├── .gitignore ├── .mvn └── extensions.xml ├── .travis.settings.xml ├── .travis.yml ├── LICENSE ├── META-INF └── maven │ └── aptasuite │ └── aptasuite │ └── pom.xml ├── README.md ├── pom.xml ├── repo └── fr │ └── orsay │ └── lri │ └── varna │ ├── 3.93 │ ├── varna-3.93.jar │ ├── varna-3.93.jar.md5 │ ├── varna-3.93.jar.sha1 │ ├── varna-3.93.pom │ ├── varna-3.93.pom.md5 │ └── varna-3.93.pom.sha1 │ ├── maven-metadata.xml │ ├── maven-metadata.xml.md5 │ └── maven-metadata.xml.sha1 └── src └── main ├── java ├── aptasuite │ ├── Aptasuite.java │ └── CLI.java ├── benchmarks │ └── MapDB.java ├── exceptions │ ├── DuplicateSelectionCycleException.java │ ├── InformationNotFoundException.java │ ├── InvalidAlphabetException.java │ ├── InvalidConfigurationException.java │ ├── InvalidSelectionCycleException.java │ └── InvalidSequenceReadFileException.java ├── gui │ ├── activity │ │ ├── BlockingOverlayPane.java │ │ ├── ProgressPane.fxml │ │ ├── ProgressPaneController.java │ │ ├── ProgressPaneLoggerHandler.java │ │ └── package-info.java │ ├── aptatrace │ │ └── logo │ │ │ ├── Logo.java │ │ │ ├── LogoBarPainter.java │ │ │ ├── LogoSummary.java │ │ │ └── LogoSummary2.java │ ├── charts │ │ └── logo │ │ │ ├── Alphabet.java │ │ │ ├── Bar.fxml │ │ │ ├── BarColumn.fxml │ │ │ ├── BarColumnBackup.fxml │ │ │ ├── BarColumnController.java │ │ │ ├── BarController.java │ │ │ ├── LogoChartPanel.fxml │ │ │ ├── LogoChartPanelController.java │ │ │ ├── Scale.java │ │ │ ├── SvgAlphabet.java │ │ │ ├── YAxis.fxml │ │ │ ├── YAxisController.java │ │ │ └── package-info.java │ ├── core │ │ ├── Initializable.java │ │ ├── RootClass.java │ │ ├── RootLayout.fxml │ │ ├── RootLayoutController.java │ │ ├── aptamer │ │ │ ├── family │ │ │ │ └── analysis │ │ │ │ │ ├── AptamerFamilyAnalysisRoot.fxml │ │ │ │ │ ├── AptamerFamilyAnalysisRootController.java │ │ │ │ │ ├── ClusterTableRowData.java │ │ │ │ │ ├── SequenceTableRowData.java │ │ │ │ │ ├── package-info.java │ │ │ │ │ ├── style.css │ │ │ │ │ ├── style_cardinality.css │ │ │ │ │ └── style_cluster_enrichment.css │ │ │ └── pool │ │ │ │ ├── AptamerPoolRoot.fxml │ │ │ │ ├── AptamerPoolRootController.java │ │ │ │ ├── TableRowData.java │ │ │ │ ├── package-info.java │ │ │ │ └── style.css │ │ ├── experiment │ │ │ └── overview │ │ │ │ ├── ExperimentOverviewRandomizedRegionSizeDistribution.fxml │ │ │ │ ├── ExperimentOverviewRandomizedRegionSizeDistributionController.java │ │ │ │ ├── ExperimentOverviewRoot.fxml │ │ │ │ ├── ExperimentOverviewRootController.java │ │ │ │ ├── ExperimentOverviewSelectionCycleComposition.fxml │ │ │ │ ├── ExperimentOverviewSelectionCycleCompositionController.java │ │ │ │ └── package-info.java │ │ ├── motifs │ │ │ ├── MotifAnalysisRoot.fxml │ │ │ ├── MotifAnalysisRootController.java │ │ │ ├── MotifFileHook.java │ │ │ ├── TableRowData.java │ │ │ └── package-info.java │ │ └── sequencing │ │ │ └── data │ │ │ ├── SequencingDataCycle.fxml │ │ │ ├── SequencingDataCycleController.java │ │ │ ├── SequencingDataRoot.fxml │ │ │ ├── SequencingDataRootController.java │ │ │ ├── package-info.java │ │ │ └── style.css │ ├── misc │ │ ├── ControlFXValidatorFactory.java │ │ ├── FXConcurrent.java │ │ ├── decorations.css │ │ └── package-info.java │ └── wizards │ │ ├── aptamut │ │ ├── AppMutScore.java │ │ ├── AptaMutRoot.fxml │ │ ├── AptaMutRootController.java │ │ ├── MutantScore.java │ │ ├── TableRowData.java │ │ ├── hide_scrollbar.css │ │ ├── package-info.java │ │ └── style.css │ │ ├── aptasim │ │ ├── AptaSimWizard.fxml │ │ ├── AptaSimWizardController.java │ │ └── package-info.java │ │ ├── export │ │ ├── ExportWizardController.java │ │ ├── exportWizard.fxml │ │ └── package-info.java │ │ ├── newexperiment │ │ ├── ActionBarController.java │ │ ├── DataModel.java │ │ ├── SelectionCycleDataModel.java │ │ ├── SelectionCycleDetailsController.java │ │ ├── Wizard1Controller.java │ │ ├── Wizard2Controller.java │ │ ├── Wizard2ControllerLogHandler.java │ │ ├── WizardAdvancedOptionsController.java │ │ ├── WizardStartController.java │ │ ├── actionBar.fxml │ │ ├── package-info.java │ │ ├── selectionCycleDetails.fxml │ │ ├── wizard1.fxml │ │ ├── wizard2.fxml │ │ ├── wizardAdvancedOptions.fxml │ │ └── wizardStart.fxml │ │ └── structureprofileprediction │ │ ├── StructureProfilePredictionWizard.fxml │ │ ├── StructureProfilePredictionWizardController.java │ │ └── package-info.java ├── lib │ ├── aptacluster │ │ ├── AptaCluster.java │ │ ├── Buckets.java │ │ ├── Distances.java │ │ ├── HashAptaCluster.java │ │ ├── HashAptaClusterLINEAR.java │ │ ├── LSHConsumer.java │ │ ├── LSHInitializationConsumer.java │ │ ├── LSHInitializationProducer.java │ │ ├── LSHProducer.java │ │ ├── LSHQueueItem.java │ │ └── LocalitySensitiveHash.java │ ├── aptamer │ │ └── datastructures │ │ │ ├── AptamerBounds.java │ │ │ ├── AptamerPool.java │ │ │ ├── BitMatrix.java │ │ │ ├── ClusterContainer.java │ │ │ ├── Experiment.java │ │ │ ├── GenericStorage.java │ │ │ ├── MapDBAptamerPool.java │ │ │ ├── MapDBClusterContainer.java │ │ │ ├── MapDBGenericStorage.java │ │ │ ├── MapDBSelectionCycle.java │ │ │ ├── MapDBStructurePool.java │ │ │ ├── Metadata.java │ │ │ ├── SelectionCycle.java │ │ │ └── StructurePool.java │ ├── aptanet │ │ ├── AptamerLabelPair.java │ │ ├── DataInputIterator.java │ │ ├── DataType.java │ │ ├── Inequality.java │ │ ├── PlayGround.java │ │ ├── ScoreMethod.java │ │ ├── SelectionCycleSplitDataInputIterator.java │ │ ├── SequenceStructureDatasetIterator.java │ │ └── input │ │ │ ├── AptamerLabelGenerator.java │ │ │ ├── AptamerRecordMetaData.java │ │ │ ├── InputEncoding.java │ │ │ ├── SequenceBPPMRecordReader.java │ │ │ ├── TensorFactory.java │ │ │ └── package-info.java │ ├── aptatrace │ │ ├── AptaTraceMotif.java │ │ ├── ExternalSort.java │ │ ├── KContextTrace.java │ │ ├── MotifProfile.java │ │ └── QuickSort.java │ ├── export │ │ ├── CompressedExportWriter.java │ │ ├── Export.java │ │ ├── ExportFormat.java │ │ ├── ExportWriter.java │ │ ├── FastaExportFormat.java │ │ ├── FastqExportFormat.java │ │ ├── SequencingDirection.java │ │ ├── StructureExportFormat.java │ │ └── UncompressedExportWriter.java │ ├── parser │ │ ├── Parser.java │ │ ├── ParserProgress.java │ │ ├── aptaplex │ │ │ ├── .gitignore │ │ │ ├── AptaPlexConsumer.java │ │ │ ├── AptaPlexParser.java │ │ │ ├── AptaPlexProducer.java │ │ │ ├── AptaPlexProgress.java │ │ │ ├── FastqReader.java │ │ │ ├── FileFormat.java │ │ │ ├── RawReader.java │ │ │ ├── Read.java │ │ │ ├── Reader.java │ │ │ └── distances │ │ │ │ ├── BitapDistance.java │ │ │ │ ├── Distance.java │ │ │ │ ├── EditDistance.java │ │ │ │ └── Result.java │ │ └── aptasim │ │ │ ├── AptaSimParser.java │ │ │ ├── AptaSimProgress.java │ │ │ ├── HMMData.java │ │ │ └── HMMSequenceGenerator.java │ └── structure │ │ ├── capr │ │ ├── CapR.java │ │ ├── CapRFactory.java │ │ ├── CapRFactoryConsumer.java │ │ ├── CapRFactoryProducer.java │ │ ├── DataMatrix.java │ │ ├── EnergyPar.java │ │ ├── InitLoops.java │ │ └── LICENSE.txt │ │ └── rnafold │ │ ├── BondT.java │ │ ├── CentroidData.java │ │ ├── EnergyConst.java │ │ ├── EnergyPar.java │ │ ├── Fold.java │ │ ├── FoldVars.java │ │ ├── LItem.java │ │ ├── LItemList.java │ │ ├── MEA.java │ │ ├── MEAdat.java │ │ ├── MFEData.java │ │ ├── PFParamT.java │ │ ├── PList.java │ │ ├── PairMat.java │ │ ├── ParamT.java │ │ ├── Params.java │ │ ├── PartFunc.java │ │ ├── RNAFold.java │ │ ├── RNAFoldAPI.java │ │ ├── RNAFoldFactory.java │ │ ├── RNAFoldFactoryConsumer.java │ │ ├── RNAFoldFactoryProducer.java │ │ ├── Sector.java │ │ ├── Utils.java │ │ └── package-info.java └── utilities │ ├── Accumulator.java │ ├── AptaColors.java │ ├── AptaLogger.java │ ├── AptaLoggerFormat.java │ ├── CLIOptions.java │ ├── Configuration.java │ ├── FileUtilities.java │ ├── GUIUtilities.java │ ├── Index.java │ ├── Pair.java │ ├── QSComparator.java │ ├── QSDoubleComparator.java │ ├── Quicksort.java │ ├── SequenceTableUtils.java │ ├── Serialization.java │ └── Version.java └── resources ├── RNAFold_int11_37.txt ├── RNAFold_int11_H.txt ├── 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