cd6f8cc 100644 --- a/src/main/java/com/milaboratory/migec2/core/consalign/entity/AlignerReferenceLibrary.java +++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/entity/AlignerReferenceLibrary.java @@ -13,18 +13,17 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.consalign.entity; +package com.milaboratory.oncomigec.core.consalign.entity; -import com.milaboratory.migec2.core.align.entity.SAlignmentResult; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; -import com.milaboratory.migec2.core.assemble.entity.SConsensus; -import com.milaboratory.migec2.core.consalign.mutations.MutationsAndCoverage; -import com.milaboratory.migec2.core.mutations.MigecMutationsCollection; +import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.assemble.entity.SConsensus; +import com.milaboratory.oncomigec.core.consalign.mutations.MutationsAndCoverage; +import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection; import java.util.HashMap; import java.util.Map; -import java.util.Set; public final class AlignerReferenceLibrary { private final Map mutationsAndCoverageByReference = diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/misc/ConsensusAlignerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/ConsensusAlignerFactory.java similarity index 66% rename from src/main/java/com/milaboratory/migec2/core/consalign/misc/ConsensusAlignerFactory.java rename to src/main/java/com/milaboratory/oncomigec/core/consalign/misc/ConsensusAlignerFactory.java index 71d488e..05c2378 100644 --- a/src/main/java/com/milaboratory/migec2/core/consalign/misc/ConsensusAlignerFactory.java +++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/ConsensusAlignerFactory.java @@ -1,8 +1,8 @@ -package com.milaboratory.migec2.core.consalign.misc; +package com.milaboratory.oncomigec.core.consalign.misc; -import com.milaboratory.migec2.core.align.processor.AlignerFactoryWithReference; -import com.milaboratory.migec2.core.assemble.entity.Consensus; -import com.milaboratory.migec2.core.consalign.processor.ConsensusAligner; +import com.milaboratory.oncomigec.core.align.processor.AlignerFactoryWithReference; +import com.milaboratory.oncomigec.core.assemble.entity.Consensus; +import com.milaboratory.oncomigec.core.consalign.processor.ConsensusAligner; public abstract class ConsensusAlignerFactory { protected final AlignerFactoryWithReference alignerFactory; diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/misc/ConsensusAlignerParameters.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/ConsensusAlignerParameters.java similarity index 96% rename from src/main/java/com/milaboratory/migec2/core/consalign/misc/ConsensusAlignerParameters.java rename to src/main/java/com/milaboratory/oncomigec/core/consalign/misc/ConsensusAlignerParameters.java index 5044844..3fc9d6f 100644 --- a/src/main/java/com/milaboratory/migec2/core/consalign/misc/ConsensusAlignerParameters.java +++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/ConsensusAlignerParameters.java @@ -1,6 +1,6 @@ -package com.milaboratory.migec2.core.consalign.misc; +package com.milaboratory.oncomigec.core.consalign.misc; -import com.milaboratory.migec2.util.ParameterSet; +import com.milaboratory.oncomigec.util.ParameterSet; import org.jdom.Element; public final class ConsensusAlignerParameters implements ParameterSet { diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/misc/PConsensusAlignerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/PConsensusAlignerFactory.java similarity index 66% rename from src/main/java/com/milaboratory/migec2/core/consalign/misc/PConsensusAlignerFactory.java rename to src/main/java/com/milaboratory/oncomigec/core/consalign/misc/PConsensusAlignerFactory.java index 50d4260..63083f3 100644 --- a/src/main/java/com/milaboratory/migec2/core/consalign/misc/PConsensusAlignerFactory.java +++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/PConsensusAlignerFactory.java @@ -1,8 +1,8 @@ -package com.milaboratory.migec2.core.consalign.misc; +package com.milaboratory.oncomigec.core.consalign.misc; -import com.milaboratory.migec2.core.align.processor.AlignerFactoryWithReference; -import com.milaboratory.migec2.core.assemble.entity.PConsensus; -import com.milaboratory.migec2.core.consalign.processor.PConsensusAligner; +import com.milaboratory.oncomigec.core.align.processor.AlignerFactoryWithReference; +import com.milaboratory.oncomigec.core.assemble.entity.PConsensus; +import com.milaboratory.oncomigec.core.consalign.processor.PConsensusAligner; public final class PConsensusAlignerFactory extends ConsensusAlignerFactory { diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/misc/SConsensusAlignerFactory.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/SConsensusAlignerFactory.java similarity index 66% rename from src/main/java/com/milaboratory/migec2/core/consalign/misc/SConsensusAlignerFactory.java rename to src/main/java/com/milaboratory/oncomigec/core/consalign/misc/SConsensusAlignerFactory.java index b3da769..5354234 100644 --- a/src/main/java/com/milaboratory/migec2/core/consalign/misc/SConsensusAlignerFactory.java +++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/misc/SConsensusAlignerFactory.java @@ -1,8 +1,8 @@ -package com.milaboratory.migec2.core.consalign.misc; +package com.milaboratory.oncomigec.core.consalign.misc; -import com.milaboratory.migec2.core.align.processor.AlignerFactoryWithReference; -import com.milaboratory.migec2.core.assemble.entity.SConsensus; -import com.milaboratory.migec2.core.consalign.processor.SConsensusAligner; +import com.milaboratory.oncomigec.core.align.processor.AlignerFactoryWithReference; +import com.milaboratory.oncomigec.core.assemble.entity.SConsensus; +import com.milaboratory.oncomigec.core.consalign.processor.SConsensusAligner; public final class SConsensusAlignerFactory extends ConsensusAlignerFactory { diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationQualityPair.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationQualityPair.java similarity index 86% rename from src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationQualityPair.java rename to src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationQualityPair.java index 49a60cc..2ae7191 100644 --- a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationQualityPair.java +++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationQualityPair.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.core.consalign.mutations; +package com.milaboratory.oncomigec.core.consalign.mutations; public class MutationQualityPair { private final int mutationCode; diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationsAndCoverage.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsAndCoverage.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationsAndCoverage.java rename to src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsAndCoverage.java index f899b5e..4564eb9 100644 --- a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationsAndCoverage.java +++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsAndCoverage.java @@ -13,17 +13,17 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.consalign.mutations; +package com.milaboratory.oncomigec.core.consalign.mutations; import com.milaboratory.core.sequence.Range; import com.milaboratory.core.sequence.alignment.LocalAlignment; import com.milaboratory.core.sequence.mutations.Mutations; import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.assemble.entity.SConsensus; -import com.milaboratory.migec2.core.mutations.MigecMutation; -import com.milaboratory.migec2.core.mutations.MigecMutationsCollection; -import com.milaboratory.migec2.util.Basics; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.assemble.entity.SConsensus; +import com.milaboratory.oncomigec.core.mutations.MigecMutation; +import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection; +import com.milaboratory.oncomigec.util.Basics; import java.util.HashSet; import java.util.Map; diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationsExtractor.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsExtractor.java similarity index 96% rename from src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationsExtractor.java rename to src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsExtractor.java index 6bc98eb..baf8470 100644 --- a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/MutationsExtractor.java +++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsExtractor.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.core.consalign.mutations; +package com.milaboratory.oncomigec.core.consalign.mutations; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequence.alignment.KAligner; @@ -8,10 +8,10 @@ import com.milaboratory.core.sequence.mutations.Mutations; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; import com.milaboratory.core.sequence.quality.SequenceQualityPhred; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.assemble.entity.SConsensus; -import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters; -import com.milaboratory.migec2.core.mutations.MigecMutationsCollection; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.assemble.entity.SConsensus; +import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerParameters; +import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection; import java.util.*; diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/NucleotideCoverage.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/NucleotideCoverage.java similarity index 98% rename from src/main/java/com/milaboratory/migec2/core/consalign/mutations/NucleotideCoverage.java rename to src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/NucleotideCoverage.java index d6bb28d..7a75a65 100644 --- a/src/main/java/com/milaboratory/migec2/core/consalign/mutations/NucleotideCoverage.java +++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/mutations/NucleotideCoverage.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.consalign.mutations; +package com.milaboratory.oncomigec.core.consalign.mutations; import java.util.concurrent.atomic.AtomicIntegerArray; diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/processor/ConsensusAligner.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/processor/ConsensusAligner.java similarity index 79% rename from src/main/java/com/milaboratory/migec2/core/consalign/processor/ConsensusAligner.java rename to src/main/java/com/milaboratory/oncomigec/core/consalign/processor/ConsensusAligner.java index ccc0c21..2cd5695 100644 --- a/src/main/java/com/milaboratory/migec2/core/consalign/processor/ConsensusAligner.java +++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/processor/ConsensusAligner.java @@ -13,15 +13,15 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.consalign.processor; +package com.milaboratory.oncomigec.core.consalign.processor; import cc.redberry.pipe.Processor; -import com.milaboratory.migec2.core.align.processor.Aligner; -import com.milaboratory.migec2.core.assemble.entity.Consensus; -import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus; -import com.milaboratory.migec2.core.consalign.entity.AlignerReferenceLibrary; -import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters; -import com.milaboratory.migec2.util.ProcessorResultWrapper; +import com.milaboratory.oncomigec.core.align.processor.Aligner; +import com.milaboratory.oncomigec.core.assemble.entity.Consensus; +import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus; +import com.milaboratory.oncomigec.core.consalign.entity.AlignerReferenceLibrary; +import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerParameters; +import com.milaboratory.oncomigec.util.ProcessorResultWrapper; public abstract class ConsensusAligner implements Processor, ProcessorResultWrapper> { diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/processor/PConsensusAligner.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/processor/PConsensusAligner.java similarity index 87% rename from src/main/java/com/milaboratory/migec2/core/consalign/processor/PConsensusAligner.java rename to src/main/java/com/milaboratory/oncomigec/core/consalign/processor/PConsensusAligner.java index 98e8a3d..b49900c 100644 --- a/src/main/java/com/milaboratory/migec2/core/consalign/processor/PConsensusAligner.java +++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/processor/PConsensusAligner.java @@ -1,16 +1,16 @@ -package com.milaboratory.migec2.core.consalign.processor; +package com.milaboratory.oncomigec.core.consalign.processor; import com.milaboratory.core.sequence.alignment.LocalAlignment; -import com.milaboratory.migec2.core.align.entity.PAlignmentResult; -import com.milaboratory.migec2.core.align.entity.SAlignmentResult; -import com.milaboratory.migec2.core.align.processor.Aligner; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.assemble.entity.PConsensus; -import com.milaboratory.migec2.core.assemble.entity.SConsensus; -import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus; -import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters; -import com.milaboratory.migec2.core.consalign.mutations.MutationsExtractor; -import com.milaboratory.migec2.core.mutations.MigecMutationsCollection; +import com.milaboratory.oncomigec.core.align.entity.PAlignmentResult; +import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult; +import com.milaboratory.oncomigec.core.align.processor.Aligner; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.assemble.entity.PConsensus; +import com.milaboratory.oncomigec.core.assemble.entity.SConsensus; +import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus; +import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerParameters; +import com.milaboratory.oncomigec.core.consalign.mutations.MutationsExtractor; +import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection; import java.util.ArrayList; import java.util.HashMap; diff --git a/src/main/java/com/milaboratory/migec2/core/consalign/processor/SConsensusAligner.java b/src/main/java/com/milaboratory/oncomigec/core/consalign/processor/SConsensusAligner.java similarity index 78% rename from src/main/java/com/milaboratory/migec2/core/consalign/processor/SConsensusAligner.java rename to src/main/java/com/milaboratory/oncomigec/core/consalign/processor/SConsensusAligner.java index dca5a82..8c3f68f 100644 --- a/src/main/java/com/milaboratory/migec2/core/consalign/processor/SConsensusAligner.java +++ b/src/main/java/com/milaboratory/oncomigec/core/consalign/processor/SConsensusAligner.java @@ -1,14 +1,14 @@ -package com.milaboratory.migec2.core.consalign.processor; +package com.milaboratory.oncomigec.core.consalign.processor; import com.milaboratory.core.sequence.alignment.LocalAlignment; -import com.milaboratory.migec2.core.align.entity.SAlignmentResult; -import com.milaboratory.migec2.core.align.processor.Aligner; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.assemble.entity.SConsensus; -import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus; -import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters; -import com.milaboratory.migec2.core.consalign.mutations.MutationsExtractor; -import com.milaboratory.migec2.core.mutations.MigecMutationsCollection; +import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult; +import com.milaboratory.oncomigec.core.align.processor.Aligner; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.assemble.entity.SConsensus; +import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus; +import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerParameters; +import com.milaboratory.oncomigec.core.consalign.mutations.MutationsExtractor; +import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection; import java.util.ArrayList; import java.util.HashMap; diff --git a/src/main/java/com/milaboratory/migec2/core/correct/CorrectedConsensus.java b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectedConsensus.java similarity index 93% rename from src/main/java/com/milaboratory/migec2/core/correct/CorrectedConsensus.java rename to src/main/java/com/milaboratory/oncomigec/core/correct/CorrectedConsensus.java index 44b356d..4c22825 100644 --- a/src/main/java/com/milaboratory/migec2/core/correct/CorrectedConsensus.java +++ b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectedConsensus.java @@ -13,17 +13,17 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.correct; +package com.milaboratory.oncomigec.core.correct; import com.milaboratory.core.sequence.Range; import com.milaboratory.core.sequence.mutations.Mutations; import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus; -import com.milaboratory.migec2.core.haplotype.Haplotype; -import com.milaboratory.migec2.core.mutations.MutationDifference; -import com.milaboratory.migec2.core.mutations.wrappers.MutationWrapperCollection; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus; +import com.milaboratory.oncomigec.core.haplotype.Haplotype; +import com.milaboratory.oncomigec.core.mutations.MutationDifference; +import com.milaboratory.oncomigec.core.mutations.wrappers.MutationWrapperCollection; import java.util.ArrayList; import java.util.List; diff --git a/src/main/java/com/milaboratory/migec2/core/correct/Corrector.java b/src/main/java/com/milaboratory/oncomigec/core/correct/Corrector.java similarity index 89% rename from src/main/java/com/milaboratory/migec2/core/correct/Corrector.java rename to src/main/java/com/milaboratory/oncomigec/core/correct/Corrector.java index f197939..e7458b5 100644 --- a/src/main/java/com/milaboratory/migec2/core/correct/Corrector.java +++ b/src/main/java/com/milaboratory/oncomigec/core/correct/Corrector.java @@ -13,16 +13,16 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.correct; +package com.milaboratory.oncomigec.core.correct; import com.milaboratory.core.sequence.Range; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus; -import com.milaboratory.migec2.core.consalign.entity.AlignerReferenceLibrary; -import com.milaboratory.migec2.core.mutations.MigecMutation; -import com.milaboratory.migec2.core.mutations.MigecMutationsCollection; -import com.milaboratory.migec2.model.classifier.BaseVariantClassifier; -import com.milaboratory.migec2.model.classifier.VariantClassifier; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus; +import com.milaboratory.oncomigec.core.consalign.entity.AlignerReferenceLibrary; +import com.milaboratory.oncomigec.core.mutations.MigecMutation; +import com.milaboratory.oncomigec.core.mutations.MigecMutationsCollection; +import com.milaboratory.oncomigec.model.classifier.BaseVariantClassifier; +import com.milaboratory.oncomigec.model.classifier.VariantClassifier; import java.util.HashSet; import java.util.Set; diff --git a/src/main/java/com/milaboratory/migec2/core/correct/CorrectorParameters.java b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorParameters.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/core/correct/CorrectorParameters.java rename to src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorParameters.java index 2bcae95..a7794d0 100644 --- a/src/main/java/com/milaboratory/migec2/core/correct/CorrectorParameters.java +++ b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorParameters.java @@ -1,7 +1,7 @@ -package com.milaboratory.migec2.core.correct; +package com.milaboratory.oncomigec.core.correct; -import com.milaboratory.migec2.util.ParameterSet; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.util.ParameterSet; +import com.milaboratory.oncomigec.util.Util; import org.jdom.Element; public final class CorrectorParameters implements ParameterSet { diff --git a/src/main/java/com/milaboratory/migec2/core/correct/CorrectorReferenceLibrary.java b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorReferenceLibrary.java similarity index 96% rename from src/main/java/com/milaboratory/migec2/core/correct/CorrectorReferenceLibrary.java rename to src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorReferenceLibrary.java index 3aaea3d..73acafb 100644 --- a/src/main/java/com/milaboratory/migec2/core/correct/CorrectorReferenceLibrary.java +++ b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorReferenceLibrary.java @@ -13,18 +13,18 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.correct; +package com.milaboratory.oncomigec.core.correct; import com.milaboratory.core.sequence.mutations.Mutations; import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.consalign.entity.AlignerReferenceLibrary; -import com.milaboratory.migec2.core.consalign.mutations.MutationsAndCoverage; -import com.milaboratory.migec2.model.classifier.ClassifierResult; -import com.milaboratory.migec2.model.classifier.VariantClassifier; -import com.milaboratory.migec2.model.variant.Variant; -import com.milaboratory.migec2.model.variant.VariantContainer; -import com.milaboratory.migec2.model.variant.VariantLibrary; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.consalign.entity.AlignerReferenceLibrary; +import com.milaboratory.oncomigec.core.consalign.mutations.MutationsAndCoverage; +import com.milaboratory.oncomigec.model.classifier.ClassifierResult; +import com.milaboratory.oncomigec.model.classifier.VariantClassifier; +import com.milaboratory.oncomigec.model.variant.Variant; +import com.milaboratory.oncomigec.model.variant.VariantContainer; +import com.milaboratory.oncomigec.model.variant.VariantLibrary; import java.util.*; diff --git a/src/main/java/com/milaboratory/migec2/core/correct/MutationFilter.java b/src/main/java/com/milaboratory/oncomigec/core/correct/MutationFilter.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/core/correct/MutationFilter.java rename to src/main/java/com/milaboratory/oncomigec/core/correct/MutationFilter.java index 8423f9b..1ace036 100644 --- a/src/main/java/com/milaboratory/migec2/core/correct/MutationFilter.java +++ b/src/main/java/com/milaboratory/oncomigec/core/correct/MutationFilter.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.correct; +package com.milaboratory.oncomigec.core.correct; import java.util.Set; diff --git a/src/main/java/com/milaboratory/migec2/core/haplotype/Haplotype.java b/src/main/java/com/milaboratory/oncomigec/core/haplotype/Haplotype.java similarity index 94% rename from src/main/java/com/milaboratory/migec2/core/haplotype/Haplotype.java rename to src/main/java/com/milaboratory/oncomigec/core/haplotype/Haplotype.java index 3907cef..4817593 100644 --- a/src/main/java/com/milaboratory/migec2/core/haplotype/Haplotype.java +++ b/src/main/java/com/milaboratory/oncomigec/core/haplotype/Haplotype.java @@ -13,11 +13,11 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.haplotype; +package com.milaboratory.oncomigec.core.haplotype; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.core.correct.CorrectedConsensus; -import com.milaboratory.migec2.core.mutations.MutationDifference; +import com.milaboratory.oncomigec.core.correct.CorrectedConsensus; +import com.milaboratory.oncomigec.core.mutations.MutationDifference; import java.util.List; diff --git a/src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeCounters.java b/src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeCounters.java similarity index 95% rename from src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeCounters.java rename to src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeCounters.java index 0e18606..64c0007 100644 --- a/src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeCounters.java +++ b/src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeCounters.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.haplotype; +package com.milaboratory.oncomigec.core.haplotype; public final class HaplotypeCounters { private int count = 0, readCount = 0; diff --git a/src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeTree.java b/src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTree.java similarity index 96% rename from src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeTree.java rename to src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTree.java index 2cbb7fa..a66e131 100644 --- a/src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeTree.java +++ b/src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTree.java @@ -13,15 +13,15 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.haplotype; +package com.milaboratory.oncomigec.core.haplotype; import com.milaboratory.core.sequence.mutations.Mutations; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.correct.CorrectedConsensus; -import com.milaboratory.migec2.core.correct.CorrectorReferenceLibrary; -import com.milaboratory.migec2.core.mutations.MutationDifference; -import com.milaboratory.migec2.model.variant.VariantLibrary; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.correct.CorrectedConsensus; +import com.milaboratory.oncomigec.core.correct.CorrectorReferenceLibrary; +import com.milaboratory.oncomigec.core.mutations.MutationDifference; +import com.milaboratory.oncomigec.model.variant.VariantLibrary; import org.apache.commons.math.MathException; import org.apache.commons.math.distribution.BinomialDistribution; import org.apache.commons.math.distribution.BinomialDistributionImpl; diff --git a/src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeTreeParameters.java b/src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTreeParameters.java similarity index 96% rename from src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeTreeParameters.java rename to src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTreeParameters.java index b3d8f40..1797576 100644 --- a/src/main/java/com/milaboratory/migec2/core/haplotype/HaplotypeTreeParameters.java +++ b/src/main/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTreeParameters.java @@ -1,6 +1,6 @@ -package com.milaboratory.migec2.core.haplotype; +package com.milaboratory.oncomigec.core.haplotype; -import com.milaboratory.migec2.util.ParameterSet; +import com.milaboratory.oncomigec.util.ParameterSet; import org.jdom.Element; public final class HaplotypeTreeParameters implements ParameterSet { diff --git a/src/main/java/com/milaboratory/migec2/core/io/entity/Mig.java b/src/main/java/com/milaboratory/oncomigec/core/io/entity/Mig.java similarity index 94% rename from src/main/java/com/milaboratory/migec2/core/io/entity/Mig.java rename to src/main/java/com/milaboratory/oncomigec/core/io/entity/Mig.java index 774c077..f022cc7 100644 --- a/src/main/java/com/milaboratory/migec2/core/io/entity/Mig.java +++ b/src/main/java/com/milaboratory/oncomigec/core/io/entity/Mig.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.core.io.entity; +package com.milaboratory.oncomigec.core.io.entity; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; diff --git a/src/main/java/com/milaboratory/migec2/core/io/entity/PMig.java b/src/main/java/com/milaboratory/oncomigec/core/io/entity/PMig.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/core/io/entity/PMig.java rename to src/main/java/com/milaboratory/oncomigec/core/io/entity/PMig.java index 3932f6f..120fa22 100644 --- a/src/main/java/com/milaboratory/migec2/core/io/entity/PMig.java +++ b/src/main/java/com/milaboratory/oncomigec/core/io/entity/PMig.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.io.entity; +package com.milaboratory.oncomigec.core.io.entity; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; diff --git a/src/main/java/com/milaboratory/migec2/core/io/entity/SMig.java b/src/main/java/com/milaboratory/oncomigec/core/io/entity/SMig.java similarity index 96% rename from src/main/java/com/milaboratory/migec2/core/io/entity/SMig.java rename to src/main/java/com/milaboratory/oncomigec/core/io/entity/SMig.java index 27004f4..7098639 100644 --- a/src/main/java/com/milaboratory/migec2/core/io/entity/SMig.java +++ b/src/main/java/com/milaboratory/oncomigec/core/io/entity/SMig.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.io.entity; +package com.milaboratory.oncomigec.core.io.entity; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; diff --git a/src/main/java/com/milaboratory/migec2/core/io/misc/MigReaderParameters.java b/src/main/java/com/milaboratory/oncomigec/core/io/misc/MigReaderParameters.java similarity index 94% rename from src/main/java/com/milaboratory/migec2/core/io/misc/MigReaderParameters.java rename to src/main/java/com/milaboratory/oncomigec/core/io/misc/MigReaderParameters.java index 0f12305..5ca4da2 100644 --- a/src/main/java/com/milaboratory/migec2/core/io/misc/MigReaderParameters.java +++ b/src/main/java/com/milaboratory/oncomigec/core/io/misc/MigReaderParameters.java @@ -1,6 +1,6 @@ -package com.milaboratory.migec2.core.io.misc; +package com.milaboratory.oncomigec.core.io.misc; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.util.Util; public class MigReaderParameters { private final byte umiQualThreshold; diff --git a/src/main/java/com/milaboratory/migec2/core/io/misc/ReadInfo.java b/src/main/java/com/milaboratory/oncomigec/core/io/misc/ReadInfo.java similarity index 91% rename from src/main/java/com/milaboratory/migec2/core/io/misc/ReadInfo.java rename to src/main/java/com/milaboratory/oncomigec/core/io/misc/ReadInfo.java index b4276b4..fb63059 100644 --- a/src/main/java/com/milaboratory/migec2/core/io/misc/ReadInfo.java +++ b/src/main/java/com/milaboratory/oncomigec/core/io/misc/ReadInfo.java @@ -13,10 +13,10 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.io.misc; +package com.milaboratory.oncomigec.core.io.misc; import com.milaboratory.core.sequencing.read.SequencingRead; -import com.milaboratory.migec2.preproc.demultiplex.entity.CheckoutResult; +import com.milaboratory.oncomigec.preproc.demultiplex.entity.CheckoutResult; public class ReadInfo { private final ReadType read; diff --git a/src/main/java/com/milaboratory/migec2/core/io/misc/UmiHistogram.java b/src/main/java/com/milaboratory/oncomigec/core/io/misc/UmiHistogram.java similarity index 99% rename from src/main/java/com/milaboratory/migec2/core/io/misc/UmiHistogram.java rename to src/main/java/com/milaboratory/oncomigec/core/io/misc/UmiHistogram.java index 74a2ddd..b8bb86b 100644 --- a/src/main/java/com/milaboratory/migec2/core/io/misc/UmiHistogram.java +++ b/src/main/java/com/milaboratory/oncomigec/core/io/misc/UmiHistogram.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.io.misc; +package com.milaboratory.oncomigec.core.io.misc; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; import com.milaboratory.util.Bit2Array; diff --git a/src/main/java/com/milaboratory/migec2/core/io/misc/index/IndexingInfo.java b/src/main/java/com/milaboratory/oncomigec/core/io/misc/index/IndexingInfo.java similarity index 89% rename from src/main/java/com/milaboratory/migec2/core/io/misc/index/IndexingInfo.java rename to src/main/java/com/milaboratory/oncomigec/core/io/misc/index/IndexingInfo.java index e86c4c7..f6f78c8 100644 --- a/src/main/java/com/milaboratory/migec2/core/io/misc/index/IndexingInfo.java +++ b/src/main/java/com/milaboratory/oncomigec/core/io/misc/index/IndexingInfo.java @@ -1,7 +1,7 @@ -package com.milaboratory.migec2.core.io.misc.index; +package com.milaboratory.oncomigec.core.io.misc.index; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.core.io.misc.ReadInfo; +import com.milaboratory.oncomigec.core.io.misc.ReadInfo; public class IndexingInfo { private final ReadInfo readInfo; diff --git a/src/main/java/com/milaboratory/migec2/core/io/misc/index/UmiIndexer.java b/src/main/java/com/milaboratory/oncomigec/core/io/misc/index/UmiIndexer.java similarity index 81% rename from src/main/java/com/milaboratory/migec2/core/io/misc/index/UmiIndexer.java rename to src/main/java/com/milaboratory/oncomigec/core/io/misc/index/UmiIndexer.java index d4f66cf..6dcd89e 100644 --- a/src/main/java/com/milaboratory/migec2/core/io/misc/index/UmiIndexer.java +++ b/src/main/java/com/milaboratory/oncomigec/core/io/misc/index/UmiIndexer.java @@ -1,12 +1,12 @@ -package com.milaboratory.migec2.core.io.misc.index; +package com.milaboratory.oncomigec.core.io.misc.index; import cc.redberry.pipe.Processor; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; import com.milaboratory.core.sequencing.read.SequencingRead; -import com.milaboratory.migec2.core.io.misc.ReadInfo; -import com.milaboratory.migec2.preproc.demultiplex.entity.CheckoutResult; -import com.milaboratory.migec2.preproc.demultiplex.processor.CheckoutProcessor; -import com.milaboratory.migec2.util.ProcessorResultWrapper; +import com.milaboratory.oncomigec.core.io.misc.ReadInfo; +import com.milaboratory.oncomigec.preproc.demultiplex.entity.CheckoutResult; +import com.milaboratory.oncomigec.preproc.demultiplex.processor.CheckoutProcessor; +import com.milaboratory.oncomigec.util.ProcessorResultWrapper; public class UmiIndexer implements Processor> { private final CheckoutProcessor checkoutProcessor; diff --git a/src/main/java/com/milaboratory/migec2/core/io/readers/MigReader.java b/src/main/java/com/milaboratory/oncomigec/core/io/readers/MigReader.java similarity index 90% rename from src/main/java/com/milaboratory/migec2/core/io/readers/MigReader.java rename to src/main/java/com/milaboratory/oncomigec/core/io/readers/MigReader.java index f89af94..a2bc176 100644 --- a/src/main/java/com/milaboratory/migec2/core/io/readers/MigReader.java +++ b/src/main/java/com/milaboratory/oncomigec/core/io/readers/MigReader.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.core.io.readers; +package com.milaboratory.oncomigec.core.io.readers; import cc.redberry.pipe.OutputPort; import cc.redberry.pipe.OutputPortCloseable; @@ -8,16 +8,16 @@ import cc.redberry.pipe.util.CountingOutputPort; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; import com.milaboratory.core.sequencing.read.SequencingRead; -import com.milaboratory.migec2.core.io.entity.Mig; -import com.milaboratory.migec2.core.io.misc.MigReaderParameters; -import com.milaboratory.migec2.core.io.misc.ReadInfo; -import com.milaboratory.migec2.core.io.misc.UmiHistogram; -import com.milaboratory.migec2.core.io.misc.index.IndexingInfo; -import com.milaboratory.migec2.core.io.misc.index.UmiIndexer; -import com.milaboratory.migec2.pipeline.MigecCli; -import com.milaboratory.migec2.preproc.demultiplex.processor.CheckoutProcessor; -import com.milaboratory.migec2.preproc.demultiplex.processor.HeaderParser; -import com.milaboratory.migec2.util.ProcessorResultWrapper; +import com.milaboratory.oncomigec.core.io.entity.Mig; +import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters; +import com.milaboratory.oncomigec.core.io.misc.ReadInfo; +import com.milaboratory.oncomigec.core.io.misc.UmiHistogram; +import com.milaboratory.oncomigec.core.io.misc.index.IndexingInfo; +import com.milaboratory.oncomigec.core.io.misc.index.UmiIndexer; +import com.milaboratory.oncomigec.pipeline.MigecCli; +import com.milaboratory.oncomigec.preproc.demultiplex.processor.CheckoutProcessor; +import com.milaboratory.oncomigec.preproc.demultiplex.processor.HeaderParser; +import com.milaboratory.oncomigec.util.ProcessorResultWrapper; import java.util.*; diff --git a/src/main/java/com/milaboratory/migec2/core/io/readers/PMigReader.java b/src/main/java/com/milaboratory/oncomigec/core/io/readers/PMigReader.java similarity index 92% rename from src/main/java/com/milaboratory/migec2/core/io/readers/PMigReader.java rename to src/main/java/com/milaboratory/oncomigec/core/io/readers/PMigReader.java index 78a4630..41b8d61 100644 --- a/src/main/java/com/milaboratory/migec2/core/io/readers/PMigReader.java +++ b/src/main/java/com/milaboratory/oncomigec/core/io/readers/PMigReader.java @@ -13,26 +13,25 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.io.readers; +package com.milaboratory.oncomigec.core.io.readers; import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; import com.milaboratory.core.sequence.quality.QualityFormat; import com.milaboratory.core.sequencing.io.fastq.PFastqReader; -import com.milaboratory.core.sequencing.io.fastq.SRandomAccessFastqReader; import com.milaboratory.core.sequencing.read.PSequencingRead; import com.milaboratory.core.sequencing.read.PSequencingReadImpl; import com.milaboratory.core.sequencing.read.SSequencingRead; import com.milaboratory.core.sequencing.read.SequencingRead; -import com.milaboratory.migec2.core.io.entity.PMig; -import com.milaboratory.migec2.core.io.entity.SMig; -import com.milaboratory.migec2.core.io.misc.MigReaderParameters; -import com.milaboratory.migec2.core.io.misc.ReadInfo; -import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult; -import com.milaboratory.migec2.preproc.demultiplex.entity.PCheckoutResult; -import com.milaboratory.migec2.preproc.demultiplex.processor.PCheckoutProcessor; -import com.milaboratory.migec2.preproc.misc.ReadOverlapper; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.core.io.entity.PMig; +import com.milaboratory.oncomigec.core.io.entity.SMig; +import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters; +import com.milaboratory.oncomigec.core.io.misc.ReadInfo; +import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult; +import com.milaboratory.oncomigec.preproc.demultiplex.entity.PCheckoutResult; +import com.milaboratory.oncomigec.preproc.demultiplex.processor.PCheckoutProcessor; +import com.milaboratory.oncomigec.preproc.misc.ReadOverlapper; +import com.milaboratory.oncomigec.util.Util; import java.io.File; import java.io.IOException; diff --git a/src/main/java/com/milaboratory/migec2/core/io/readers/SMigReader.java b/src/main/java/com/milaboratory/oncomigec/core/io/readers/SMigReader.java similarity index 90% rename from src/main/java/com/milaboratory/migec2/core/io/readers/SMigReader.java rename to src/main/java/com/milaboratory/oncomigec/core/io/readers/SMigReader.java index 584b344..aef03f7 100644 --- a/src/main/java/com/milaboratory/migec2/core/io/readers/SMigReader.java +++ b/src/main/java/com/milaboratory/oncomigec/core/io/readers/SMigReader.java @@ -13,18 +13,18 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.io.readers; +package com.milaboratory.oncomigec.core.io.readers; import cc.redberry.pipe.OutputPortCloseable; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; import com.milaboratory.core.sequencing.io.fastq.SFastqReader; import com.milaboratory.core.sequencing.read.SSequencingRead; import com.milaboratory.core.sequencing.read.SequencingRead; -import com.milaboratory.migec2.core.io.entity.SMig; -import com.milaboratory.migec2.core.io.misc.MigReaderParameters; -import com.milaboratory.migec2.core.io.misc.ReadInfo; -import com.milaboratory.migec2.preproc.demultiplex.processor.SCheckoutProcessor; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.core.io.entity.SMig; +import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters; +import com.milaboratory.oncomigec.core.io.misc.ReadInfo; +import com.milaboratory.oncomigec.preproc.demultiplex.processor.SCheckoutProcessor; +import com.milaboratory.oncomigec.util.Util; import java.io.File; import java.io.IOException; diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/MigecMutation.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/MigecMutation.java similarity index 96% rename from src/main/java/com/milaboratory/migec2/core/mutations/MigecMutation.java rename to src/main/java/com/milaboratory/oncomigec/core/mutations/MigecMutation.java index ac556b2..baf9df2 100644 --- a/src/main/java/com/milaboratory/migec2/core/mutations/MigecMutation.java +++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/MigecMutation.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.core.mutations; +package com.milaboratory.oncomigec.core.mutations; import com.milaboratory.core.sequence.mutations.MutationType; import com.milaboratory.core.sequence.mutations.Mutations; diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/MigecMutationsCollection.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/MigecMutationsCollection.java similarity index 95% rename from src/main/java/com/milaboratory/migec2/core/mutations/MigecMutationsCollection.java rename to src/main/java/com/milaboratory/oncomigec/core/mutations/MigecMutationsCollection.java index ff88868..8c8d0c3 100644 --- a/src/main/java/com/milaboratory/migec2/core/mutations/MigecMutationsCollection.java +++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/MigecMutationsCollection.java @@ -1,9 +1,8 @@ -package com.milaboratory.migec2.core.mutations; +package com.milaboratory.oncomigec.core.mutations; import com.milaboratory.core.sequence.Range; import com.milaboratory.core.sequence.mutations.Mutations; -import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet; -import com.milaboratory.migec2.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.Reference; import java.util.Iterator; import java.util.LinkedList; diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/MutationDifference.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/MutationDifference.java similarity index 93% rename from src/main/java/com/milaboratory/migec2/core/mutations/MutationDifference.java rename to src/main/java/com/milaboratory/oncomigec/core/mutations/MutationDifference.java index a84789b..6e1d63d 100644 --- a/src/main/java/com/milaboratory/migec2/core/mutations/MutationDifference.java +++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/MutationDifference.java @@ -1,11 +1,9 @@ -package com.milaboratory.migec2.core.mutations; +package com.milaboratory.oncomigec.core.mutations; import com.milaboratory.core.sequence.mutations.Mutations; -import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet; -import com.milaboratory.migec2.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.Reference; import org.apache.commons.collections.iterators.ArrayIterator; -import java.lang.reflect.Array; import java.util.Arrays; import java.util.Iterator; diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/MutationsCollection.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/MutationsCollection.java similarity index 73% rename from src/main/java/com/milaboratory/migec2/core/mutations/MutationsCollection.java rename to src/main/java/com/milaboratory/oncomigec/core/mutations/MutationsCollection.java index 239a066..3629f43 100644 --- a/src/main/java/com/milaboratory/migec2/core/mutations/MutationsCollection.java +++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/MutationsCollection.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.core.mutations; +package com.milaboratory.oncomigec.core.mutations; public interface MutationsCollection { public int[] getMutationCodes(); diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/DeletionWrapper.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/DeletionWrapper.java similarity index 93% rename from src/main/java/com/milaboratory/migec2/core/mutations/wrappers/DeletionWrapper.java rename to src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/DeletionWrapper.java index e73b977..ad42019 100644 --- a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/DeletionWrapper.java +++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/DeletionWrapper.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.core.mutations.wrappers; +package com.milaboratory.oncomigec.core.mutations.wrappers; import com.milaboratory.core.sequence.mutations.MutationType; import com.milaboratory.core.sequence.mutations.Mutations; diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/IndelWrapper.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/IndelWrapper.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/core/mutations/wrappers/IndelWrapper.java rename to src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/IndelWrapper.java index 726e254..e56295f 100644 --- a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/IndelWrapper.java +++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/IndelWrapper.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.core.mutations.wrappers; +package com.milaboratory.oncomigec.core.mutations.wrappers; import com.milaboratory.core.sequence.mutations.MutationType; import com.milaboratory.core.sequence.mutations.Mutations; diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/InsertionWrapper.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/InsertionWrapper.java similarity index 92% rename from src/main/java/com/milaboratory/migec2/core/mutations/wrappers/InsertionWrapper.java rename to src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/InsertionWrapper.java index a0bacae..da5dd21 100644 --- a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/InsertionWrapper.java +++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/InsertionWrapper.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.core.mutations.wrappers; +package com.milaboratory.oncomigec.core.mutations.wrappers; import com.milaboratory.core.sequence.mutations.MutationType; import com.milaboratory.core.sequence.mutations.Mutations; diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/MutationWrapper.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/MutationWrapper.java similarity index 90% rename from src/main/java/com/milaboratory/migec2/core/mutations/wrappers/MutationWrapper.java rename to src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/MutationWrapper.java index 7dfdfcd..9dda03a 100644 --- a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/MutationWrapper.java +++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/MutationWrapper.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.core.mutations.wrappers; +package com.milaboratory.oncomigec.core.mutations.wrappers; import com.milaboratory.core.sequence.mutations.MutationType; import com.milaboratory.core.sequence.mutations.Mutations; diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/MutationWrapperCollection.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/MutationWrapperCollection.java similarity index 92% rename from src/main/java/com/milaboratory/migec2/core/mutations/wrappers/MutationWrapperCollection.java rename to src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/MutationWrapperCollection.java index 59b2b5a..859b137 100644 --- a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/MutationWrapperCollection.java +++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/MutationWrapperCollection.java @@ -1,10 +1,9 @@ -package com.milaboratory.migec2.core.mutations.wrappers; +package com.milaboratory.oncomigec.core.mutations.wrappers; import com.milaboratory.core.sequence.mutations.MutationType; import com.milaboratory.core.sequence.mutations.Mutations; -import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.mutations.MutationsCollection; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.mutations.MutationsCollection; import java.util.LinkedList; import java.util.List; diff --git a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/SubstitutionWrapper.java b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/SubstitutionWrapper.java similarity index 94% rename from src/main/java/com/milaboratory/migec2/core/mutations/wrappers/SubstitutionWrapper.java rename to src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/SubstitutionWrapper.java index 737f4ee..26959ff 100644 --- a/src/main/java/com/milaboratory/migec2/core/mutations/wrappers/SubstitutionWrapper.java +++ b/src/main/java/com/milaboratory/oncomigec/core/mutations/wrappers/SubstitutionWrapper.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.core.mutations.wrappers; +package com.milaboratory.oncomigec.core.mutations.wrappers; import com.milaboratory.core.sequence.mutations.MutationType; import com.milaboratory.core.sequence.mutations.Mutations; diff --git a/src/main/java/com/milaboratory/migec2/model/classifier/BaseInstanceFactory.java b/src/main/java/com/milaboratory/oncomigec/model/classifier/BaseInstanceFactory.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/model/classifier/BaseInstanceFactory.java rename to src/main/java/com/milaboratory/oncomigec/model/classifier/BaseInstanceFactory.java index 4303262..3522065 100644 --- a/src/main/java/com/milaboratory/migec2/model/classifier/BaseInstanceFactory.java +++ b/src/main/java/com/milaboratory/oncomigec/model/classifier/BaseInstanceFactory.java @@ -16,9 +16,9 @@ * Last modified on 25.11.2014 by mikesh */ -package com.milaboratory.migec2.model.classifier; +package com.milaboratory.oncomigec.model.classifier; -import com.milaboratory.migec2.model.variant.Variant; +import com.milaboratory.oncomigec.model.variant.Variant; import weka.core.Instance; import weka.core.Instances; import weka.core.converters.ArffLoader; diff --git a/src/main/java/com/milaboratory/migec2/model/classifier/BaseVariantClassifier.java b/src/main/java/com/milaboratory/oncomigec/model/classifier/BaseVariantClassifier.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/model/classifier/BaseVariantClassifier.java rename to src/main/java/com/milaboratory/oncomigec/model/classifier/BaseVariantClassifier.java index 47a6aab..c64360d 100644 --- a/src/main/java/com/milaboratory/migec2/model/classifier/BaseVariantClassifier.java +++ b/src/main/java/com/milaboratory/oncomigec/model/classifier/BaseVariantClassifier.java @@ -16,9 +16,9 @@ * Last modified on 25.11.2014 by mikesh */ -package com.milaboratory.migec2.model.classifier; +package com.milaboratory.oncomigec.model.classifier; -import com.milaboratory.migec2.model.variant.Variant; +import com.milaboratory.oncomigec.model.variant.Variant; import weka.classifiers.Classifier; import weka.classifiers.misc.SerializedClassifier; import weka.core.Instance; diff --git a/src/main/java/com/milaboratory/migec2/model/classifier/ClassifierResult.java b/src/main/java/com/milaboratory/oncomigec/model/classifier/ClassifierResult.java similarity index 95% rename from src/main/java/com/milaboratory/migec2/model/classifier/ClassifierResult.java rename to src/main/java/com/milaboratory/oncomigec/model/classifier/ClassifierResult.java index 9df90e0..c743241 100644 --- a/src/main/java/com/milaboratory/migec2/model/classifier/ClassifierResult.java +++ b/src/main/java/com/milaboratory/oncomigec/model/classifier/ClassifierResult.java @@ -16,7 +16,7 @@ * Last modified on 23.11.2014 by mikesh */ -package com.milaboratory.migec2.model.classifier; +package com.milaboratory.oncomigec.model.classifier; public class ClassifierResult { private final boolean passed; diff --git a/src/main/java/com/milaboratory/migec2/model/classifier/InstanceFactory.java b/src/main/java/com/milaboratory/oncomigec/model/classifier/InstanceFactory.java similarity index 91% rename from src/main/java/com/milaboratory/migec2/model/classifier/InstanceFactory.java rename to src/main/java/com/milaboratory/oncomigec/model/classifier/InstanceFactory.java index ce43930..c635cfb 100644 --- a/src/main/java/com/milaboratory/migec2/model/classifier/InstanceFactory.java +++ b/src/main/java/com/milaboratory/oncomigec/model/classifier/InstanceFactory.java @@ -16,9 +16,9 @@ * Last modified on 23.11.2014 by mikesh */ -package com.milaboratory.migec2.model.classifier; +package com.milaboratory.oncomigec.model.classifier; -import com.milaboratory.migec2.model.variant.Variant; +import com.milaboratory.oncomigec.model.variant.Variant; import weka.core.Instance; import weka.core.Instances; diff --git a/src/main/java/com/milaboratory/migec2/model/classifier/VariantClassifier.java b/src/main/java/com/milaboratory/oncomigec/model/classifier/VariantClassifier.java similarity index 87% rename from src/main/java/com/milaboratory/migec2/model/classifier/VariantClassifier.java rename to src/main/java/com/milaboratory/oncomigec/model/classifier/VariantClassifier.java index 7292b27..8943663 100644 --- a/src/main/java/com/milaboratory/migec2/model/classifier/VariantClassifier.java +++ b/src/main/java/com/milaboratory/oncomigec/model/classifier/VariantClassifier.java @@ -16,9 +16,9 @@ * Last modified on 26.11.2014 by mikesh */ -package com.milaboratory.migec2.model.classifier; +package com.milaboratory.oncomigec.model.classifier; -import com.milaboratory.migec2.model.variant.Variant; +import com.milaboratory.oncomigec.model.variant.Variant; public interface VariantClassifier { public ClassifierResult classify(Variant variant); diff --git a/src/main/java/com/milaboratory/migec2/model/variant/Variant.java b/src/main/java/com/milaboratory/oncomigec/model/variant/Variant.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/model/variant/Variant.java rename to src/main/java/com/milaboratory/oncomigec/model/variant/Variant.java index a127f81..2097639 100644 --- a/src/main/java/com/milaboratory/migec2/model/variant/Variant.java +++ b/src/main/java/com/milaboratory/oncomigec/model/variant/Variant.java @@ -16,10 +16,10 @@ * Last modified on 20.11.2014 by mikesh */ -package com.milaboratory.migec2.model.variant; +package com.milaboratory.oncomigec.model.variant; import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet; -import com.milaboratory.migec2.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.Reference; public class Variant { private final int pos; diff --git a/src/main/java/com/milaboratory/migec2/model/variant/VariantContainer.java b/src/main/java/com/milaboratory/oncomigec/model/variant/VariantContainer.java similarity index 98% rename from src/main/java/com/milaboratory/migec2/model/variant/VariantContainer.java rename to src/main/java/com/milaboratory/oncomigec/model/variant/VariantContainer.java index 1dbdb3a..59e595d 100644 --- a/src/main/java/com/milaboratory/migec2/model/variant/VariantContainer.java +++ b/src/main/java/com/milaboratory/oncomigec/model/variant/VariantContainer.java @@ -16,10 +16,10 @@ * Last modified on 23.11.2014 by mikesh */ -package com.milaboratory.migec2.model.variant; +package com.milaboratory.oncomigec.model.variant; import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet; -import com.milaboratory.migec2.core.consalign.mutations.MutationsAndCoverage; +import com.milaboratory.oncomigec.core.consalign.mutations.MutationsAndCoverage; import java.util.Collections; import java.util.LinkedList; diff --git a/src/main/java/com/milaboratory/migec2/model/variant/VariantLibrary.java b/src/main/java/com/milaboratory/oncomigec/model/variant/VariantLibrary.java similarity index 93% rename from src/main/java/com/milaboratory/migec2/model/variant/VariantLibrary.java rename to src/main/java/com/milaboratory/oncomigec/model/variant/VariantLibrary.java index fff52af..a603f5e 100644 --- a/src/main/java/com/milaboratory/migec2/model/variant/VariantLibrary.java +++ b/src/main/java/com/milaboratory/oncomigec/model/variant/VariantLibrary.java @@ -16,11 +16,11 @@ * Last modified on 1.12.2014 by mikesh */ -package com.milaboratory.migec2.model.variant; +package com.milaboratory.oncomigec.model.variant; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; -import com.milaboratory.migec2.core.consalign.entity.AlignerReferenceLibrary; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.consalign.entity.AlignerReferenceLibrary; import java.util.HashMap; import java.util.Map; diff --git a/src/main/java/com/milaboratory/migec2/pipeline/ExomePipeline.java b/src/main/java/com/milaboratory/oncomigec/pipeline/ExomePipeline.java similarity index 81% rename from src/main/java/com/milaboratory/migec2/pipeline/ExomePipeline.java rename to src/main/java/com/milaboratory/oncomigec/pipeline/ExomePipeline.java index 4cc3659..04b3531 100644 --- a/src/main/java/com/milaboratory/migec2/pipeline/ExomePipeline.java +++ b/src/main/java/com/milaboratory/oncomigec/pipeline/ExomePipeline.java @@ -13,23 +13,22 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.pipeline; +package com.milaboratory.oncomigec.pipeline; -import com.milaboratory.migec2.core.align.processor.AlignerFactoryWithReference; -import com.milaboratory.migec2.core.align.processor.aligners.ExtendedExomeAlignerFactory; -import com.milaboratory.migec2.core.align.processor.aligners.SimpleExomeAlignerFactory; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; -import com.milaboratory.migec2.core.assemble.misc.AssemblerFactory; -import com.milaboratory.migec2.core.assemble.misc.PAssemblerFactory; -import com.milaboratory.migec2.core.assemble.misc.SAssemblerFactory; -import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerFactory; -import com.milaboratory.migec2.core.consalign.misc.PConsensusAlignerFactory; -import com.milaboratory.migec2.core.consalign.misc.SConsensusAlignerFactory; -import com.milaboratory.migec2.core.io.misc.MigReaderParameters; -import com.milaboratory.migec2.core.io.readers.MigReader; -import com.milaboratory.migec2.core.io.readers.PMigReader; -import com.milaboratory.migec2.core.io.readers.SMigReader; -import com.milaboratory.migec2.preproc.demultiplex.config.BarcodeListParser; +import com.milaboratory.oncomigec.core.align.processor.AlignerFactoryWithReference; +import com.milaboratory.oncomigec.core.align.processor.aligners.ExtendedExomeAlignerFactory; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.assemble.misc.AssemblerFactory; +import com.milaboratory.oncomigec.core.assemble.misc.PAssemblerFactory; +import com.milaboratory.oncomigec.core.assemble.misc.SAssemblerFactory; +import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerFactory; +import com.milaboratory.oncomigec.core.consalign.misc.PConsensusAlignerFactory; +import com.milaboratory.oncomigec.core.consalign.misc.SConsensusAlignerFactory; +import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters; +import com.milaboratory.oncomigec.core.io.readers.MigReader; +import com.milaboratory.oncomigec.core.io.readers.PMigReader; +import com.milaboratory.oncomigec.core.io.readers.SMigReader; +import com.milaboratory.oncomigec.preproc.demultiplex.config.BarcodeListParser; import org.apache.commons.io.FileUtils; import java.io.File; diff --git a/src/main/java/com/milaboratory/migec2/pipeline/MigecCli.java b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecCli.java similarity index 99% rename from src/main/java/com/milaboratory/migec2/pipeline/MigecCli.java rename to src/main/java/com/milaboratory/oncomigec/pipeline/MigecCli.java index 90b88cd..398552a 100644 --- a/src/main/java/com/milaboratory/migec2/pipeline/MigecCli.java +++ b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecCli.java @@ -1,7 +1,7 @@ -package com.milaboratory.migec2.pipeline; +package com.milaboratory.oncomigec.pipeline; -import com.milaboratory.migec2.core.io.misc.MigReaderParameters; -import com.milaboratory.migec2.core.io.misc.UmiHistogram; +import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters; +import com.milaboratory.oncomigec.core.io.misc.UmiHistogram; import org.apache.commons.cli.*; import org.apache.commons.io.FileUtils; import org.apache.commons.io.FilenameUtils; diff --git a/src/main/java/com/milaboratory/migec2/pipeline/MigecParameterSet.java b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecParameterSet.java similarity index 95% rename from src/main/java/com/milaboratory/migec2/pipeline/MigecParameterSet.java rename to src/main/java/com/milaboratory/oncomigec/pipeline/MigecParameterSet.java index 6265f41..27e91f2 100644 --- a/src/main/java/com/milaboratory/migec2/pipeline/MigecParameterSet.java +++ b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecParameterSet.java @@ -1,12 +1,12 @@ -package com.milaboratory.migec2.pipeline; - -import com.milaboratory.migec2.core.assemble.misc.AssemblerParameters; -import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters; -import com.milaboratory.migec2.core.correct.CorrectorParameters; -import com.milaboratory.migec2.core.haplotype.HaplotypeTreeParameters; -import com.milaboratory.migec2.preproc.demultiplex.entity.DemultiplexParameters; -import com.milaboratory.migec2.util.ParameterSet; -import com.milaboratory.migec2.util.Util; +package com.milaboratory.oncomigec.pipeline; + +import com.milaboratory.oncomigec.core.assemble.misc.AssemblerParameters; +import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerParameters; +import com.milaboratory.oncomigec.core.correct.CorrectorParameters; +import com.milaboratory.oncomigec.core.haplotype.HaplotypeTreeParameters; +import com.milaboratory.oncomigec.preproc.demultiplex.entity.DemultiplexParameters; +import com.milaboratory.oncomigec.util.ParameterSet; +import com.milaboratory.oncomigec.util.Util; import org.jdom.Document; import org.jdom.Element; import org.jdom.JDOMException; diff --git a/src/main/java/com/milaboratory/migec2/pipeline/MigecPipeline.java b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecPipeline.java similarity index 86% rename from src/main/java/com/milaboratory/migec2/pipeline/MigecPipeline.java rename to src/main/java/com/milaboratory/oncomigec/pipeline/MigecPipeline.java index 99899a3..e9e8e66 100644 --- a/src/main/java/com/milaboratory/migec2/pipeline/MigecPipeline.java +++ b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecPipeline.java @@ -1,30 +1,30 @@ -package com.milaboratory.migec2.pipeline; +package com.milaboratory.oncomigec.pipeline; import cc.redberry.pipe.OutputPort; import cc.redberry.pipe.blocks.Merger; import cc.redberry.pipe.blocks.ParallelProcessor; import cc.redberry.pipe.util.CountingOutputPort; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.assemble.entity.Consensus; -import com.milaboratory.migec2.core.assemble.misc.AssemblerFactory; -import com.milaboratory.migec2.core.assemble.processor.Assembler; -import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus; -import com.milaboratory.migec2.core.consalign.entity.AlignerReferenceLibrary; -import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerFactory; -import com.milaboratory.migec2.core.consalign.mutations.MutationsAndCoverage; -import com.milaboratory.migec2.core.consalign.processor.ConsensusAligner; -import com.milaboratory.migec2.core.correct.CorrectedConsensus; -import com.milaboratory.migec2.core.correct.Corrector; -import com.milaboratory.migec2.core.haplotype.HaplotypeTree; -import com.milaboratory.migec2.core.io.entity.Mig; -import com.milaboratory.migec2.core.io.misc.UmiHistogram; -import com.milaboratory.migec2.core.io.readers.MigReader; -import com.milaboratory.migec2.model.classifier.BaseVariantClassifier; -import com.milaboratory.migec2.model.classifier.VariantClassifier; -import com.milaboratory.migec2.model.variant.Variant; -import com.milaboratory.migec2.model.variant.VariantContainer; -import com.milaboratory.migec2.model.variant.VariantLibrary; -import com.milaboratory.migec2.util.ProcessorResultWrapper; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.assemble.entity.Consensus; +import com.milaboratory.oncomigec.core.assemble.misc.AssemblerFactory; +import com.milaboratory.oncomigec.core.assemble.processor.Assembler; +import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus; +import com.milaboratory.oncomigec.core.consalign.entity.AlignerReferenceLibrary; +import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerFactory; +import com.milaboratory.oncomigec.core.consalign.mutations.MutationsAndCoverage; +import com.milaboratory.oncomigec.core.consalign.processor.ConsensusAligner; +import com.milaboratory.oncomigec.core.correct.CorrectedConsensus; +import com.milaboratory.oncomigec.core.correct.Corrector; +import com.milaboratory.oncomigec.core.haplotype.HaplotypeTree; +import com.milaboratory.oncomigec.core.io.entity.Mig; +import com.milaboratory.oncomigec.core.io.misc.UmiHistogram; +import com.milaboratory.oncomigec.core.io.readers.MigReader; +import com.milaboratory.oncomigec.model.classifier.BaseVariantClassifier; +import com.milaboratory.oncomigec.model.classifier.VariantClassifier; +import com.milaboratory.oncomigec.model.variant.Variant; +import com.milaboratory.oncomigec.model.variant.VariantContainer; +import com.milaboratory.oncomigec.model.variant.VariantLibrary; +import com.milaboratory.oncomigec.util.ProcessorResultWrapper; import java.util.*; diff --git a/src/main/java/com/milaboratory/migec2/pipeline/TestPipeline.java b/src/main/java/com/milaboratory/oncomigec/pipeline/TestPipeline.java similarity index 70% rename from src/main/java/com/milaboratory/migec2/pipeline/TestPipeline.java rename to src/main/java/com/milaboratory/oncomigec/pipeline/TestPipeline.java index a3f83cb..255b3f9 100644 --- a/src/main/java/com/milaboratory/migec2/pipeline/TestPipeline.java +++ b/src/main/java/com/milaboratory/oncomigec/pipeline/TestPipeline.java @@ -1,12 +1,12 @@ -package com.milaboratory.migec2.pipeline; - -import com.milaboratory.migec2.core.io.misc.MigReaderParameters; -import com.milaboratory.migec2.core.io.readers.PMigReader; -import com.milaboratory.migec2.core.io.readers.SMigReader; -import com.milaboratory.migec2.preproc.demultiplex.config.BarcodeListParser; -import com.milaboratory.migec2.preproc.demultiplex.processor.CheckoutProcessor; -import com.milaboratory.migec2.preproc.demultiplex.processor.PCheckoutProcessor; -import com.milaboratory.migec2.preproc.demultiplex.processor.SCheckoutProcessor; +package com.milaboratory.oncomigec.pipeline; + +import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters; +import com.milaboratory.oncomigec.core.io.readers.PMigReader; +import com.milaboratory.oncomigec.core.io.readers.SMigReader; +import com.milaboratory.oncomigec.preproc.demultiplex.config.BarcodeListParser; +import com.milaboratory.oncomigec.preproc.demultiplex.processor.CheckoutProcessor; +import com.milaboratory.oncomigec.preproc.demultiplex.processor.PCheckoutProcessor; +import com.milaboratory.oncomigec.preproc.demultiplex.processor.SCheckoutProcessor; import org.apache.commons.io.FileUtils; import java.io.File; diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcher.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcher.java similarity index 98% rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcher.java rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcher.java index a3a706b..9e6738f 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcher.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcher.java @@ -13,11 +13,11 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.preproc.demultiplex.barcode; +package com.milaboratory.oncomigec.preproc.demultiplex.barcode; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.util.Util; import java.util.HashSet; import java.util.Set; diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcherResult.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcherResult.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcherResult.java rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcherResult.java index 1485b73..5a2667b 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcherResult.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcherResult.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.preproc.demultiplex.barcode; +package com.milaboratory.oncomigec.preproc.demultiplex.barcode; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/config/BarcodeListParser.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/config/BarcodeListParser.java similarity index 95% rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/config/BarcodeListParser.java rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/config/BarcodeListParser.java index 6a069b5..f577944 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/config/BarcodeListParser.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/config/BarcodeListParser.java @@ -13,12 +13,12 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.preproc.demultiplex.config; +package com.milaboratory.oncomigec.preproc.demultiplex.config; -import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcher; -import com.milaboratory.migec2.preproc.demultiplex.entity.DemultiplexParameters; -import com.milaboratory.migec2.preproc.demultiplex.processor.PCheckoutProcessor; -import com.milaboratory.migec2.preproc.demultiplex.processor.SCheckoutProcessor; +import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcher; +import com.milaboratory.oncomigec.preproc.demultiplex.entity.DemultiplexParameters; +import com.milaboratory.oncomigec.preproc.demultiplex.processor.PCheckoutProcessor; +import com.milaboratory.oncomigec.preproc.demultiplex.processor.SCheckoutProcessor; import java.util.ArrayList; import java.util.HashSet; diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/CheckoutResult.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/CheckoutResult.java similarity index 92% rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/CheckoutResult.java rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/CheckoutResult.java index aea547a..5624e0c 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/CheckoutResult.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/CheckoutResult.java @@ -13,10 +13,10 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.preproc.demultiplex.entity; +package com.milaboratory.oncomigec.preproc.demultiplex.entity; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult; +import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult; public class CheckoutResult { protected final int sampleId; diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/DemultiplexParameters.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/DemultiplexParameters.java similarity index 96% rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/DemultiplexParameters.java rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/DemultiplexParameters.java index 56c01f4..6297faa 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/DemultiplexParameters.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/DemultiplexParameters.java @@ -1,7 +1,7 @@ -package com.milaboratory.migec2.preproc.demultiplex.entity; +package com.milaboratory.oncomigec.preproc.demultiplex.entity; -import com.milaboratory.migec2.util.ParameterSet; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.util.ParameterSet; +import com.milaboratory.oncomigec.util.Util; import org.jdom.Element; public class DemultiplexParameters implements ParameterSet{ diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/PCheckoutResult.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/PCheckoutResult.java similarity index 92% rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/PCheckoutResult.java rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/PCheckoutResult.java index d993213..39974ff 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/PCheckoutResult.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/PCheckoutResult.java @@ -13,10 +13,10 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.preproc.demultiplex.entity; +package com.milaboratory.oncomigec.preproc.demultiplex.entity; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult; +import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult; public final class PCheckoutResult extends CheckoutResult { private final boolean masterFirst; diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/SCheckoutResult.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/SCheckoutResult.java similarity index 62% rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/SCheckoutResult.java rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/SCheckoutResult.java index 57b1f9c..4c4c71a 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/SCheckoutResult.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/SCheckoutResult.java @@ -1,6 +1,6 @@ -package com.milaboratory.migec2.preproc.demultiplex.entity; +package com.milaboratory.oncomigec.preproc.demultiplex.entity; -import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult; +import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult; public final class SCheckoutResult extends CheckoutResult { public SCheckoutResult(int sampleId, String sampleName, boolean foundInRC, BarcodeSearcherResult masterResult) { diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/SimpleCheckoutResult.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/SimpleCheckoutResult.java similarity index 72% rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/SimpleCheckoutResult.java rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/SimpleCheckoutResult.java index 315a99f..8d6e4bd 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/entity/SimpleCheckoutResult.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/entity/SimpleCheckoutResult.java @@ -1,7 +1,7 @@ -package com.milaboratory.migec2.preproc.demultiplex.entity; +package com.milaboratory.oncomigec.preproc.demultiplex.entity; import com.milaboratory.core.sequence.NucleotideSQPair; -import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult; +import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult; public final class SimpleCheckoutResult extends CheckoutResult { public SimpleCheckoutResult(String sampleName, NucleotideSQPair umiSQPair) { diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/CheckoutProcessor.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/CheckoutProcessor.java similarity index 94% rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/CheckoutProcessor.java rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/CheckoutProcessor.java index 1cad24d..76937c5 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/CheckoutProcessor.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/CheckoutProcessor.java @@ -13,11 +13,11 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.preproc.demultiplex.processor; +package com.milaboratory.oncomigec.preproc.demultiplex.processor; import com.milaboratory.core.sequencing.read.SequencingRead; -import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcher; -import com.milaboratory.migec2.preproc.demultiplex.entity.CheckoutResult; +import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcher; +import com.milaboratory.oncomigec.preproc.demultiplex.entity.CheckoutResult; import java.util.ArrayList; import java.util.Arrays; diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/HeaderParser.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/HeaderParser.java similarity index 72% rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/HeaderParser.java rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/HeaderParser.java index cd5538e..2fce8d9 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/HeaderParser.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/HeaderParser.java @@ -1,11 +1,11 @@ -package com.milaboratory.migec2.preproc.demultiplex.processor; +package com.milaboratory.oncomigec.preproc.demultiplex.processor; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequencing.read.SequencingRead; -import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcher; -import com.milaboratory.migec2.preproc.demultiplex.entity.CheckoutResult; -import com.milaboratory.migec2.preproc.demultiplex.entity.SimpleCheckoutResult; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcher; +import com.milaboratory.oncomigec.preproc.demultiplex.entity.CheckoutResult; +import com.milaboratory.oncomigec.preproc.demultiplex.entity.SimpleCheckoutResult; +import com.milaboratory.oncomigec.util.Util; public final class HeaderParser extends CheckoutProcessor { private final String sampleName; diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/PCheckoutProcessor.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/PCheckoutProcessor.java similarity index 95% rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/PCheckoutProcessor.java rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/PCheckoutProcessor.java index 2e225cf..2168437 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/PCheckoutProcessor.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/PCheckoutProcessor.java @@ -13,13 +13,13 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.preproc.demultiplex.processor; +package com.milaboratory.oncomigec.preproc.demultiplex.processor; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequencing.read.PSequencingRead; -import com.milaboratory.migec2.preproc.demultiplex.entity.PCheckoutResult; -import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcher; -import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult; +import com.milaboratory.oncomigec.preproc.demultiplex.entity.PCheckoutResult; +import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcher; +import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult; import java.util.List; import java.util.concurrent.atomic.AtomicLong; diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/ReadPositionUmiExtractor.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/ReadPositionUmiExtractor.java similarity index 81% rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/ReadPositionUmiExtractor.java rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/ReadPositionUmiExtractor.java index fb07223..705699f 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/ReadPositionUmiExtractor.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/ReadPositionUmiExtractor.java @@ -14,14 +14,14 @@ * limitations under the License. */ -package com.milaboratory.migec2.preproc.demultiplex.processor; +package com.milaboratory.oncomigec.preproc.demultiplex.processor; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequencing.read.SequencingRead; -import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcher; -import com.milaboratory.migec2.preproc.demultiplex.entity.CheckoutResult; -import com.milaboratory.migec2.preproc.demultiplex.entity.SimpleCheckoutResult; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcher; +import com.milaboratory.oncomigec.preproc.demultiplex.entity.CheckoutResult; +import com.milaboratory.oncomigec.preproc.demultiplex.entity.SimpleCheckoutResult; +import com.milaboratory.oncomigec.util.Util; public class ReadPositionUmiExtractor extends CheckoutProcessor { private final String sampleName; diff --git a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/SCheckoutProcessor.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/SCheckoutProcessor.java similarity index 85% rename from src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/SCheckoutProcessor.java rename to src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/SCheckoutProcessor.java index 7569c06..df8a0de 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/demultiplex/processor/SCheckoutProcessor.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/SCheckoutProcessor.java @@ -13,14 +13,12 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.preproc.demultiplex.processor; +package com.milaboratory.oncomigec.preproc.demultiplex.processor; import com.milaboratory.core.sequencing.read.SSequencingRead; -import com.milaboratory.migec2.preproc.demultiplex.entity.SCheckoutResult; -import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcher; -import com.milaboratory.migec2.preproc.demultiplex.barcode.BarcodeSearcherResult; - -import java.util.Arrays; +import com.milaboratory.oncomigec.preproc.demultiplex.entity.SCheckoutResult; +import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcher; +import com.milaboratory.oncomigec.preproc.demultiplex.barcode.BarcodeSearcherResult; public final class SCheckoutProcessor extends CheckoutProcessor { public SCheckoutProcessor(String[] sampleNames, BarcodeSearcher[] masterBarcodes) { diff --git a/src/main/java/com/milaboratory/migec2/preproc/misc/ReadOverlapper.java b/src/main/java/com/milaboratory/oncomigec/preproc/misc/ReadOverlapper.java similarity index 99% rename from src/main/java/com/milaboratory/migec2/preproc/misc/ReadOverlapper.java rename to src/main/java/com/milaboratory/oncomigec/preproc/misc/ReadOverlapper.java index 97b0a89..ec74028 100644 --- a/src/main/java/com/milaboratory/migec2/preproc/misc/ReadOverlapper.java +++ b/src/main/java/com/milaboratory/oncomigec/preproc/misc/ReadOverlapper.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.preproc.misc; +package com.milaboratory.oncomigec.preproc.misc; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequencing.read.PSequencingRead; diff --git a/src/main/java/com/milaboratory/migec2/util/Basics.java b/src/main/java/com/milaboratory/oncomigec/util/Basics.java similarity index 99% rename from src/main/java/com/milaboratory/migec2/util/Basics.java rename to src/main/java/com/milaboratory/oncomigec/util/Basics.java index 112c9eb..029d29f 100644 --- a/src/main/java/com/milaboratory/migec2/util/Basics.java +++ b/src/main/java/com/milaboratory/oncomigec/util/Basics.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.util; +package com.milaboratory.oncomigec.util; import org.jdom.Document; import org.jdom.Element; diff --git a/src/main/java/com/milaboratory/migec2/util/ParameterSet.java b/src/main/java/com/milaboratory/oncomigec/util/ParameterSet.java similarity index 68% rename from src/main/java/com/milaboratory/migec2/util/ParameterSet.java rename to src/main/java/com/milaboratory/oncomigec/util/ParameterSet.java index 6f1570a..25f7942 100644 --- a/src/main/java/com/milaboratory/migec2/util/ParameterSet.java +++ b/src/main/java/com/milaboratory/oncomigec/util/ParameterSet.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.util; +package com.milaboratory.oncomigec.util; import org.jdom.Element; diff --git a/src/main/java/com/milaboratory/migec2/util/ProcessorResultWrapper.java b/src/main/java/com/milaboratory/oncomigec/util/ProcessorResultWrapper.java similarity index 92% rename from src/main/java/com/milaboratory/migec2/util/ProcessorResultWrapper.java rename to src/main/java/com/milaboratory/oncomigec/util/ProcessorResultWrapper.java index b61722e..96e466f 100644 --- a/src/main/java/com/milaboratory/migec2/util/ProcessorResultWrapper.java +++ b/src/main/java/com/milaboratory/oncomigec/util/ProcessorResultWrapper.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.util; +package com.milaboratory.oncomigec.util; public class ProcessorResultWrapper { private final T result; diff --git a/src/main/java/com/milaboratory/migec2/util/QualityHistogram.java b/src/main/java/com/milaboratory/oncomigec/util/QualityHistogram.java similarity index 97% rename from src/main/java/com/milaboratory/migec2/util/QualityHistogram.java rename to src/main/java/com/milaboratory/oncomigec/util/QualityHistogram.java index 569fee3..9e593b3 100644 --- a/src/main/java/com/milaboratory/migec2/util/QualityHistogram.java +++ b/src/main/java/com/milaboratory/oncomigec/util/QualityHistogram.java @@ -14,7 +14,7 @@ * limitations under the License. */ -package com.milaboratory.migec2.util; +package com.milaboratory.oncomigec.util; import com.milaboratory.core.sequence.quality.SequenceQualityPhred; diff --git a/src/main/java/com/milaboratory/migec2/util/Util.java b/src/main/java/com/milaboratory/oncomigec/util/Util.java similarity index 99% rename from src/main/java/com/milaboratory/migec2/util/Util.java rename to src/main/java/com/milaboratory/oncomigec/util/Util.java index c164c5f..cbf9924 100644 --- a/src/main/java/com/milaboratory/migec2/util/Util.java +++ b/src/main/java/com/milaboratory/oncomigec/util/Util.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.util; +package com.milaboratory.oncomigec.util; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequence.SequenceBuilder; diff --git a/src/test/java/com/milaboratory/migec2/core/align/kmer/KMerFinderTest.java b/src/test/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinderTest.java similarity index 87% rename from src/test/java/com/milaboratory/migec2/core/align/kmer/KMerFinderTest.java rename to src/test/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinderTest.java index 40aacf0..193fe88 100644 --- a/src/test/java/com/milaboratory/migec2/core/align/kmer/KMerFinderTest.java +++ b/src/test/java/com/milaboratory/oncomigec/core/align/kmer/KMerFinderTest.java @@ -1,11 +1,10 @@ -package com.milaboratory.migec2.core.align.kmer; +package com.milaboratory.oncomigec.core.align.kmer; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; -import com.milaboratory.migec2.util.testing.IntRange; -import com.milaboratory.migec2.util.testing.PercentRange; -import com.milaboratory.migec2.util.testing.generators.GeneratorMutationModel; -import com.milaboratory.migec2.util.testing.generators.RandomReferenceGenerator; -import org.junit.Test; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.util.testing.IntRange; +import com.milaboratory.oncomigec.util.testing.PercentRange; +import com.milaboratory.oncomigec.util.testing.generators.GeneratorMutationModel; +import com.milaboratory.oncomigec.util.testing.generators.RandomReferenceGenerator; import java.util.Arrays; diff --git a/src/test/java/com/milaboratory/migec2/core/align/processor/aligners/AlignersTest.java b/src/test/java/com/milaboratory/oncomigec/core/align/processor/aligners/AlignersTest.java similarity index 91% rename from src/test/java/com/milaboratory/migec2/core/align/processor/aligners/AlignersTest.java rename to src/test/java/com/milaboratory/oncomigec/core/align/processor/aligners/AlignersTest.java index 8a09258..8e1cdd0 100644 --- a/src/test/java/com/milaboratory/migec2/core/align/processor/aligners/AlignersTest.java +++ b/src/test/java/com/milaboratory/oncomigec/core/align/processor/aligners/AlignersTest.java @@ -13,16 +13,16 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.align.processor.aligners; +package com.milaboratory.oncomigec.core.align.processor.aligners; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.core.align.entity.SAlignmentResult; -import com.milaboratory.migec2.core.align.processor.Aligner; -import com.milaboratory.migec2.core.align.processor.AlignerFactory; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; -import com.milaboratory.migec2.util.testing.PercentRange; -import com.milaboratory.migec2.util.testing.generators.RandomIndelGenerator; -import com.milaboratory.migec2.util.testing.generators.RandomReferenceGenerator; +import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult; +import com.milaboratory.oncomigec.core.align.processor.Aligner; +import com.milaboratory.oncomigec.core.align.processor.AlignerFactory; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.util.testing.PercentRange; +import com.milaboratory.oncomigec.util.testing.generators.RandomIndelGenerator; +import com.milaboratory.oncomigec.util.testing.generators.RandomReferenceGenerator; import org.junit.Test; import java.io.IOException; diff --git a/src/test/java/com/milaboratory/migec2/core/assemble/processor/AssemblerTest.java b/src/test/java/com/milaboratory/oncomigec/core/assemble/processor/AssemblerTest.java similarity index 92% rename from src/test/java/com/milaboratory/migec2/core/assemble/processor/AssemblerTest.java rename to src/test/java/com/milaboratory/oncomigec/core/assemble/processor/AssemblerTest.java index 75adbb8..4e38380 100644 --- a/src/test/java/com/milaboratory/migec2/core/assemble/processor/AssemblerTest.java +++ b/src/test/java/com/milaboratory/oncomigec/core/assemble/processor/AssemblerTest.java @@ -13,24 +13,24 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.assemble.processor; +package com.milaboratory.oncomigec.core.assemble.processor; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; import com.milaboratory.core.sequencing.read.SSequencingRead; -import com.milaboratory.migec2.core.assemble.entity.Consensus; -import com.milaboratory.migec2.core.assemble.entity.SConsensus; -import com.milaboratory.migec2.core.io.entity.Mig; -import com.milaboratory.migec2.core.io.entity.SMig; -import com.milaboratory.migec2.util.Basics; -import com.milaboratory.migec2.util.testing.generators.RandomMigGenerator; -import com.milaboratory.migec2.util.testing.generators.RandomReferenceGenerator; +import com.milaboratory.oncomigec.core.assemble.entity.Consensus; +import com.milaboratory.oncomigec.core.assemble.entity.SConsensus; +import com.milaboratory.oncomigec.core.io.entity.Mig; +import com.milaboratory.oncomigec.core.io.entity.SMig; +import com.milaboratory.oncomigec.util.Basics; +import com.milaboratory.oncomigec.util.testing.generators.RandomMigGenerator; +import com.milaboratory.oncomigec.util.testing.generators.RandomReferenceGenerator; import org.junit.Assert; import org.junit.Test; import java.util.ArrayList; import java.util.List; -import static com.milaboratory.migec2.util.Util.*; +import static com.milaboratory.oncomigec.util.Util.*; public class AssemblerTest { private static final int nRepetitions = 1000, randomTestAssertThreshold = 70, randomTestAssertIDHThreshold = 60; diff --git a/src/test/java/com/milaboratory/migec2/core/consalign/mutations/MutationsExtractorTest.java b/src/test/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsExtractorTest.java similarity index 95% rename from src/test/java/com/milaboratory/migec2/core/consalign/mutations/MutationsExtractorTest.java rename to src/test/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsExtractorTest.java index 6ba6deb..c61f150 100644 --- a/src/test/java/com/milaboratory/migec2/core/consalign/mutations/MutationsExtractorTest.java +++ b/src/test/java/com/milaboratory/oncomigec/core/consalign/mutations/MutationsExtractorTest.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.core.consalign.mutations; +package com.milaboratory.oncomigec.core.consalign.mutations; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequence.alignment.KAligner; @@ -8,17 +8,17 @@ import com.milaboratory.core.sequence.mutations.MutationType; import com.milaboratory.core.sequence.mutations.Mutations; import com.milaboratory.core.sequence.nucleotide.NucleotideAlphabet; -import com.milaboratory.migec2.core.align.entity.SAlignmentResult; -import com.milaboratory.migec2.core.align.processor.aligners.ExtendedExomeAligner; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; -import com.milaboratory.migec2.core.assemble.entity.SConsensus; -import com.milaboratory.migec2.core.assemble.processor.SAssembler; -import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters; -import com.milaboratory.migec2.core.io.entity.SMig; -import com.milaboratory.migec2.util.Basics; -import com.milaboratory.migec2.util.testing.generators.GeneratorMutationModel; -import com.milaboratory.migec2.util.testing.generators.RandomMigGenerator; -import com.milaboratory.migec2.util.testing.generators.RandomReferenceGenerator; +import com.milaboratory.oncomigec.core.align.entity.SAlignmentResult; +import com.milaboratory.oncomigec.core.align.processor.aligners.ExtendedExomeAligner; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.assemble.entity.SConsensus; +import com.milaboratory.oncomigec.core.assemble.processor.SAssembler; +import com.milaboratory.oncomigec.core.consalign.misc.ConsensusAlignerParameters; +import com.milaboratory.oncomigec.core.io.entity.SMig; +import com.milaboratory.oncomigec.util.Basics; +import com.milaboratory.oncomigec.util.testing.generators.GeneratorMutationModel; +import com.milaboratory.oncomigec.util.testing.generators.RandomMigGenerator; +import com.milaboratory.oncomigec.util.testing.generators.RandomReferenceGenerator; import org.junit.Assert; import org.junit.Test; diff --git a/src/test/java/com/milaboratory/migec2/core/consalign/processor/ConsensusAlignerTest.java b/src/test/java/com/milaboratory/oncomigec/core/consalign/processor/ConsensusAlignerTest.java similarity index 85% rename from src/test/java/com/milaboratory/migec2/core/consalign/processor/ConsensusAlignerTest.java rename to src/test/java/com/milaboratory/oncomigec/core/consalign/processor/ConsensusAlignerTest.java index 8f01621..239ccc9 100644 --- a/src/test/java/com/milaboratory/migec2/core/consalign/processor/ConsensusAlignerTest.java +++ b/src/test/java/com/milaboratory/oncomigec/core/consalign/processor/ConsensusAlignerTest.java @@ -13,24 +13,24 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.consalign.processor; - -import com.milaboratory.migec2.core.align.processor.aligners.ExtendedExomeAligner; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; -import com.milaboratory.migec2.core.assemble.entity.Consensus; -import com.milaboratory.migec2.core.assemble.misc.AssemblerParameters; -import com.milaboratory.migec2.core.assemble.processor.Assembler; -import com.milaboratory.migec2.core.assemble.processor.SAssembler; -import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus; -import com.milaboratory.migec2.core.consalign.mutations.MutationsAndCoverage; -import com.milaboratory.migec2.core.io.entity.SMig; -import com.milaboratory.migec2.util.Basics; -import com.milaboratory.migec2.util.testing.DoubleRange; -import com.milaboratory.migec2.util.testing.PercentRange; -import com.milaboratory.migec2.util.testing.generators.GeneratorMutationModel; -import com.milaboratory.migec2.util.testing.generators.RandomMigGenerator; -import com.milaboratory.migec2.util.testing.generators.RandomReferenceGenerator; +package com.milaboratory.oncomigec.core.consalign.processor; + +import com.milaboratory.oncomigec.core.align.processor.aligners.ExtendedExomeAligner; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.assemble.entity.Consensus; +import com.milaboratory.oncomigec.core.assemble.misc.AssemblerParameters; +import com.milaboratory.oncomigec.core.assemble.processor.Assembler; +import com.milaboratory.oncomigec.core.assemble.processor.SAssembler; +import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus; +import com.milaboratory.oncomigec.core.consalign.mutations.MutationsAndCoverage; +import com.milaboratory.oncomigec.core.io.entity.SMig; +import com.milaboratory.oncomigec.util.Basics; +import com.milaboratory.oncomigec.util.testing.DoubleRange; +import com.milaboratory.oncomigec.util.testing.PercentRange; +import com.milaboratory.oncomigec.util.testing.generators.GeneratorMutationModel; +import com.milaboratory.oncomigec.util.testing.generators.RandomMigGenerator; +import com.milaboratory.oncomigec.util.testing.generators.RandomReferenceGenerator; import org.junit.Test; import java.util.Arrays; diff --git a/src/test/java/com/milaboratory/migec2/core/correct/CorrectorTest.java b/src/test/java/com/milaboratory/oncomigec/core/correct/CorrectorTest.java similarity index 82% rename from src/test/java/com/milaboratory/migec2/core/correct/CorrectorTest.java rename to src/test/java/com/milaboratory/oncomigec/core/correct/CorrectorTest.java index b8503f7..e2a17f9 100644 --- a/src/test/java/com/milaboratory/migec2/core/correct/CorrectorTest.java +++ b/src/test/java/com/milaboratory/oncomigec/core/correct/CorrectorTest.java @@ -13,21 +13,20 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.correct; +package com.milaboratory.oncomigec.core.correct; -import com.milaboratory.migec2.core.align.processor.aligners.ExtendedExomeAligner; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; -import com.milaboratory.migec2.core.assemble.entity.SConsensus; -import com.milaboratory.migec2.core.assemble.processor.SAssembler; -import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus; -import com.milaboratory.migec2.core.consalign.misc.ConsensusAlignerParameters; -import com.milaboratory.migec2.core.consalign.processor.ConsensusAligner; -import com.milaboratory.migec2.core.consalign.processor.SConsensusAligner; -import com.milaboratory.migec2.core.io.entity.SMig; -import com.milaboratory.migec2.util.testing.generators.GeneratorMutationModel; -import com.milaboratory.migec2.util.testing.generators.RandomMigGenerator; -import com.milaboratory.migec2.util.testing.generators.RandomReferenceGenerator; +import com.milaboratory.oncomigec.core.align.processor.aligners.ExtendedExomeAligner; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.assemble.entity.SConsensus; +import com.milaboratory.oncomigec.core.assemble.processor.SAssembler; +import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus; +import com.milaboratory.oncomigec.core.consalign.processor.ConsensusAligner; +import com.milaboratory.oncomigec.core.consalign.processor.SConsensusAligner; +import com.milaboratory.oncomigec.core.io.entity.SMig; +import com.milaboratory.oncomigec.util.testing.generators.GeneratorMutationModel; +import com.milaboratory.oncomigec.util.testing.generators.RandomMigGenerator; +import com.milaboratory.oncomigec.util.testing.generators.RandomReferenceGenerator; import org.junit.Assert; import org.junit.Test; diff --git a/src/test/java/com/milaboratory/migec2/core/haplotype/HaplotypeTreeDataTest.java b/src/test/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTreeDataTest.java similarity index 85% rename from src/test/java/com/milaboratory/migec2/core/haplotype/HaplotypeTreeDataTest.java rename to src/test/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTreeDataTest.java index 51c6968..a68bf77 100644 --- a/src/test/java/com/milaboratory/migec2/core/haplotype/HaplotypeTreeDataTest.java +++ b/src/test/java/com/milaboratory/oncomigec/core/haplotype/HaplotypeTreeDataTest.java @@ -13,22 +13,22 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.haplotype; +package com.milaboratory.oncomigec.core.haplotype; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.core.align.processor.aligners.ExtendedExomeAligner; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; -import com.milaboratory.migec2.core.assemble.entity.Consensus; -import com.milaboratory.migec2.core.assemble.processor.Assembler; -import com.milaboratory.migec2.core.assemble.processor.PAssembler; -import com.milaboratory.migec2.core.consalign.entity.AlignedConsensus; -import com.milaboratory.migec2.core.consalign.processor.ConsensusAligner; -import com.milaboratory.migec2.core.consalign.processor.PConsensusAligner; -import com.milaboratory.migec2.core.correct.CorrectedConsensus; -import com.milaboratory.migec2.core.correct.Corrector; -import com.milaboratory.migec2.core.io.entity.PMig; -import com.milaboratory.migec2.core.io.readers.PMigReader; -import com.milaboratory.migec2.util.testing.TestResources; +import com.milaboratory.oncomigec.core.align.processor.aligners.ExtendedExomeAligner; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.assemble.entity.Consensus; +import com.milaboratory.oncomigec.core.assemble.processor.Assembler; +import com.milaboratory.oncomigec.core.assemble.processor.PAssembler; +import com.milaboratory.oncomigec.core.consalign.entity.AlignedConsensus; +import com.milaboratory.oncomigec.core.consalign.processor.ConsensusAligner; +import com.milaboratory.oncomigec.core.consalign.processor.PConsensusAligner; +import com.milaboratory.oncomigec.core.correct.CorrectedConsensus; +import com.milaboratory.oncomigec.core.correct.Corrector; +import com.milaboratory.oncomigec.core.io.entity.PMig; +import com.milaboratory.oncomigec.core.io.readers.PMigReader; +import com.milaboratory.oncomigec.util.testing.TestResources; import org.junit.Assert; import java.util.ArrayList; diff --git a/src/test/java/com/milaboratory/migec2/core/io/misc/UmiHistogramTest.java b/src/test/java/com/milaboratory/oncomigec/core/io/misc/UmiHistogramTest.java similarity index 94% rename from src/test/java/com/milaboratory/migec2/core/io/misc/UmiHistogramTest.java rename to src/test/java/com/milaboratory/oncomigec/core/io/misc/UmiHistogramTest.java index ca131ed..95e98af 100644 --- a/src/test/java/com/milaboratory/migec2/core/io/misc/UmiHistogramTest.java +++ b/src/test/java/com/milaboratory/oncomigec/core/io/misc/UmiHistogramTest.java @@ -1,7 +1,7 @@ -package com.milaboratory.migec2.core.io.misc; +package com.milaboratory.oncomigec.core.io.misc; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.util.Util; import org.apache.commons.math.random.MersenneTwister; import org.apache.commons.math.random.RandomGenerator; import org.junit.Assert; diff --git a/src/test/java/com/milaboratory/migec2/core/io/readers/PMigReaderTest.java b/src/test/java/com/milaboratory/oncomigec/core/io/readers/PMigReaderTest.java similarity index 91% rename from src/test/java/com/milaboratory/migec2/core/io/readers/PMigReaderTest.java rename to src/test/java/com/milaboratory/oncomigec/core/io/readers/PMigReaderTest.java index 6f4502d..bc6e2ed 100644 --- a/src/test/java/com/milaboratory/migec2/core/io/readers/PMigReaderTest.java +++ b/src/test/java/com/milaboratory/oncomigec/core/io/readers/PMigReaderTest.java @@ -13,19 +13,18 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.io.readers; +package com.milaboratory.oncomigec.core.io.readers; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; import com.milaboratory.core.sequencing.io.fastq.SFastqReader; import com.milaboratory.core.sequencing.read.SSequencingRead; -import com.milaboratory.migec2.core.io.entity.PMig; -import com.milaboratory.migec2.core.io.misc.MigReaderParameters; -import com.milaboratory.migec2.core.io.misc.UmiHistogram; -import com.milaboratory.migec2.preproc.demultiplex.config.BarcodeListParser; -import com.milaboratory.migec2.util.testing.TestResources; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.core.io.entity.PMig; +import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters; +import com.milaboratory.oncomigec.core.io.misc.UmiHistogram; +import com.milaboratory.oncomigec.preproc.demultiplex.config.BarcodeListParser; +import com.milaboratory.oncomigec.util.testing.TestResources; +import com.milaboratory.oncomigec.util.Util; import org.junit.Assert; -import org.junit.Test; import java.io.File; import java.util.ArrayList; diff --git a/src/test/java/com/milaboratory/migec2/core/io/readers/SMigReaderTest.java b/src/test/java/com/milaboratory/oncomigec/core/io/readers/SMigReaderTest.java similarity index 86% rename from src/test/java/com/milaboratory/migec2/core/io/readers/SMigReaderTest.java rename to src/test/java/com/milaboratory/oncomigec/core/io/readers/SMigReaderTest.java index cfb2617..811680f 100644 --- a/src/test/java/com/milaboratory/migec2/core/io/readers/SMigReaderTest.java +++ b/src/test/java/com/milaboratory/oncomigec/core/io/readers/SMigReaderTest.java @@ -13,16 +13,15 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.core.io.readers; +package com.milaboratory.oncomigec.core.io.readers; import com.milaboratory.core.sequencing.io.fastq.SFastqReader; import com.milaboratory.core.sequencing.read.SSequencingRead; -import com.milaboratory.migec2.core.io.entity.SMig; -import com.milaboratory.migec2.core.io.misc.MigReaderParameters; +import com.milaboratory.oncomigec.core.io.entity.SMig; +import com.milaboratory.oncomigec.core.io.misc.MigReaderParameters; import org.junit.Assert; -import org.junit.Test; -import com.milaboratory.migec2.util.testing.TestResources; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.util.testing.TestResources; +import com.milaboratory.oncomigec.util.Util; import java.io.File; diff --git a/src/test/java/com/milaboratory/migec2/model/classifier/ClassifierTest.java b/src/test/java/com/milaboratory/oncomigec/model/classifier/ClassifierTest.java similarity index 94% rename from src/test/java/com/milaboratory/migec2/model/classifier/ClassifierTest.java rename to src/test/java/com/milaboratory/oncomigec/model/classifier/ClassifierTest.java index 0d7eb1e..4092d68 100644 --- a/src/test/java/com/milaboratory/migec2/model/classifier/ClassifierTest.java +++ b/src/test/java/com/milaboratory/oncomigec/model/classifier/ClassifierTest.java @@ -16,7 +16,7 @@ * Last modified on 27.11.2014 by mikesh */ -package com.milaboratory.migec2.model.classifier; +package com.milaboratory.oncomigec.model.classifier; import org.junit.Assert; import org.junit.Test; diff --git a/src/test/java/com/milaboratory/migec2/pipeline/MigecParameterSetTest.java b/src/test/java/com/milaboratory/oncomigec/pipeline/MigecParameterSetTest.java similarity index 91% rename from src/test/java/com/milaboratory/migec2/pipeline/MigecParameterSetTest.java rename to src/test/java/com/milaboratory/oncomigec/pipeline/MigecParameterSetTest.java index 1677ee3..06f1ce0 100644 --- a/src/test/java/com/milaboratory/migec2/pipeline/MigecParameterSetTest.java +++ b/src/test/java/com/milaboratory/oncomigec/pipeline/MigecParameterSetTest.java @@ -1,6 +1,6 @@ -package com.milaboratory.migec2.pipeline; +package com.milaboratory.oncomigec.pipeline; -import com.milaboratory.migec2.util.Basics; +import com.milaboratory.oncomigec.util.Basics; import org.jdom.Element; import org.jdom.JDOMException; import org.junit.Assert; @@ -8,7 +8,6 @@ import java.io.ByteArrayInputStream; import java.io.ByteArrayOutputStream; -import java.io.File; import java.io.IOException; public class MigecParameterSetTest { diff --git a/src/test/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcherTest.java b/src/test/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcherTest.java similarity index 98% rename from src/test/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcherTest.java rename to src/test/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcherTest.java index 9cf4134..417f687 100644 --- a/src/test/java/com/milaboratory/migec2/preproc/demultiplex/barcode/BarcodeSearcherTest.java +++ b/src/test/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcherTest.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.preproc.demultiplex.barcode; +package com.milaboratory.oncomigec.preproc.demultiplex.barcode; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequence.mutations.GenericNucleotideMutationModel; @@ -24,8 +24,8 @@ import com.milaboratory.core.sequence.quality.SequenceQualityPhred; import com.milaboratory.core.sequencing.io.fastq.SFastqReader; import com.milaboratory.core.sequencing.read.SSequencingRead; -import com.milaboratory.migec2.util.testing.TestResources; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.util.testing.TestResources; +import com.milaboratory.oncomigec.util.Util; import org.junit.Assert; import org.junit.Test; diff --git a/src/test/java/com/milaboratory/migec2/preproc/demultiplex/processor/CheckoutProcessorTest.java b/src/test/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/CheckoutProcessorTest.java similarity index 87% rename from src/test/java/com/milaboratory/migec2/preproc/demultiplex/processor/CheckoutProcessorTest.java rename to src/test/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/CheckoutProcessorTest.java index 7b02df8..82b4599 100644 --- a/src/test/java/com/milaboratory/migec2/preproc/demultiplex/processor/CheckoutProcessorTest.java +++ b/src/test/java/com/milaboratory/oncomigec/preproc/demultiplex/processor/CheckoutProcessorTest.java @@ -13,19 +13,18 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.preproc.demultiplex.processor; +package com.milaboratory.oncomigec.preproc.demultiplex.processor; import com.milaboratory.core.sequence.quality.QualityFormat; import com.milaboratory.core.sequencing.io.fastq.PFastqReader; import com.milaboratory.core.sequencing.read.PSequencingRead; -import com.milaboratory.migec2.preproc.demultiplex.config.BarcodeListParser; -import com.milaboratory.migec2.preproc.demultiplex.entity.DemultiplexParameters; -import com.milaboratory.migec2.util.testing.TestResources; +import com.milaboratory.oncomigec.preproc.demultiplex.config.BarcodeListParser; +import com.milaboratory.oncomigec.preproc.demultiplex.entity.DemultiplexParameters; +import com.milaboratory.oncomigec.util.testing.TestResources; import com.milaboratory.util.CompressionType; import org.apache.commons.io.FileUtils; import org.junit.Assert; import org.junit.Rule; -import org.junit.Test; import org.junit.rules.ExpectedException; import java.util.List; diff --git a/src/test/java/com/milaboratory/migec2/preproc/misc/OverlapTest.java b/src/test/java/com/milaboratory/oncomigec/preproc/misc/OverlapTest.java similarity index 98% rename from src/test/java/com/milaboratory/migec2/preproc/misc/OverlapTest.java rename to src/test/java/com/milaboratory/oncomigec/preproc/misc/OverlapTest.java index 6dc0062..6ed7d85 100644 --- a/src/test/java/com/milaboratory/migec2/preproc/misc/OverlapTest.java +++ b/src/test/java/com/milaboratory/oncomigec/preproc/misc/OverlapTest.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.preproc.misc; +package com.milaboratory.oncomigec.preproc.misc; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequence.mutations.MutationModels; @@ -31,7 +31,7 @@ import java.util.Arrays; -import static com.milaboratory.migec2.util.Util.randomSequence; +import static com.milaboratory.oncomigec.util.Util.randomSequence; public class OverlapTest { diff --git a/src/test/java/com/milaboratory/migec2/util/testing/DoubleRange.java b/src/test/java/com/milaboratory/oncomigec/util/testing/DoubleRange.java similarity index 97% rename from src/test/java/com/milaboratory/migec2/util/testing/DoubleRange.java rename to src/test/java/com/milaboratory/oncomigec/util/testing/DoubleRange.java index 31800c1..45c5998 100644 --- a/src/test/java/com/milaboratory/migec2/util/testing/DoubleRange.java +++ b/src/test/java/com/milaboratory/oncomigec/util/testing/DoubleRange.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.util.testing; +package com.milaboratory.oncomigec.util.testing; import org.junit.Assert; diff --git a/src/test/java/com/milaboratory/migec2/util/testing/IntRange.java b/src/test/java/com/milaboratory/oncomigec/util/testing/IntRange.java similarity index 97% rename from src/test/java/com/milaboratory/migec2/util/testing/IntRange.java rename to src/test/java/com/milaboratory/oncomigec/util/testing/IntRange.java index 40f1857..9619cb2 100644 --- a/src/test/java/com/milaboratory/migec2/util/testing/IntRange.java +++ b/src/test/java/com/milaboratory/oncomigec/util/testing/IntRange.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.util.testing; +package com.milaboratory.oncomigec.util.testing; import org.junit.Assert; diff --git a/src/test/java/com/milaboratory/migec2/util/testing/PercentRange.java b/src/test/java/com/milaboratory/oncomigec/util/testing/PercentRange.java similarity index 95% rename from src/test/java/com/milaboratory/migec2/util/testing/PercentRange.java rename to src/test/java/com/milaboratory/oncomigec/util/testing/PercentRange.java index abf87ca..caa0f65 100644 --- a/src/test/java/com/milaboratory/migec2/util/testing/PercentRange.java +++ b/src/test/java/com/milaboratory/oncomigec/util/testing/PercentRange.java @@ -1,6 +1,6 @@ -package com.milaboratory.migec2.util.testing; +package com.milaboratory.oncomigec.util.testing; -import com.milaboratory.migec2.util.Basics; +import com.milaboratory.oncomigec.util.Basics; import org.junit.Assert; public class PercentRange { diff --git a/src/test/java/com/milaboratory/migec2/util/testing/TestResources.java b/src/test/java/com/milaboratory/oncomigec/util/testing/TestResources.java similarity index 95% rename from src/test/java/com/milaboratory/migec2/util/testing/TestResources.java rename to src/test/java/com/milaboratory/oncomigec/util/testing/TestResources.java index 5e590cc..6cd1d60 100644 --- a/src/test/java/com/milaboratory/migec2/util/testing/TestResources.java +++ b/src/test/java/com/milaboratory/oncomigec/util/testing/TestResources.java @@ -13,7 +13,7 @@ * See the License for the specific language governing permissions and * limitations under the License. */ -package com.milaboratory.migec2.util.testing; +package com.milaboratory.oncomigec.util.testing; import org.junit.Assume; diff --git a/src/test/java/com/milaboratory/migec2/util/testing/generators/GeneratorMutationModel.java b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/GeneratorMutationModel.java similarity index 95% rename from src/test/java/com/milaboratory/migec2/util/testing/generators/GeneratorMutationModel.java rename to src/test/java/com/milaboratory/oncomigec/util/testing/generators/GeneratorMutationModel.java index 8e10579..88d4039 100644 --- a/src/test/java/com/milaboratory/migec2/util/testing/generators/GeneratorMutationModel.java +++ b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/GeneratorMutationModel.java @@ -1,11 +1,11 @@ -package com.milaboratory.migec2.util.testing.generators; +package com.milaboratory.oncomigec.util.testing.generators; import com.milaboratory.core.sequence.mutations.GenericNucleotideMutationModel; import com.milaboratory.core.sequence.mutations.Mutations; import com.milaboratory.core.sequence.mutations.NucleotideMutationModel; import com.milaboratory.core.sequence.mutations.SubstitutionModels; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.Reference; import java.util.Random; diff --git a/src/test/java/com/milaboratory/migec2/util/testing/generators/RandomIndelGenerator.java b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomIndelGenerator.java similarity index 92% rename from src/test/java/com/milaboratory/migec2/util/testing/generators/RandomIndelGenerator.java rename to src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomIndelGenerator.java index 68527f9..3950697 100644 --- a/src/test/java/com/milaboratory/migec2/util/testing/generators/RandomIndelGenerator.java +++ b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomIndelGenerator.java @@ -1,7 +1,7 @@ -package com.milaboratory.migec2.util.testing.generators; +package com.milaboratory.oncomigec.util.testing.generators; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; -import com.milaboratory.migec2.util.Util; +import com.milaboratory.oncomigec.util.Util; public class RandomIndelGenerator { private final int minIndelSize, maxIndelSize; diff --git a/src/test/java/com/milaboratory/migec2/util/testing/generators/RandomMigGenerator.java b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomMigGenerator.java similarity index 95% rename from src/test/java/com/milaboratory/migec2/util/testing/generators/RandomMigGenerator.java rename to src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomMigGenerator.java index 81b64cb..c201312 100644 --- a/src/test/java/com/milaboratory/migec2/util/testing/generators/RandomMigGenerator.java +++ b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomMigGenerator.java @@ -1,4 +1,4 @@ -package com.milaboratory.migec2.util.testing.generators; +package com.milaboratory.oncomigec.util.testing.generators; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequence.mutations.Mutations; @@ -6,12 +6,12 @@ import com.milaboratory.core.sequence.quality.SequenceQualityPhred; import com.milaboratory.core.sequencing.read.SSequencingRead; import com.milaboratory.core.sequencing.read.SSequencingReadImpl; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.io.entity.SMig; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.io.entity.SMig; import java.util.*; -import static com.milaboratory.migec2.util.Util.randomSequence; +import static com.milaboratory.oncomigec.util.Util.randomSequence; public class RandomMigGenerator { private int migSizeMin, migSizeMax; diff --git a/src/test/java/com/milaboratory/migec2/util/testing/generators/RandomReferenceGenerator.java b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomReferenceGenerator.java similarity index 95% rename from src/test/java/com/milaboratory/migec2/util/testing/generators/RandomReferenceGenerator.java rename to src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomReferenceGenerator.java index 806dc2d..b1b92ba 100644 --- a/src/test/java/com/milaboratory/migec2/util/testing/generators/RandomReferenceGenerator.java +++ b/src/test/java/com/milaboratory/oncomigec/util/testing/generators/RandomReferenceGenerator.java @@ -1,12 +1,12 @@ -package com.milaboratory.migec2.util.testing.generators; +package com.milaboratory.oncomigec.util.testing.generators; import com.milaboratory.core.sequence.NucleotideSQPair; import com.milaboratory.core.sequence.mutations.Mutations; import com.milaboratory.core.sequence.nucleotide.NucleotideSequence; import com.milaboratory.core.sequencing.read.SSequencingRead; import com.milaboratory.core.sequencing.read.SSequencingReadImpl; -import com.milaboratory.migec2.core.align.reference.Reference; -import com.milaboratory.migec2.core.align.reference.ReferenceLibrary; +import com.milaboratory.oncomigec.core.align.reference.Reference; +import com.milaboratory.oncomigec.core.align.reference.ReferenceLibrary; import java.util.HashSet; import java.util.LinkedList; @@ -14,7 +14,7 @@ import java.util.Set; import java.util.concurrent.atomic.AtomicInteger; -import static com.milaboratory.migec2.util.Util.randomSequence; +import static com.milaboratory.oncomigec.util.Util.randomSequence; public class RandomReferenceGenerator { private int referenceSizeMin, referenceSizeMax;