path	# lines of code
desktop/index.html	23
desktop/css/loader.css	86
desktop/css/main.css	15
desktop/src/ScriptUtils.js	61
server/ngb-cli/config/pmd/pmd-ruleset.xml	31
server/ngb-cli/src/main/resources/log4j2.xml	23
server/ngb-cli/src/main/resources/command-configuration.xml	329
server/ngb-cli/src/main/java/com/epam/ngb/cli/app/ConfigurationLoader.java	101
server/ngb-cli/src/main/java/com/epam/ngb/cli/app/Application.java	315
server/ngb-cli/src/main/java/com/epam/ngb/cli/app/Utils.java	12
server/ngb-cli/src/main/java/com/epam/ngb/cli/app/ApplicationOptions.java	48
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/BiologicalDataItem.java	113
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/UrlWithAliasItem.java	11
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/IDList.java	9
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/RequestPayload.java	3
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/RegistrationRequest.java	95
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/BlastDatabase.java	60
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/ProjectItem.java	23
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/PermissionsContainer.java	55
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/BaseEntity.java	24
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/ProjectDescription.java	16
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/BlastDatabaseVO.java	22
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/lineage/LineageTree.java	76
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/lineage/LineageTreeRegistrationRequest.java	15
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/AclSecuredEntry.java	40
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/ExtendedRole.java	9
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/SpeciesEntity.java	59
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/NgbUser.java	66
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/pathway/NGBPathway.java	76
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/pathway/PathwayDatabaseSource.java	28
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/pathway/PathwayRegistrationRequest.java	16
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/pathway/BioPAXRegistrationRequest.java	14
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/Project.java	124
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/Role.java	75
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/SortRequest.java	24
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/heatmap/HeatmapRegistrationRequest.java	22
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/heatmap/HeatmapAnnotationType.java	15
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/heatmap/Heatmap.java	86
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/UserContext.java	14
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/NgbUserVO.java	10
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/BiologicalDataItemResourceType.java	51
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/coverage/BamCoverage.java	65
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/pdb/PdbFileRegistrationRequest.java	16
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/pdb/PdbFile.java	72
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/BiologicalDataItemFormat.java	131
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/ResponseResult.java	24
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/AclClass.java	15
server/ngb-cli/src/main/java/com/epam/ngb/cli/entity/PermissionGrantRequest.java	47
server/ngb-cli/src/main/java/com/epam/ngb/cli/constants/MessageConstants.java	47
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/printer/AbstractResultPrinter.java	48
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/printer/Printable.java	7
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/request/RequestManager.java	57
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/Command.java	14
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/simple/SetServerCommandHandler.java	19
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/simple/VersionCommandHandler.java	28
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/simple/SetTokenCommandHandler.java	24
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/simple/SetPropertyCommandHandler.java	43
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/simple/AbstractSimpleCommandHandler.java	15
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/AbstractEntityRenameHandler.java	54
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/FileDeletionHandler.java	22
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/SortHandler.java	82
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/FileIndexingHandler.java	46
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/FileRenameHandler.java	7
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/SearchHandler.java	58
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/UserGroupUserRemovingHandler.java	83
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/dataset/DatasetItemAddingHandler.java	55
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/dataset/DatasetListHandler.java	98
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/dataset/DatasetRenameHandler.java	8
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/dataset/DatasetDescriptionAdditionHandler.java	61
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/dataset/DatasetDescriptionDeletionHandler.java	50
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/dataset/DatasetMovingHandler.java	44
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/dataset/DatasetDeletionHandler.java	49
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/dataset/DatasetItemDeletionHandler.java	32
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/dataset/DatasetRegistrationHandler.java	86
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/user/DeleteUserHandler.java	62
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/user/CreateUserHandler.java	84
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/user/DeleteUserGroupHandler.java	45
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/species/SpeciesAddingHandler.java	48
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/species/SpeciesRegistrationHandler.java	45
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/species/SpeciesRemovingHandler.java	32
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/species/SpeciesDeletionHandler.java	41
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/species/SpeciesListHandler.java	58
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/gene/GeneRemovingHandler.java	31
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/gene/GeneAddingHandler.java	66
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/UrlGeneratorHandler.java	122
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/lineage/LineageTreeRegistrationHandler.java	49
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/lineage/LineageTreeDeletionHandler.java	40
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/lineage/LineageTreeListHandler.java	56
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/CreateUserGroupHandler.java	78
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/FileRegistrationHandler.java	122
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/blast/BlastDatabasesListHandler.java	79
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/blast/BlastDatabaseDeletionHandler.java	27
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/blast/BlastDatabaseRegistrationHandler.java	42
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/pathway/PathwayRegistrationHandler.java	69
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/pathway/BioPAXRegistrationHandler.java	52
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/pathway/PathwayDeletionHandler.java	40
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/pathway/PathwayListHandler.java	56
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/heatmap/HeatmapListHandler.java	56
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/heatmap/AbstractHeatmapUpdateHandler.java	54
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/heatmap/HeatmapDeletionHandler.java	39
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/heatmap/HeatmapColumnTreeHandler.java	5
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/heatmap/HeatmapRowTreeHandler.java	5
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/heatmap/HeatmapCellAnnotationHandler.java	19
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/heatmap/HeatmapRegistrationHandler.java	54
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/heatmap/HeatmapLabelAnnotationHandler.java	24
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/PrintPermissionsHelper.java	81
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/coverage/CoverageDeletionHandler.java	52
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/coverage/CoverageRegistrationHandler.java	48
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/coverage/CoverageListHandler.java	56
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/pdb/PdbFileListHandler.java	56
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/pdb/PdbFileRegistrationHandler.java	62
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/pdb/PdbFileDeletionHandler.java	40
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/reference/AnnotationReferenceRemovingHandler.java	10
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/reference/ReferenceDeletionHandler.java	23
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/reference/ProteinAddingHandler.java	48
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/reference/ReferenceListHandler.java	59
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/reference/ReferenceRenameHandler.java	8
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/reference/AnnotationReferenceAddingHandler.java	10
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/reference/AbstractAnnotationReferenceHandler.java	70
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/reference/ReferenceRegistrationHandler.java	86
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/UserGroupUserAddingHandler.java	79
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/AbstractHTTPCommandHandler.java	629
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/http/GrantPermissionHandler.java	193
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/handler/CommandHandler.java	7
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/CommandManager.java	129
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/ServerParameters.java	24
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/command/CommandConfiguration.java	34
server/ngb-cli/src/main/java/com/epam/ngb/cli/manager/JsonMapper.java	22
server/ngb-cli/src/main/java/com/epam/ngb/cli/exception/ApplicationException.java	9
server/catgenome/config/pmd/pmd-ruleset.xml	34
server/catgenome/config/pmd/pmd-ruleset-feature-index-manager.xml	35
server/catgenome/profiles/staging/log4j.xml	49
server/catgenome/profiles/h2/applicationContext-flyway.xml	18
server/catgenome/profiles/h2/dao/dao-helper.xml	22
server/catgenome/profiles/h2/test-applicationContext-flyway.xml	23
server/catgenome/profiles/jar/log4j.xml	55
server/catgenome/profiles/desktop/log4j.xml	37
server/catgenome/profiles/release/log4j.xml	40
server/catgenome/profiles/postgres/applicationContext-flyway.xml	18
server/catgenome/profiles/postgres/dao/dao-helper.xml	22
server/catgenome/profiles/postgres/test-applicationContext-flyway.xml	23
server/catgenome/profiles/dev/log4j.xml	69
server/catgenome/src/main/resources/database/catgenome/h2/v2023.03.18_18.00__target.sql	18
server/catgenome/src/main/resources/database/catgenome/h2/v2021.08.04_16.00__issue_496_activity.sql	14
server/catgenome/src/main/resources/database/catgenome/h2/v2023.07.28_18.00__target_owner.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2024.03.11_18.00__ref_protein_seq.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2016.12.16_12.07__EPMCMBI-1257_bookmark_name_idx.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2022.03.02_16.00__pathway_database_source.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2021.06.08_13.00__issue_398_species_taxid.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2016.12.12_14.35__project_created_by_index.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2022.01.21_16.00__pathway.sql	7
server/catgenome/src/main/resources/database/catgenome/h2/v2021.12.20_16.00__strain_lineage_dataset.sql	2
server/catgenome/src/main/resources/database/catgenome/h2/v2022.02.16_16.00__coverage.sql	8
server/catgenome/src/main/resources/database/catgenome/h2/v2017.03.31_15.20__EPMCMBI-1710_annotation_files.sql	7
server/catgenome/src/main/resources/database/catgenome/h2/v2021.09.09_17.00__project_note_empty_content.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2021.10.06_18.00__issue_581_heatmap_annotation_type.sql	3
server/catgenome/src/main/resources/database/catgenome/h2/v2021.08.30_18.00__issue_524_metadata.sql	6
server/catgenome/src/main/resources/database/catgenome/h2/v2024.01.26_16.00__identification_translational_not_requred.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2023.09.18_18.00__target_identification.sql	11
server/catgenome/src/main/resources/database/catgenome/h2/v2021.06.09_17.00__issue_397_blast_database_ref.sql	4
server/catgenome/src/main/resources/database/catgenome/h2/v2021.09.14_12.00__heatmap.sql	21
server/catgenome/src/main/resources/database/catgenome/h2/v2018.10.11_15.03__drop_created_by_related_things.sql	5
server/catgenome/src/main/resources/database/catgenome/h2/v2021.10.15_14.00__issue_667_blast_db_reference.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2022.03.22_16.00__pathway_organism.sql	7
server/catgenome/src/main/resources/database/catgenome/h2/v2016.11.30_11.59__parent_projects.sql	2
server/catgenome/src/main/resources/database/catgenome/h2/v2023.11.25_18.00__target_patents_search.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2017.07.04_11.20__EPMCMBI-1810_short_url.sql	6
server/catgenome/src/main/resources/database/catgenome/h2/v2017.03.24_18.00__EPMCMBI-1725_pretty_name.sql	2
server/catgenome/src/main/resources/database/catgenome/h2/v2017.01.17_18.00__EPMCMBI-1211_unique_names.sql	27
server/catgenome/src/main/resources/database/catgenome/h2/v2021.10.4_12.00__drop_heatmap_label_annotation.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2024.02.19_18.00__acl_target_manager_role.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2021.08.27_16.00__issue_534_session_sharing.sql	14
server/catgenome/src/main/resources/database/catgenome/h2/v2016.12.15_19.50__EPMCMBI-0_set_path_name_length.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2017.07.13_01.17__EPMCMBI-1806_bedGraph_support.sql	2
server/catgenome/src/main/resources/database/catgenome/h2/v2021.08.27_12.00__homologs.sql	56
server/catgenome/src/main/resources/database/catgenome/h2/v2023.07.29_18.00__pdb_file.sql	7
server/catgenome/src/main/resources/database/catgenome/h2/v2022.03.28_18.00__pathways_store_organism_name.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2022.02.22_16.00__pathway_database_source.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2021.11.03_12.00__lineage_tree.sql	30
server/catgenome/src/main/resources/database/catgenome/h2/v2024.02.22_18.00__additional_target_genes.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2021.05.12_12.00__task.sql	36
server/catgenome/src/main/resources/database/catgenome/h2/v2021.12.13_16.00__session_reference_not_requred.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2024.01.15_18.00__target_type.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2021.06.16_17.00__issue_438_project_description.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2017.02.16_18.00__EPMCMBI-1553_Create_ref_index.sql	19
server/catgenome/src/main/resources/database/catgenome/h2/v2017.10.26_14.45__blat_search_support.sql	7
server/catgenome/src/main/resources/database/catgenome/h2/v2021.06.02_21.00__blast_database.sql	8
server/catgenome/src/main/resources/database/catgenome/h2/v2016.12.13_15.38__EPMCMBI-1255_reference_associated_genes.sql	3
server/catgenome/src/main/resources/database/catgenome/h2/v2023.08.15_18.00__target_alignment.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2021.05.27_16.00__task_column_lengths.sql	5
server/catgenome/src/main/resources/database/catgenome/h2/v2018.09.17_11.03__ACL_tables.sql	102
server/catgenome/src/main/resources/database/catgenome/h2/v2021.10.13_12.00__project_description.sql	10
server/catgenome/src/main/resources/database/catgenome/h2/v2024.03.21_19.00__blast_task_id.sql	5
server/catgenome/src/main/resources/database/catgenome/h2/v2016.12.16_12.06__EPMCMBI-1257_global_bookmarks.sql	7
server/catgenome/src/main/resources/database/catgenome/h2/v2021.08.31_12.00__project_note.sql	8
server/catgenome/src/main/resources/database/catgenome/h2/v2016.11.21_17.58__Database_create_script.sql	254
server/catgenome/src/main/resources/database/catgenome/h2/v2022.02.14_16.00__vcf_sample_alias.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2021.12.03_12.00__multi_sample_vcf.sql	1
server/catgenome/src/main/resources/database/catgenome/h2/v2021.06.24_17.00__issue_441_biological_data_item_source.sql	3
server/catgenome/src/main/resources/database/catgenome/h2/v2018.12.03_12.00__default_admin.sql	4
server/catgenome/src/main/resources/database/catgenome/postgres/v2023.03.18_18.00__target.sql	18
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.08.04_16.00__issue_496_activity.sql	14
server/catgenome/src/main/resources/database/catgenome/postgres/v2016.11.21_12.52__Database_create_script.sql	251
server/catgenome/src/main/resources/database/catgenome/postgres/v2023.07.28_18.00__target_owner.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2024.03.11_18.00__ref_protein_seq.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2016.12.16_12.07__EPMCMBI-1257_bookmark_name_idx.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.06.08_13.00__issue_398_species_taxid.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2016.12.12_14.35__project_created_by_index.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2022.01.21_16.00__pathway.sql	7
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.12.20_16.00__strain_lineage_dataset.sql	2
server/catgenome/src/main/resources/database/catgenome/postgres/v2022.02.16_16.00__coverage.sql	8
server/catgenome/src/main/resources/database/catgenome/postgres/v2017.03.31_15.20__EPMCMBI-1710_annotation_files.sql	7
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.09.09_17.00__project_note_empty_content.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.10.06_18.00__issue_581_heatmap_annotation_type.sql	3
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.08.30_18.00__issue_524_metadata.sql	6
server/catgenome/src/main/resources/database/catgenome/postgres/v2024.01.26_16.00__identification_translational_not_requred.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2023.09.18_18.00__target_identification.sql	11
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.06.09_17.00__issue_397_blast_database_ref.sql	4
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.09.14_12.00__heatmap.sql	21
server/catgenome/src/main/resources/database/catgenome/postgres/v2018.10.11_15.03__drop_created_by_related_things.sql	5
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.10.15_14.00__issue_667_blast_db_reference.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2022.03.22_16.00__pathway_organism.sql	7
server/catgenome/src/main/resources/database/catgenome/postgres/v2023.11.25_18.00__target_patents_search.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2016.12.02_18.26__Oauth_tables.sql	37
server/catgenome/src/main/resources/database/catgenome/postgres/v2017.07.04_11.20__EPMCMBI-1810_short_url.sql	6
server/catgenome/src/main/resources/database/catgenome/postgres/v2017.03.24_18.00__EPMCMBI-1725_pretty_name.sql	2
server/catgenome/src/main/resources/database/catgenome/postgres/v2017.01.17_18.00__EPMCMBI-1211_unique_names.sql	27
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.10.4_12.00__drop_heatmap_label_annotation.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2024.02.19_18.00__acl_target_manager_role.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.08.27_16.00__issue_534_session_sharing.sql	14
server/catgenome/src/main/resources/database/catgenome/postgres/v2016.12.15_19.50__EPMCMBI-0_set_path_name_length.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2017.07.13_01.17__EPMCMBI-1806_bedGraph_support.sql	2
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.08.27_12.00__homologs.sql	56
server/catgenome/src/main/resources/database/catgenome/postgres/v2023.07.29_18.00__pdb_file.sql	7
server/catgenome/src/main/resources/database/catgenome/postgres/v2022.03.28_18.00__pathways_store_organism_name.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2022.02.22_16.00__pathway_database_source.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.11.03_12.00__lineage_tree.sql	30
server/catgenome/src/main/resources/database/catgenome/postgres/v2024.02.22_18.00__additional_target_genes.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.05.12_12.00__task.sql	36
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.12.13_16.00__session_reference_not_requred.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2024.01.15_18.00__target_type.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.06.16_17.00__issue_438_project_description.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2017.02.16_18.00__EPMCMBI-1553_Create_ref_index.sql	18
server/catgenome/src/main/resources/database/catgenome/postgres/v2017.10.26_14.45__blat_search_support.sql	7
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.06.02_21.00__blast_database.sql	8
server/catgenome/src/main/resources/database/catgenome/postgres/v2016.12.13_15.38__EPMCMBI-1255_reference_associated_genes.sql	3
server/catgenome/src/main/resources/database/catgenome/postgres/v2023.08.15_18.00__target_alignment.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2016.12.03_11.59__parent_projects.sql	2
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.05.27_16.00__task_column_lengths.sql	5
server/catgenome/src/main/resources/database/catgenome/postgres/v2018.09.17_11.03__ACL_tables.sql	99
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.10.13_12.00__project_description.sql	10
server/catgenome/src/main/resources/database/catgenome/postgres/v2024.03.21_19.00__blast_task_id.sql	5
server/catgenome/src/main/resources/database/catgenome/postgres/v2016.12.16_12.06__EPMCMBI-1257_global_bookmarks.sql	7
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.08.31_12.00__project_note.sql	8
server/catgenome/src/main/resources/database/catgenome/postgres/v2022.02.14_16.00__vcf_sample_alias.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.12.03_12.00__multi_sample_vcf.sql	1
server/catgenome/src/main/resources/database/catgenome/postgres/v2021.06.24_17.00__issue_441_biological_data_item_source.sql	3
server/catgenome/src/main/resources/database/catgenome/postgres/v2018.12.03_12.00__default_admin.sql	3
server/catgenome/src/main/resources/applicationContext.xml	11
server/catgenome/src/main/resources/static/blastx.html	188
server/catgenome/src/main/resources/static/swagger-ui/index.html	82
server/catgenome/src/main/resources/static/tblastn.html	183
server/catgenome/src/main/resources/static/miew/index.html	1
server/catgenome/src/main/resources/static/blastp.html	168
server/catgenome/src/main/resources/static/tblastx.html	155
server/catgenome/src/main/resources/static/blastn.html	203
server/catgenome/src/main/resources/scripts/run_tmap.py	53
server/catgenome/src/main/resources/templates/error-401.html	15
server/catgenome/src/main/resources/conf/catgenome/ehcache.xml	22
server/catgenome/src/main/resources/conf/catgenome/applicationContext-database.xml	68
server/catgenome/src/main/resources/conf/catgenome/dao/bam-coverage-dao.xml	58
server/catgenome/src/main/resources/conf/catgenome/dao/homolog-group-dao.xml	34
server/catgenome/src/main/resources/conf/catgenome/dao/role-dao.xml	173
server/catgenome/src/main/resources/conf/catgenome/dao/user-dao.xml	435
server/catgenome/src/main/resources/conf/catgenome/dao/lineage-tree-node-dao.xml	72
server/catgenome/src/main/resources/conf/catgenome/dao/homolog-gene-description-dao.xml	44
server/catgenome/src/main/resources/conf/catgenome/dao/homolog-database-dao.xml	30
server/catgenome/src/main/resources/conf/catgenome/dao/blast-task-dao.xml	247
server/catgenome/src/main/resources/conf/catgenome/dao/bucket-dao.xml	63
server/catgenome/src/main/resources/conf/catgenome/dao/bam-file-dao.xml	71
server/catgenome/src/main/resources/conf/catgenome/dao/homolog-group-gene-dao.xml	73
server/catgenome/src/main/resources/conf/catgenome/dao/reference-genome-dao.xml	363
server/catgenome/src/main/resources/conf/catgenome/dao/activity-dao.xml	55
server/catgenome/src/main/resources/conf/catgenome/dao/species-dao.xml	52
server/catgenome/src/main/resources/conf/catgenome/dao/vcf-file-dao.xml	156
server/catgenome/src/main/resources/conf/catgenome/dao/pathway-dao.xml	85
server/catgenome/src/main/resources/conf/catgenome/dao/target-dao.xml	194
server/catgenome/src/main/resources/conf/catgenome/dao/lineage-tree-edge-dao.xml	94
server/catgenome/src/main/resources/conf/catgenome/dao/maf-file-dao.xml	61
server/catgenome/src/main/resources/conf/catgenome/dao/gene-file-dao.xml	133
server/catgenome/src/main/resources/conf/catgenome/dao/heatmap-dao.xml	228
server/catgenome/src/main/resources/conf/catgenome/dao/project-description-dao.xml	109
server/catgenome/src/main/resources/conf/catgenome/dao/url-shorter-dao.xml	30
server/catgenome/src/main/resources/conf/catgenome/dao/bed-graph-file-dao.xml	57
server/catgenome/src/main/resources/conf/catgenome/dao/bookmark-dao.xml	241
server/catgenome/src/main/resources/conf/catgenome/dao/pathway-organism-dao.xml	56
server/catgenome/src/main/resources/conf/catgenome/dao/pdb-file-dao.xml	95
server/catgenome/src/main/resources/conf/catgenome/dao/bed-file-dao.xml	57
server/catgenome/src/main/resources/conf/catgenome/dao/biological-data-item-dao.xml	620
server/catgenome/src/main/resources/conf/catgenome/dao/target-gene-dao.xml	92
server/catgenome/src/main/resources/conf/catgenome/dao/lineage-tree-dao.xml	113
server/catgenome/src/main/resources/conf/catgenome/dao/homolog-gene-domain-dao.xml	38
server/catgenome/src/main/resources/conf/catgenome/dao/seg-file-dao.xml	123
server/catgenome/src/main/resources/conf/catgenome/dao/target-identification-dao.xml	109
server/catgenome/src/main/resources/conf/catgenome/dao/project-dao.xml	653
server/catgenome/src/main/resources/conf/catgenome/dao/homolog-gene-alias-dao.xml	30
server/catgenome/src/main/resources/conf/catgenome/dao/blast-database-dao.xml	64
server/catgenome/src/main/resources/conf/catgenome/dao/person-dao.xml	64
server/catgenome/src/main/resources/conf/catgenome/dao/session-dao.xml	78
server/catgenome/src/main/resources/conf/catgenome/dao/metadata-dao.xml	57
server/catgenome/src/main/resources/conf/catgenome/acl-dao.xml	139
server/catgenome/src/main/resources/conf/catgenome/applicationContext-cache.xml	24
server/catgenome/src/main/resources/conf/catgenome/applicationContext-messages.xml	13
server/catgenome/src/main/resources/conf/catgenome/applicationContext-config.xml	22
server/catgenome/src/main/webapp/swagger-ui/index.html	82
server/catgenome/src/main/webapp/WEB-INF/applicationContext.xml	18
server/catgenome/src/main/webapp/WEB-INF/web.xml	19
server/catgenome/src/main/webapp/WEB-INF/oauth-servlet.xml	11
server/catgenome/src/main/webapp/WEB-INF/catgenome-servlet.xml	26
server/catgenome/src/main/java/com/epam/catgenome/app/CustomRequestLoggingFilter.java	8
server/catgenome/src/main/java/com/epam/catgenome/app/AclSecurityConfiguration.java	122
server/catgenome/src/main/java/com/epam/catgenome/app/TomcatConfigurerImpl.java	18
server/catgenome/src/main/java/com/epam/catgenome/app/NoSecurityConfiguration.java	21
server/catgenome/src/main/java/com/epam/catgenome/app/Application.java	113
server/catgenome/src/main/java/com/epam/catgenome/app/AppMVCConfiguration.java	102
server/catgenome/src/main/java/com/epam/catgenome/app/JWTSecurityConfiguration.java	122
server/catgenome/src/main/java/com/epam/catgenome/app/CustomAwareAuthenticationSuccessHandler.java	37
server/catgenome/src/main/java/com/epam/catgenome/app/AppConfiguration.java	24
server/catgenome/src/main/java/com/epam/catgenome/app/SecurityConfiguration.java	8
server/catgenome/src/main/java/com/epam/catgenome/app/SAMLSecurityConfiguration.java	434
server/catgenome/src/main/java/com/epam/catgenome/app/TomcatConfigurer.java	6
server/catgenome/src/main/java/com/epam/catgenome/util/NggbIntervalTreeMap.java	117
server/catgenome/src/main/java/com/epam/catgenome/util/FileFormat.java	25
server/catgenome/src/main/java/com/epam/catgenome/util/comparator/FeatureComparator.java	13
server/catgenome/src/main/java/com/epam/catgenome/util/FeatureIterator.java	146
server/catgenome/src/main/java/com/epam/catgenome/util/QueryUtils.java	32
server/catgenome/src/main/java/com/epam/catgenome/util/motif/MotifSearcher.java	36
server/catgenome/src/main/java/com/epam/catgenome/util/motif/MotifSearchIterator.java	130
server/catgenome/src/main/java/com/epam/catgenome/util/motif/SimpleMotifSearchIterator.java	133
server/catgenome/src/main/java/com/epam/catgenome/util/motif/IupacRegexConverter.java	32
server/catgenome/src/main/java/com/epam/catgenome/util/motif/RegexReverser.java	83
server/catgenome/src/main/java/com/epam/catgenome/util/motif/IupacRegex.java	40
server/catgenome/src/main/java/com/epam/catgenome/util/motif/ReversingRegexMotifSearchIterator.java	55
server/catgenome/src/main/java/com/epam/catgenome/util/PositionalOutputStream.java	34
server/catgenome/src/main/java/com/epam/catgenome/util/BlockCompressedDataInputStream.java	104
server/catgenome/src/main/java/com/epam/catgenome/util/sort/FeatureSorterFactory.java	39
server/catgenome/src/main/java/com/epam/catgenome/util/sort/VCFSorter.java	31
server/catgenome/src/main/java/com/epam/catgenome/util/sort/Parser.java	50
server/catgenome/src/main/java/com/epam/catgenome/util/sort/BedSorter.java	35
server/catgenome/src/main/java/com/epam/catgenome/util/sort/SortableRecordCodec.java	72
server/catgenome/src/main/java/com/epam/catgenome/util/sort/AbstractFeatureSorter.java	89
server/catgenome/src/main/java/com/epam/catgenome/util/sort/SortableRecord.java	20
server/catgenome/src/main/java/com/epam/catgenome/util/sort/GFFSorter.java	31
server/catgenome/src/main/java/com/epam/catgenome/util/azure/AzureBlobInputStream.java	41
server/catgenome/src/main/java/com/epam/catgenome/util/azure/AzureSeekableStreamFactory.java	33
server/catgenome/src/main/java/com/epam/catgenome/util/azure/AzureBlobSeekableStream.java	34
server/catgenome/src/main/java/com/epam/catgenome/util/azure/AzureBlobClient.java	167
server/catgenome/src/main/java/com/epam/catgenome/util/azure/AzureCredentialConfiguration.java	13
server/catgenome/src/main/java/com/epam/catgenome/util/IOHelper.java	50
server/catgenome/src/main/java/com/epam/catgenome/util/NgbFileUtils.java	169
server/catgenome/src/main/java/com/epam/catgenome/util/InfoFieldParser.java	111
server/catgenome/src/main/java/com/epam/catgenome/util/HdfsSeekableInputStream.java	43
server/catgenome/src/main/java/com/epam/catgenome/util/Utils.java	379
server/catgenome/src/main/java/com/epam/catgenome/util/ConsensusSequenceUtils.java	101
server/catgenome/src/main/java/com/epam/catgenome/util/BamUtil.java	137
server/catgenome/src/main/java/com/epam/catgenome/util/ProteinSequenceUtils.java	147
server/catgenome/src/main/java/com/epam/catgenome/util/db/PagingInfo.java	13
server/catgenome/src/main/java/com/epam/catgenome/util/db/Page.java	16
server/catgenome/src/main/java/com/epam/catgenome/util/db/QueryParameters.java	17
server/catgenome/src/main/java/com/epam/catgenome/util/db/SortInfo.java	15
server/catgenome/src/main/java/com/epam/catgenome/util/db/Condition.java	12
server/catgenome/src/main/java/com/epam/catgenome/util/db/DBQueryUtils.java	22
server/catgenome/src/main/java/com/epam/catgenome/util/db/Filter.java	16
server/catgenome/src/main/java/com/epam/catgenome/util/DiskBasedList.java	218
server/catgenome/src/main/java/com/epam/catgenome/util/ListMapCollector.java	48
server/catgenome/src/main/java/com/epam/catgenome/util/aws/S3Client.java	166
server/catgenome/src/main/java/com/epam/catgenome/util/aws/S3SeekableStream.java	31
server/catgenome/src/main/java/com/epam/catgenome/util/aws/S3ObjectChunkInputStream.java	39
server/catgenome/src/main/java/com/epam/catgenome/util/aws/S3SeekableStreamFactory.java	46
server/catgenome/src/main/java/com/epam/catgenome/util/feature/reader/AbstractFeatureReader.java	123
server/catgenome/src/main/java/com/epam/catgenome/util/feature/reader/EhCacheBasedIndexCache.java	60
server/catgenome/src/main/java/com/epam/catgenome/util/feature/reader/TabixFeatureReader.java	167
server/catgenome/src/main/java/com/epam/catgenome/util/feature/reader/AbstractEnhancedFeatureReader.java	96
server/catgenome/src/main/java/com/epam/catgenome/util/feature/reader/TabixReader.java	516
server/catgenome/src/main/java/com/epam/catgenome/util/feature/reader/TabixIteratorLineReader.java	19
server/catgenome/src/main/java/com/epam/catgenome/util/feature/reader/TribbleIndexedFeatureReader.java	412
server/catgenome/src/main/java/com/epam/catgenome/util/feature/reader/EnhancedUrlHelper.java	67
server/catgenome/src/main/java/com/epam/catgenome/util/feature/reader/IndexCache.java	3
server/catgenome/src/main/java/com/epam/catgenome/util/FeatureSeekableStream.java	53
server/catgenome/src/main/java/com/epam/catgenome/util/BlockCompressedDataOutputStream.java	95
server/catgenome/src/main/java/com/epam/catgenome/util/FeatureInputStream.java	29
server/catgenome/src/main/java/com/epam/catgenome/util/IndexUtils.java	449
server/catgenome/src/main/java/com/epam/catgenome/util/NgbSeekableStreamFactory.java	57
server/catgenome/src/main/java/com/epam/catgenome/util/HistogramUtils.java	67
server/catgenome/src/main/java/com/epam/catgenome/config/SwaggerConfig.java	49
server/catgenome/src/main/java/com/epam/catgenome/security/jwt/JwtTokenGenerator.java	85
server/catgenome/src/main/java/com/epam/catgenome/security/jwt/TokenVerificationException.java	9
server/catgenome/src/main/java/com/epam/catgenome/security/jwt/JwtFilterAuthenticationFilter.java	62
server/catgenome/src/main/java/com/epam/catgenome/security/jwt/JwtInitializationException.java	6
server/catgenome/src/main/java/com/epam/catgenome/security/jwt/RestAuthenticationEntryPoint.java	15
server/catgenome/src/main/java/com/epam/catgenome/security/jwt/JwtAuthenticationToken.java	36
server/catgenome/src/main/java/com/epam/catgenome/security/jwt/JwtAuthenticationProvider.java	32
server/catgenome/src/main/java/com/epam/catgenome/security/jwt/JwtTokenVerifier.java	100
server/catgenome/src/main/java/com/epam/catgenome/security/PersonService.java	26
server/catgenome/src/main/java/com/epam/catgenome/security/BrowserUser.java	35
server/catgenome/src/main/java/com/epam/catgenome/security/UserContext.java	92
server/catgenome/src/main/java/com/epam/catgenome/security/acl/LookupStrategyImpl.java	366
server/catgenome/src/main/java/com/epam/catgenome/security/acl/AclPermissionSecurityService.java	42
server/catgenome/src/main/java/com/epam/catgenome/security/acl/PermissionHelper.java	302
server/catgenome/src/main/java/com/epam/catgenome/security/acl/PermissionGrantingStrategyImpl.java	55
server/catgenome/src/main/java/com/epam/catgenome/security/acl/JdbcMutableAclServiceImpl.java	138
server/catgenome/src/main/java/com/epam/catgenome/security/acl/aspect/AclMapFilter.java	11
server/catgenome/src/main/java/com/epam/catgenome/security/acl/aspect/AclMaskList.java	11
server/catgenome/src/main/java/com/epam/catgenome/security/acl/aspect/AclMaskPage.java	11
server/catgenome/src/main/java/com/epam/catgenome/security/acl/aspect/AclSync.java	11
server/catgenome/src/main/java/com/epam/catgenome/security/acl/aspect/AclFilterAndTree.java	11
server/catgenome/src/main/java/com/epam/catgenome/security/acl/aspect/AclMask.java	11
server/catgenome/src/main/java/com/epam/catgenome/security/acl/aspect/AclAspect.java	124
server/catgenome/src/main/java/com/epam/catgenome/security/acl/aspect/AclTree.java	11
server/catgenome/src/main/java/com/epam/catgenome/security/acl/aspect/AclFilter.java	11
server/catgenome/src/main/java/com/epam/catgenome/security/acl/customexpression/NGBMethodSecurityExpressionRoot.java	200
server/catgenome/src/main/java/com/epam/catgenome/security/acl/customexpression/NGBMethodSecurityExpressionHandler.java	27
server/catgenome/src/main/java/com/epam/catgenome/security/acl/AclPermissionFactory.java	9
server/catgenome/src/main/java/com/epam/catgenome/security/acl/AclPermission.java	61
server/catgenome/src/main/java/com/epam/catgenome/security/acl/SecurityExpressions.java	23
server/catgenome/src/main/java/com/epam/catgenome/security/acl/GrantPermissionManager.java	291
server/catgenome/src/main/java/com/epam/catgenome/security/acl/PermissionUtils.java	130
server/catgenome/src/main/java/com/epam/catgenome/security/saml/OptionalSAMLLogoutFilter.java	132
server/catgenome/src/main/java/com/epam/catgenome/security/saml/SAMLContextProviderCustomSignKey.java	100
server/catgenome/src/main/java/com/epam/catgenome/security/saml/SAMLUserDetailsServiceImpl.java	224
server/catgenome/src/main/java/com/epam/catgenome/security/saml/SamlUserRegisterStrategy.java	4
server/catgenome/src/main/java/com/epam/catgenome/security/saml/CustomSAMLProcessingFilter.java	73
server/catgenome/src/main/java/com/epam/catgenome/security/saml/SchemeInsensitiveUrlComparator.java	30
server/catgenome/src/main/java/com/epam/catgenome/security/saml/LBConfig.java	20
server/catgenome/src/main/java/com/epam/catgenome/entity/BiologicalDataItem.java	103
server/catgenome/src/main/java/com/epam/catgenome/entity/tmap/TMapDrugField.java	16
server/catgenome/src/main/java/com/epam/catgenome/entity/tmap/Compound.java	13
server/catgenome/src/main/java/com/epam/catgenome/entity/tmap/TMapDrug.java	14
server/catgenome/src/main/java/com/epam/catgenome/entity/UrlWithAliasItem.java	17
server/catgenome/src/main/java/com/epam/catgenome/entity/maf/MafRecord.java	282
server/catgenome/src/main/java/com/epam/catgenome/entity/maf/MafFile.java	38
server/catgenome/src/main/java/com/epam/catgenome/entity/IndexedDataItem.java	30
server/catgenome/src/main/java/com/epam/catgenome/entity/bed/BedFile.java	13
server/catgenome/src/main/java/com/epam/catgenome/entity/bed/BedRecord.java	138
server/catgenome/src/main/java/com/epam/catgenome/entity/bed/FileExtensionMapping.java	47
server/catgenome/src/main/java/com/epam/catgenome/entity/llm/LLMRole.java	13
server/catgenome/src/main/java/com/epam/catgenome/entity/llm/LLMProvider.java	4
server/catgenome/src/main/java/com/epam/catgenome/entity/llm/LLMMessage.java	11
server/catgenome/src/main/java/com/epam/catgenome/entity/llm/CustomLLMMessage.java	8
server/catgenome/src/main/java/com/epam/catgenome/entity/llm/CustomChatCompletion.java	9
server/catgenome/src/main/java/com/epam/catgenome/entity/llm/CustomChatResponse.java	24
server/catgenome/src/main/java/com/epam/catgenome/entity/llm/CustomLLMResponse.java	6
server/catgenome/src/main/java/com/epam/catgenome/entity/track/Track.java	53
server/catgenome/src/main/java/com/epam/catgenome/entity/track/TrackType.java	14
server/catgenome/src/main/java/com/epam/catgenome/entity/track/ReferenceTrackMode.java	6
server/catgenome/src/main/java/com/epam/catgenome/entity/track/SampledTrack.java	28
server/catgenome/src/main/java/com/epam/catgenome/entity/track/AbstractTrack.java	54
server/catgenome/src/main/java/com/epam/catgenome/entity/track/Block.java	30
server/catgenome/src/main/java/com/epam/catgenome/entity/Interval.java	11
server/catgenome/src/main/java/com/epam/catgenome/entity/file/FsDirectory.java	20
server/catgenome/src/main/java/com/epam/catgenome/entity/file/AbstractFsItem.java	11
server/catgenome/src/main/java/com/epam/catgenome/entity/file/FsFile.java	28
server/catgenome/src/main/java/com/epam/catgenome/entity/security/JwtRawToken.java	30
server/catgenome/src/main/java/com/epam/catgenome/entity/security/EntityPermission.java	11
server/catgenome/src/main/java/com/epam/catgenome/entity/security/NgbSecurityGroup.java	13
server/catgenome/src/main/java/com/epam/catgenome/entity/security/AbstractHierarchicalEntity.java	24
server/catgenome/src/main/java/com/epam/catgenome/entity/security/AclSid.java	27
server/catgenome/src/main/java/com/epam/catgenome/entity/security/AbstractSecuredEntity.java	51
server/catgenome/src/main/java/com/epam/catgenome/entity/security/SessionExpirationBehavior.java	4
server/catgenome/src/main/java/com/epam/catgenome/entity/security/AclSecuredEntry.java	19
server/catgenome/src/main/java/com/epam/catgenome/entity/security/AclPermissionEntry.java	16
server/catgenome/src/main/java/com/epam/catgenome/entity/security/JwtTokenClaims.java	34
server/catgenome/src/main/java/com/epam/catgenome/entity/security/NgbUser.java	54
server/catgenome/src/main/java/com/epam/catgenome/entity/security/AclClass.java	22
server/catgenome/src/main/java/com/epam/catgenome/entity/person/PersonRole.java	20
server/catgenome/src/main/java/com/epam/catgenome/entity/person/Person.java	39
server/catgenome/src/main/java/com/epam/catgenome/entity/notification/NotificationMessageVO.java	18
server/catgenome/src/main/java/com/epam/catgenome/entity/activity/Activity.java	23
server/catgenome/src/main/java/com/epam/catgenome/entity/activity/ActivityType.java	4
server/catgenome/src/main/java/com/epam/catgenome/entity/wig/WigFile.java	13
server/catgenome/src/main/java/com/epam/catgenome/entity/wig/Wig.java	20
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/Read.java	135
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/NgbSamTagAndValue.java	29
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/BamFile.java	13
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/PSLRecord.java	166
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/BamReferenceBuffer.java	23
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/BamTrackMode.java	6
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/TrackDirectionType.java	27
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/BasePosition.java	27
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/SpliceJunctionsEntity.java	40
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/BamQueryOption.java	119
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/BamCoverage.java	13
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/CoverageQueryParams.java	20
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/CoverageInterval.java	14
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/BamTrack.java	57
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/BamTrackQuery.java	18
server/catgenome/src/main/java/com/epam/catgenome/entity/bam/BaseCoverage.java	80
server/catgenome/src/main/java/com/epam/catgenome/entity/protein/ProteinSequenceEntry.java	68
server/catgenome/src/main/java/com/epam/catgenome/entity/protein/MrnaProteinSequenceVariants.java	19
server/catgenome/src/main/java/com/epam/catgenome/entity/protein/ProteinSequence.java	28
server/catgenome/src/main/java/com/epam/catgenome/entity/protein/ProteinSequenceConstructRequest.java	13
server/catgenome/src/main/java/com/epam/catgenome/entity/protein/ProteinSequenceInfo.java	25
server/catgenome/src/main/java/com/epam/catgenome/entity/BaseEntity.java	35
server/catgenome/src/main/java/com/epam/catgenome/entity/user/DefaultRoles.java	25
server/catgenome/src/main/java/com/epam/catgenome/entity/user/ExtendedRole.java	10
server/catgenome/src/main/java/com/epam/catgenome/entity/user/Role.java	28
server/catgenome/src/main/java/com/epam/catgenome/entity/AbstractFilterForm.java	37
server/catgenome/src/main/java/com/epam/catgenome/entity/gene/PBDGaneEntity.java	10
server/catgenome/src/main/java/com/epam/catgenome/entity/gene/GeneLowLevel.java	54
server/catgenome/src/main/java/com/epam/catgenome/entity/gene/GeneHighLevel.java	52
server/catgenome/src/main/java/com/epam/catgenome/entity/gene/GeneTranscript.java	51
server/catgenome/src/main/java/com/epam/catgenome/entity/gene/Transcript.java	46
server/catgenome/src/main/java/com/epam/catgenome/entity/gene/GeneFile.java	64
server/catgenome/src/main/java/com/epam/catgenome/entity/gene/Gene.java	110
server/catgenome/src/main/java/com/epam/catgenome/entity/gene/BaseGeneEntity.java	45
server/catgenome/src/main/java/com/epam/catgenome/entity/gene/GeneFilterInfo.java	9
server/catgenome/src/main/java/com/epam/catgenome/entity/gene/GeneFileType.java	6
server/catgenome/src/main/java/com/epam/catgenome/entity/gene/GeneFilterForm.java	223
server/catgenome/src/main/java/com/epam/catgenome/entity/project/ProjectNote.java	17
server/catgenome/src/main/java/com/epam/catgenome/entity/project/ProjectItem.java	27
server/catgenome/src/main/java/com/epam/catgenome/entity/project/ProjectDescription.java	16
server/catgenome/src/main/java/com/epam/catgenome/entity/project/Project.java	149
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/VcfFilterForm.java	363
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/VcfFieldValues.java	17
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/Pointer.java	108
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/VariationEffect.java	9
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/GenotypeData.java	20
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/VariationImpact.java	7
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/VcfFilterInfo.java	21
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/OrganismType.java	8
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/VcfSample.java	17
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/VariationQuery.java	38
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/Variation.java	47
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/VcfFile.java	20
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/VariationType.java	49
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/Filter.java	23
server/catgenome/src/main/java/com/epam/catgenome/entity/vcf/InfoItem.java	59
server/catgenome/src/main/java/com/epam/catgenome/entity/bucket/Bucket.java	34
server/catgenome/src/main/java/com/epam/catgenome/entity/lineage/LineageTreeEdge.java	18
server/catgenome/src/main/java/com/epam/catgenome/entity/lineage/LineageTree.java	23
server/catgenome/src/main/java/com/epam/catgenome/entity/lineage/LineageTreeNode.java	19
server/catgenome/src/main/java/com/epam/catgenome/entity/nucleotid/Signature.java	12
server/catgenome/src/main/java/com/epam/catgenome/entity/nucleotid/FormatCoder.java	29
server/catgenome/src/main/java/com/epam/catgenome/entity/nucleotid/NibByteFormat.java	130
server/catgenome/src/main/java/com/epam/catgenome/entity/BiologicalDataItemDownloadUrl.java	12
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/ExternalDBType.java	22
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/homologene/Alias.java	12
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/homologene/HomologeneEntry.java	19
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/homologene/Gene.java	31
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/homologene/Domain.java	20
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/DimStructure.java	36
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/patents/google/GooglePatent.java	30
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/patents/DrugPatent.java	15
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/patents/SequencePatent.java	15
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/ncbi/GeneId.java	19
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/ncbi/GeneInfo.java	16
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/ChainMinMax.java	60
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/ExternalDB.java	27
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/homolog/HomologGroup.java	24
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/homolog/HomologDatabase.java	12
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/homolog/HomologGroupGene.java	14
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/homolog/HomologType.java	32
server/catgenome/src/main/java/com/epam/catgenome/entity/externaldb/DimEntity.java	45
server/catgenome/src/main/java/com/epam/catgenome/entity/blast/BlastTask.java	27
server/catgenome/src/main/java/com/epam/catgenome/entity/blast/BlastTaskStatus.java	35
server/catgenome/src/main/java/com/epam/catgenome/entity/blast/result/BlastSequence.java	48
server/catgenome/src/main/java/com/epam/catgenome/entity/blast/result/BlastFeatureLocatable.java	15
server/catgenome/src/main/java/com/epam/catgenome/entity/blast/result/Alignment.java	72
server/catgenome/src/main/java/com/epam/catgenome/entity/blast/BlastDatabase.java	17
server/catgenome/src/main/java/com/epam/catgenome/entity/blast/BlastDatabaseType.java	23
server/catgenome/src/main/java/com/epam/catgenome/entity/blast/TaskParameter.java	11
server/catgenome/src/main/java/com/epam/catgenome/entity/blast/BlastTaskOrganism.java	10
server/catgenome/src/main/java/com/epam/catgenome/entity/blast/BlastDatabaseSource.java	20
server/catgenome/src/main/java/com/epam/catgenome/entity/index/SortType.java	12
server/catgenome/src/main/java/com/epam/catgenome/entity/index/Group.java	23
server/catgenome/src/main/java/com/epam/catgenome/entity/index/GeneIndexEntry.java	35
server/catgenome/src/main/java/com/epam/catgenome/entity/index/FeatureType.java	58
server/catgenome/src/main/java/com/epam/catgenome/entity/index/IndexSearchResult.java	62
server/catgenome/src/main/java/com/epam/catgenome/entity/index/VcfIndexEntry.java	52
server/catgenome/src/main/java/com/epam/catgenome/entity/index/FeatureIndexEntry.java	44
server/catgenome/src/main/java/com/epam/catgenome/entity/index/BookmarkIndexEntry.java	42
server/catgenome/src/main/java/com/epam/catgenome/entity/index/FilterType.java	12
server/catgenome/src/main/java/com/epam/catgenome/entity/pathway/NGBPathway.java	21
server/catgenome/src/main/java/com/epam/catgenome/entity/pathway/PathwayDatabaseSource.java	33
server/catgenome/src/main/java/com/epam/catgenome/entity/pathway/PathwayOrganism.java	13
server/catgenome/src/main/java/com/epam/catgenome/entity/pathway/PathwayQueryParams.java	15
server/catgenome/src/main/java/com/epam/catgenome/entity/pathway/SpeciesDescription.java	9
server/catgenome/src/main/java/com/epam/catgenome/entity/NucleotideContent.java	60
server/catgenome/src/main/java/com/epam/catgenome/entity/seg/SegRecord.java	33
server/catgenome/src/main/java/com/epam/catgenome/entity/seg/SegSample.java	17
server/catgenome/src/main/java/com/epam/catgenome/entity/seg/SegFile.java	39
server/catgenome/src/main/java/com/epam/catgenome/entity/heatmap/HeatmapAnnotationType.java	4
server/catgenome/src/main/java/com/epam/catgenome/entity/heatmap/HeatmapTree.java	9
server/catgenome/src/main/java/com/epam/catgenome/entity/heatmap/Heatmap.java	32
server/catgenome/src/main/java/com/epam/catgenome/entity/heatmap/HeatmapDataType.java	30
server/catgenome/src/main/java/com/epam/catgenome/entity/heatmap/HeatmapTreeNode.java	13
server/catgenome/src/main/java/com/epam/catgenome/entity/sequence/LocalProteinSequence.java	9
server/catgenome/src/main/java/com/epam/catgenome/entity/sequence/LocalMRNASequence.java	10
server/catgenome/src/main/java/com/epam/catgenome/entity/BiologicalDataItemResourceType.java	53
server/catgenome/src/main/java/com/epam/catgenome/entity/metadata/MetadataVO.java	14
server/catgenome/src/main/java/com/epam/catgenome/entity/metadata/EntityVO.java	12
server/catgenome/src/main/java/com/epam/catgenome/entity/FeatureFile.java	42
server/catgenome/src/main/java/com/epam/catgenome/entity/pdb/PdbFileQueryParams.java	18
server/catgenome/src/main/java/com/epam/catgenome/entity/pdb/PdbFile.java	20
server/catgenome/src/main/java/com/epam/catgenome/entity/BiologicalDataItemFormat.java	75
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/Sequence.java	35
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/motif/Region.java	23
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/motif/Motif.java	25
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/motif/MotifSearchType.java	6
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/motif/MotifSearchRequest.java	41
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/motif/MotifFilter.java	19
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/motif/MotifSearchResult.java	12
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/motif/MotifTrackQuery.java	11
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/Bookmark.java	43
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/Chromosome.java	60
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/Reference.java	64
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/StrandedSequence.java	16
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/cytoband/GiemsaStain.java	19
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/cytoband/Cytoband.java	27
server/catgenome/src/main/java/com/epam/catgenome/entity/reference/Species.java	8
server/catgenome/src/main/java/com/epam/catgenome/entity/BiologicalDataItemFile.java	10
server/catgenome/src/main/java/com/epam/catgenome/entity/session/NGBSessionValue.java	17
server/catgenome/src/main/java/com/epam/catgenome/entity/session/NGBSessionFilter.java	15
server/catgenome/src/main/java/com/epam/catgenome/entity/session/NGBSessionTrack.java	17
server/catgenome/src/main/java/com/epam/catgenome/entity/session/NGBSession.java	21
server/catgenome/src/main/java/com/epam/catgenome/dao/maf/MafFileDao.java	70
server/catgenome/src/main/java/com/epam/catgenome/dao/bed/BedFileDao.java	64
server/catgenome/src/main/java/com/epam/catgenome/dao/person/PersonDao.java	120
server/catgenome/src/main/java/com/epam/catgenome/dao/activity/ActivityDao.java	97
server/catgenome/src/main/java/com/epam/catgenome/dao/wig/WigFileDao.java	59
server/catgenome/src/main/java/com/epam/catgenome/dao/bam/BamFileDao.java	76
server/catgenome/src/main/java/com/epam/catgenome/dao/bam/BamCoverageDao.java	96
server/catgenome/src/main/java/com/epam/catgenome/dao/UrlShorterDao.java	52
server/catgenome/src/main/java/com/epam/catgenome/dao/user/UserDao.java	457
server/catgenome/src/main/java/com/epam/catgenome/dao/user/RoleDao.java	224
server/catgenome/src/main/java/com/epam/catgenome/dao/BiologicalDataItemDao.java	545
server/catgenome/src/main/java/com/epam/catgenome/dao/gene/GeneFileDao.java	108
server/catgenome/src/main/java/com/epam/catgenome/dao/project/ProjectDescriptionDao.java	151
server/catgenome/src/main/java/com/epam/catgenome/dao/project/ProjectDao.java	589
server/catgenome/src/main/java/com/epam/catgenome/dao/vcf/VcfFileDao.java	153
server/catgenome/src/main/java/com/epam/catgenome/dao/bucket/BucketDao.java	99
server/catgenome/src/main/java/com/epam/catgenome/dao/lineage/LineageTreeNodeDao.java	108
server/catgenome/src/main/java/com/epam/catgenome/dao/lineage/LineageTreeDao.java	120
server/catgenome/src/main/java/com/epam/catgenome/dao/lineage/LineageTreeEdgeDao.java	103
server/catgenome/src/main/java/com/epam/catgenome/dao/blast/BlastTaskDao.java	387
server/catgenome/src/main/java/com/epam/catgenome/dao/blast/BlastDatabaseDao.java	96
server/catgenome/src/main/java/com/epam/catgenome/dao/index/searcher/PagingSearcher.java	55
server/catgenome/src/main/java/com/epam/catgenome/dao/index/searcher/LuceneIndexSearcher.java	11
server/catgenome/src/main/java/com/epam/catgenome/dao/index/searcher/AbstractIndexSearcher.java	80
server/catgenome/src/main/java/com/epam/catgenome/dao/index/searcher/NextPageSearcher.java	55
server/catgenome/src/main/java/com/epam/catgenome/dao/index/field/VcfIndexSortField.java	46
server/catgenome/src/main/java/com/epam/catgenome/dao/index/field/SortedIntPoint.java	79
server/catgenome/src/main/java/com/epam/catgenome/dao/index/field/SortedStringField.java	21
server/catgenome/src/main/java/com/epam/catgenome/dao/index/field/SortedFloatPoint.java	56
server/catgenome/src/main/java/com/epam/catgenome/dao/index/field/SortedSetFloatPoint.java	55
server/catgenome/src/main/java/com/epam/catgenome/dao/index/field/GeneIndexSortField.java	48
server/catgenome/src/main/java/com/epam/catgenome/dao/index/FeatureIndexDao.java	946
server/catgenome/src/main/java/com/epam/catgenome/dao/index/IndexQueryUtils.java	47
server/catgenome/src/main/java/com/epam/catgenome/dao/index/indexer/DefaultDocumentBuilder.java	27
server/catgenome/src/main/java/com/epam/catgenome/dao/index/indexer/BigVcfDocumentBuilder.java	345
server/catgenome/src/main/java/com/epam/catgenome/dao/index/indexer/VcfFeatureIndexBuilder.java	328
server/catgenome/src/main/java/com/epam/catgenome/dao/index/indexer/FeatureIndexBuilder.java	12
server/catgenome/src/main/java/com/epam/catgenome/dao/index/indexer/BigVcfFeatureIndexBuilder.java	136
server/catgenome/src/main/java/com/epam/catgenome/dao/index/indexer/VcfDocumentBuilder.java	187
server/catgenome/src/main/java/com/epam/catgenome/dao/index/indexer/GeneDocumentBuilder.java	134
server/catgenome/src/main/java/com/epam/catgenome/dao/index/indexer/AbstractDocumentBuilder.java	209
server/catgenome/src/main/java/com/epam/catgenome/dao/homolog/HomologGroupDao.java	99
server/catgenome/src/main/java/com/epam/catgenome/dao/homolog/HomologGeneDomainDao.java	92
server/catgenome/src/main/java/com/epam/catgenome/dao/homolog/HomologGeneDescDao.java	103
server/catgenome/src/main/java/com/epam/catgenome/dao/homolog/HomologGeneAliasDao.java	80
server/catgenome/src/main/java/com/epam/catgenome/dao/homolog/HomologDatabaseDao.java	66
server/catgenome/src/main/java/com/epam/catgenome/dao/homolog/HomologGroupGeneDao.java	145
server/catgenome/src/main/java/com/epam/catgenome/dao/pathway/PathwayDao.java	132
server/catgenome/src/main/java/com/epam/catgenome/dao/pathway/PathwayOrganismDao.java	89
server/catgenome/src/main/java/com/epam/catgenome/dao/seg/SegFileDao.java	169
server/catgenome/src/main/java/com/epam/catgenome/dao/heatmap/HeatmapDao.java	275
server/catgenome/src/main/java/com/epam/catgenome/dao/metadata/MetadataDao.java	112
server/catgenome/src/main/java/com/epam/catgenome/dao/pdb/PdbFileDao.java	134
server/catgenome/src/main/java/com/epam/catgenome/dao/reference/ReferenceGenomeDao.java	446
server/catgenome/src/main/java/com/epam/catgenome/dao/reference/SpeciesDao.java	87
server/catgenome/src/main/java/com/epam/catgenome/dao/reference/BookmarkDao.java	217
server/catgenome/src/main/java/com/epam/catgenome/dao/DaoHelper.java	75
server/catgenome/src/main/java/com/epam/catgenome/dao/session/NGBSessionDao.java	166
server/catgenome/src/main/java/com/epam/catgenome/component/MessageHelper.java	40
server/catgenome/src/main/java/com/epam/catgenome/component/MessageCode.java	25
server/catgenome/src/main/java/com/epam/catgenome/controller/AbstractRESTController.java	69
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ExonViewPortQuery.java	17
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ProjectItemVO.java	29
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/registration/IndexedFileRegistrationRequest.java	25
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/registration/ReferenceRegistrationRequest.java	40
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/registration/FeatureIndexedFileRegistrationRequest.java	10
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/registration/HeatmapRegistrationRequest.java	17
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/registration/FileRegistrationRequest.java	25
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/registration/PathwayRegistrationRequest.java	15
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/registration/BioPAXRegistrationRequest.java	11
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/registration/LineageTreeRegistrationRequest.java	11
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/registration/DefaultFileRegistrationRequest.java	24
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/IDList.java	9
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/BookmarkVO.java	34
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/converter/BookmarkConverter.java	75
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/converter/UniprotConverter.java	107
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/converter/ProjectConverter.java	118
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/FilesVO.java	34
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/security/PermissionVO.java	12
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/security/EntityWithPermissionVO.java	13
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/security/PermissionGrantVO.java	12
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/VcfTrackQuery.java	10
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/SpeciesVO.java	11
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/Query2TrackConverter.java	39
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/BookmarkItemVO.java	69
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/GeneSearchQuery.java	19
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/RoleVO.java	9
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ga4gh/ReferenceSet.java	69
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ga4gh/CallSetSearch.java	22
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ga4gh/VariantsGA4GH.java	64
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ga4gh/VariantGA4GH.java	57
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ga4gh/ReferenceBasesGA4GH.java	28
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ga4gh/GenotypeGA4GH.java	58
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ga4gh/ReferenceGA4GH.java	40
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ga4gh/ReferenceBound.java	21
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ga4gh/VariantsSearch.java	22
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ga4gh/VariantCall.java	43
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ga4gh/VariantSet.java	57
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ga4gh/VariantSetMetadata.java	66
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ga4gh/CallSet.java	38
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ItemsByProject.java	24
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/UrlRequestVO.java	20
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/TrackQuery.java	60
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/RegionQuery.java	31
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ReadSequenceVO.java	10
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ProjectVO.java	26
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ReadQuery.java	45
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/NCBITaxonomyVO.java	20
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/NCBIShortVarVO.java	157
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/UniprotEntryVO.java	67
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/NCBIVariationVO.java	110
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/NCBIGeneVO.java	305
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/NCBISummaryVO.java	141
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/ensemblevo/EnsemblDBBaseVO.java	16
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/ensemblevo/EnsemblTranscriptVO.java	20
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/ensemblevo/EnsemblExonVO.java	16
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/ensemblevo/EnsemblVariationEntryVO.java	47
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/ensemblevo/EnsemblEntryVO.java	20
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/ensemblevo/EnsemblTranslationVO.java	14
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/ensemblevo/EnsemblBaseVO.java	12
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/ensemblevo/EnsemblFullBaseVO.java	16
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/NCBIClinVarVO.java	119
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/externaldb/NCBIStructVarVO.java	14
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/ExonRangeQuery.java	17
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/sequence/LocalSequenceRequest.java	13
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/sequence/SequenceDatabase.java	10
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/NgbUserVO.java	8
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/AbstractExonQuery.java	31
server/catgenome/src/main/java/com/epam/catgenome/controller/vo/TaskVO.java	25
server/catgenome/src/main/java/com/epam/catgenome/controller/tools/FeatureFileSortRequest.java	24
server/catgenome/src/main/java/com/epam/catgenome/controller/tools/ToolsController.java	37
server/catgenome/src/main/java/com/epam/catgenome/controller/bed/BedController.java	124
server/catgenome/src/main/java/com/epam/catgenome/controller/llm/LLMController.java	69
server/catgenome/src/main/java/com/epam/catgenome/controller/patents/PatentsController.java	98
server/catgenome/src/main/java/com/epam/catgenome/controller/security/PermissionController.java	94
server/catgenome/src/main/java/com/epam/catgenome/controller/person/RoleController.java	127
server/catgenome/src/main/java/com/epam/catgenome/controller/person/UserController.java	151
server/catgenome/src/main/java/com/epam/catgenome/controller/wig/WigController.java	77
server/catgenome/src/main/java/com/epam/catgenome/controller/bam/BamCoverageController.java	95
server/catgenome/src/main/java/com/epam/catgenome/controller/bam/BamController.java	157
server/catgenome/src/main/java/com/epam/catgenome/controller/dataitem/DataItemController.java	129
server/catgenome/src/main/java/com/epam/catgenome/controller/gene/ProteinSequenceVariationQuery.java	26
server/catgenome/src/main/java/com/epam/catgenome/controller/gene/GeneController.java	399
server/catgenome/src/main/java/com/epam/catgenome/controller/project/ProjectController.java	515
server/catgenome/src/main/java/com/epam/catgenome/controller/vcf/VcfController.java	221
server/catgenome/src/main/java/com/epam/catgenome/controller/UtilsController.java	193
server/catgenome/src/main/java/com/epam/catgenome/controller/lineage/LineageTreeController.java	87
server/catgenome/src/main/java/com/epam/catgenome/controller/ExceptionHandlerAdvice.java	53
server/catgenome/src/main/java/com/epam/catgenome/controller/compound/CompoundController.java	31
server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/ExternalDBController.java	352
server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/TaxonomyController.java	61
server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/HomologController.java	63
server/catgenome/src/main/java/com/epam/catgenome/controller/externaldb/HomologeneController.java	62
server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastUtilController.java	35
server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastController.java	172
server/catgenome/src/main/java/com/epam/catgenome/controller/blast/BlastDatabaseController.java	73
server/catgenome/src/main/java/com/epam/catgenome/controller/pathway/PathwayController.java	130
server/catgenome/src/main/java/com/epam/catgenome/controller/seg/SegController.java	79
server/catgenome/src/main/java/com/epam/catgenome/controller/heatmap/HeatmapController.java	158
server/catgenome/src/main/java/com/epam/catgenome/controller/filter/FilterController.java	245
server/catgenome/src/main/java/com/epam/catgenome/controller/Result.java	49
server/catgenome/src/main/java/com/epam/catgenome/controller/sequence/SequenceController.java	49
server/catgenome/src/main/java/com/epam/catgenome/controller/JsonMapper.java	64
server/catgenome/src/main/java/com/epam/catgenome/controller/metadata/MetadataController.java	44
server/catgenome/src/main/java/com/epam/catgenome/controller/pdb/PdbFileController.java	112
server/catgenome/src/main/java/com/epam/catgenome/controller/reference/BookmarkController.java	58
server/catgenome/src/main/java/com/epam/catgenome/controller/reference/CytobandController.java	71
server/catgenome/src/main/java/com/epam/catgenome/controller/reference/ReferenceController.java	387
server/catgenome/src/main/java/com/epam/catgenome/controller/ResultStatus.java	7
server/catgenome/src/main/java/com/epam/catgenome/controller/session/SessionController.java	87
server/catgenome/src/main/java/com/epam/catgenome/manager/AuthManager.java	59
server/catgenome/src/main/java/com/epam/catgenome/manager/BiologicalDataItemManager.java	191
server/catgenome/src/main/java/com/epam/catgenome/manager/maf/MafFileManager.java	75
server/catgenome/src/main/java/com/epam/catgenome/manager/maf/parser/SequenceSource.java	50
server/catgenome/src/main/java/com/epam/catgenome/manager/maf/parser/MafCodec.java	125
server/catgenome/src/main/java/com/epam/catgenome/manager/maf/parser/MutationStatus.java	30
server/catgenome/src/main/java/com/epam/catgenome/manager/maf/parser/NggbMafFeature.java	316
server/catgenome/src/main/java/com/epam/catgenome/manager/maf/parser/MafFeature.java	39
server/catgenome/src/main/java/com/epam/catgenome/manager/maf/parser/VariantClassification.java	54
server/catgenome/src/main/java/com/epam/catgenome/manager/maf/parser/ValidationStatus.java	26
server/catgenome/src/main/java/com/epam/catgenome/manager/maf/parser/VerificationStatus.java	22
server/catgenome/src/main/java/com/epam/catgenome/manager/maf/MafManager.java	234
server/catgenome/src/main/java/com/epam/catgenome/manager/SecuredEntityManager.java	8
server/catgenome/src/main/java/com/epam/catgenome/manager/parallel/ParallelTaskExecutionUtils.java	24
server/catgenome/src/main/java/com/epam/catgenome/manager/parallel/TreeListMultiset.java	117
server/catgenome/src/main/java/com/epam/catgenome/manager/parallel/BamTrackTask.java	6
server/catgenome/src/main/java/com/epam/catgenome/manager/parallel/TaskExecutorService.java	86
server/catgenome/src/main/java/com/epam/catgenome/manager/tools/ToolSecurityService.java	15
server/catgenome/src/main/java/com/epam/catgenome/manager/tools/ToolsManager.java	44
server/catgenome/src/main/java/com/epam/catgenome/manager/UpdateItemPathManager.java	185
server/catgenome/src/main/java/com/epam/catgenome/manager/bed/BedManager.java	522
server/catgenome/src/main/java/com/epam/catgenome/manager/bed/BedFileManager.java	89
server/catgenome/src/main/java/com/epam/catgenome/manager/bed/parser/NggbSimpleBedFeature.java	133
server/catgenome/src/main/java/com/epam/catgenome/manager/bed/parser/NggbMultiFormatBedCodec.java	85
server/catgenome/src/main/java/com/epam/catgenome/manager/bed/parser/NggbMultiFormatBedFeature.java	110
server/catgenome/src/main/java/com/epam/catgenome/manager/bed/parser/NggbBedCodec.java	194
server/catgenome/src/main/java/com/epam/catgenome/manager/bed/parser/NggbBedFeature.java	21
server/catgenome/src/main/java/com/epam/catgenome/manager/bed/BedSecurityService.java	49
server/catgenome/src/main/java/com/epam/catgenome/manager/llm/CustomLLMApi.java	8
server/catgenome/src/main/java/com/epam/catgenome/manager/llm/OpenAIChatGPT35.java	58
server/catgenome/src/main/java/com/epam/catgenome/manager/llm/LLMService.java	83
server/catgenome/src/main/java/com/epam/catgenome/manager/llm/CustomOpenAILLMClient.java	24
server/catgenome/src/main/java/com/epam/catgenome/manager/llm/LLMSecurityService.java	34
server/catgenome/src/main/java/com/epam/catgenome/manager/llm/GCPPaLM2.java	185
server/catgenome/src/main/java/com/epam/catgenome/manager/llm/OpenAIChatGPT40.java	58
server/catgenome/src/main/java/com/epam/catgenome/manager/llm/OpenAIClient.java	64
server/catgenome/src/main/java/com/epam/catgenome/manager/llm/CustomLLMApiClient.java	30
server/catgenome/src/main/java/com/epam/catgenome/manager/llm/CustomLLMHandler.java	57
server/catgenome/src/main/java/com/epam/catgenome/manager/llm/LLMHandler.java	35
server/catgenome/src/main/java/com/epam/catgenome/manager/person/PersonManager.java	52
server/catgenome/src/main/java/com/epam/catgenome/manager/FeatureIndexSecurityService.java	109
server/catgenome/src/main/java/com/epam/catgenome/manager/activity/ActivityService.java	31
server/catgenome/src/main/java/com/epam/catgenome/manager/TrackHelper.java	188
server/catgenome/src/main/java/com/epam/catgenome/manager/wig/reader/BedGraphCodec.java	53
server/catgenome/src/main/java/com/epam/catgenome/manager/wig/reader/BedGraphFeature.java	39
server/catgenome/src/main/java/com/epam/catgenome/manager/wig/reader/BedGraphReader.java	25
server/catgenome/src/main/java/com/epam/catgenome/manager/wig/WigSecurityService.java	29
server/catgenome/src/main/java/com/epam/catgenome/manager/wig/FacadeWigManager.java	201
server/catgenome/src/main/java/com/epam/catgenome/manager/wig/BedGraphProcessor.java	147
server/catgenome/src/main/java/com/epam/catgenome/manager/wig/AbstractWigProcessor.java	35
server/catgenome/src/main/java/com/epam/catgenome/manager/wig/WigFileManager.java	78
server/catgenome/src/main/java/com/epam/catgenome/manager/wig/WigProcessor.java	169
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/filters/RightSAMRecordFilter.java	26
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/filters/MiddleSAMRecordFilter.java	22
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/filters/LeftSAMRecordFilter.java	26
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/filters/Filter.java	10
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/BamCoverageManager.java	319
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/sifters/ConstantMemorySAMRecordSampler.java	112
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/sifters/DownsamplingSifter.java	12
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/sifters/FullResultSifter.java	38
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/sifters/StandardSAMRecordSifter.java	106
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/BamFileManager.java	71
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/BlatSearchManager.java	59
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/PSLRecordParser.java	84
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/BamHelper.java	490
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/BamSecurityService.java	51
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/BamTrackEmitter.java	73
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/handlers/Handler.java	16
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/handlers/SAMRecordHandler.java	389
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/BamCoverageSecurityService.java	38
server/catgenome/src/main/java/com/epam/catgenome/manager/bam/BamManager.java	204
server/catgenome/src/main/java/com/epam/catgenome/manager/dataitem/DataItemManager.java	206
server/catgenome/src/main/java/com/epam/catgenome/manager/dataitem/DataItemSecurityService.java	56
server/catgenome/src/main/java/com/epam/catgenome/manager/protein/ProteinSequenceSecurityService.java	39
server/catgenome/src/main/java/com/epam/catgenome/manager/protein/ProteinSequenceManager.java	367
server/catgenome/src/main/java/com/epam/catgenome/manager/protein/ProteinSequenceReconstructionManager.java	404
server/catgenome/src/main/java/com/epam/catgenome/manager/UrlShorterManager.java	42
server/catgenome/src/main/java/com/epam/catgenome/manager/user/UserManager.java	162
server/catgenome/src/main/java/com/epam/catgenome/manager/user/UserSecurityService.java	74
server/catgenome/src/main/java/com/epam/catgenome/manager/user/RoleSecurityService.java	52
server/catgenome/src/main/java/com/epam/catgenome/manager/user/RoleManager.java	135
server/catgenome/src/main/java/com/epam/catgenome/manager/CompositeSecuredEntityManager.java	44
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/reader/GffReader.java	123
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/reader/GeneIndexIterator.java	52
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/reader/GtfReader.java	120
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/reader/AbstractGeneReader.java	511
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/GeneFileManager.java	104
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/GeneUtils.java	277
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/GeneTrackManager.java	210
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/parser/GffFeature.java	244
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/parser/GffCodec.java	88
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/parser/GtfFeature.java	67
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/parser/StrandSerializable.java	37
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/parser/GeneFeature.java	19
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/GeneActivityService.java	123
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/GeneSecurityService.java	118
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/writer/Gff3FeatureImpl.java	242
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/writer/Gff3Feature.java	62
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/writer/Gff3Writer.java	123
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/writer/Gff3Codec.java	58
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/writer/Gff3Constants.java	12
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/writer/Gff3BaseData.java	106
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/featurecounts/FeatureCountsToGffConvertor.java	190
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/featurecounts/FeatureCountsParserUtils.java	25
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/featurecounts/FeatureCountsLineProcessor.java	100
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/GeneRegisterer.java	429
server/catgenome/src/main/java/com/epam/catgenome/manager/gene/GffManager.java	875
server/catgenome/src/main/java/com/epam/catgenome/manager/project/ProjectDescriptionService.java	87
server/catgenome/src/main/java/com/epam/catgenome/manager/project/ProjectManager.java	525
server/catgenome/src/main/java/com/epam/catgenome/manager/project/ProjectSecurityService.java	99
server/catgenome/src/main/java/com/epam/catgenome/manager/GeneInfo.java	20
server/catgenome/src/main/java/com/epam/catgenome/manager/DownloadFileManager.java	136
server/catgenome/src/main/java/com/epam/catgenome/manager/vcf/reader/AbstractVcfReader.java	52
server/catgenome/src/main/java/com/epam/catgenome/manager/vcf/reader/VcfReader.java	15
server/catgenome/src/main/java/com/epam/catgenome/manager/vcf/reader/VcfFileReader.java	567
server/catgenome/src/main/java/com/epam/catgenome/manager/vcf/reader/VcfGa4ghReader.java	645
server/catgenome/src/main/java/com/epam/catgenome/manager/vcf/VcfManager.java	772
server/catgenome/src/main/java/com/epam/catgenome/manager/vcf/VcfSecurityService.java	91
server/catgenome/src/main/java/com/epam/catgenome/manager/vcf/VcfFileManager.java	103
server/catgenome/src/main/java/com/epam/catgenome/manager/bucket/BucketManager.java	54
server/catgenome/src/main/java/com/epam/catgenome/manager/lineage/LineageTreeSecurityService.java	37
server/catgenome/src/main/java/com/epam/catgenome/manager/lineage/LineageTreeManager.java	221
server/catgenome/src/main/java/com/epam/catgenome/manager/cloud/pipeline/CloudPipelineManager.java	44
server/catgenome/src/main/java/com/epam/catgenome/manager/genepred/GenePredUtils.java	20
server/catgenome/src/main/java/com/epam/catgenome/manager/genepred/GenePredManager.java	124
server/catgenome/src/main/java/com/epam/catgenome/manager/FeatureIndexManager.java	611
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/homologene/HomologeneSearchRequest.java	12
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/homologene/HomologeneManager.java	502
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/homologene/HomologeneSecurityService.java	31
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ParameterNameValue.java	30
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/OpenTargetsManager.java	59
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ExtenalDBUtils.java	133
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/patents/GooglePatentManager.java	144
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/patents/PatentsManager.java	183
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/patents/PatentsSecurityService.java	49
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/NCBIGeneInfoManager.java	152
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/util/NCBIDatabase.java	51
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/util/NCBISequenceDatabase.java	10
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/util/NCBIUtility.java	7
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/NCBIShortVarManager.java	175
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/NCBIEnsemblIdsManager.java	100
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/parser/NCBIGeneInfoParser.java	283
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/NCBISequencesManager.java	38
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/NCBIGeneIdsManager.java	54
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/NCBIClinVarManager.java	36
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/NCBIStructVarManager.java	26
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/NCBIAuxiliaryManager.java	145
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/NCBIDataManager.java	277
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/ncbi/NCBIGeneManager.java	278
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/pug/NCBIPugManager.java	209
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/pug/NCBIPugSecurityService.java	16
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/HttpDataManager.java	210
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/SearchResult.java	14
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/taxonomy/TaxonomySecurityService.java	26
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/taxonomy/TaxonomyManager.java	242
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/taxonomy/Taxonomy.java	12
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/EnsemblDataManager.java	98
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/homolog/HomologSearchRequest.java	12
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/homolog/HomologManager.java	323
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/homolog/HomologSecurityService.java	32
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/PubMedService.java	135
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/ecsbpdbmap/PdbBlock.java	24
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/ecsbpdbmap/Segment.java	35
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/ecsbpdbmap/AlignObject.java	27
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/ecsbpdbmap/Dasalignment.java	24
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/ecsbpdbmap/ObjectFactory.java	20
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/ecsbpdbmap/Alignment.java	24
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/ecsbpdbmap/package-info.java	3
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/dto/FeaturePosition.java	10
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/dto/PolymerEntity.java	30
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/dto/DatasetDTO.java	6
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/dto/Data.java	6
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/dto/PolymerEntityInstance.java	11
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/dto/Structure.java	27
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/dto/StructureRequest.java	129
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/dto/DasalignmentDTO.java	6
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/dto/StructureRequestField.java	10
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/dto/Entry.java	23
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/dto/InstanceFeature.java	9
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/Dataset.java	24
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/ObjectFactory.java	11
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/rcsbpbd/Record.java	66
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/Assay.java	174
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/MapLoc.java	137
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/RsStruct.java	75
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/Component.java	112
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/ObjectFactory.java	92
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/ExchangeSet.java	242
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/Ss.java	175
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/PrimarySequence.java	56
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/Rs.java	586
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/BaseURL.java	46
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/package-info.java	3
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/Assembly.java	133
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/RsLinkout.java	27
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/bindings/dbsnp/FxnSet.java	115
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/sequence/NCBISequenceManager.java	305
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/sequence/SequenceSecurityService.java	28
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/pdb/PdbEntriesManager.java	335
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/pdb/PdbDataManager.java	137
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/pdb/PdbStructureField.java	19
server/catgenome/src/main/java/com/epam/catgenome/manager/externaldb/UniprotDataManager.java	37
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/BlastUtilManager.java	97
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/dto/TaskPage.java	11
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/dto/BlastRequestResult.java	11
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/dto/BlastRequest.java	17
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/dto/CreateDatabaseRequest.java	19
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/dto/Result.java	31
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/dto/BlastRequestInfo.java	12
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/dto/CreateDatabaseResponse.java	11
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/dto/Entry.java	37
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/BlastDatabaseManager.java	47
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/BlastTaskManager.java	284
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/BlastDatabaseSecurityService.java	32
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/BlastTaskSecurityService.java	72
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/BlastUtilSecurityService.java	17
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/BlastTaskScheduledService.java	53
server/catgenome/src/main/java/com/epam/catgenome/manager/blast/BlastRequestManager.java	102
server/catgenome/src/main/java/com/epam/catgenome/manager/index/FieldInfo.java	13
server/catgenome/src/main/java/com/epam/catgenome/manager/index/AbstractIndexManager.java	215
server/catgenome/src/main/java/com/epam/catgenome/manager/index/OrderInfo.java	11
server/catgenome/src/main/java/com/epam/catgenome/manager/index/CaseInsensitiveWhitespaceAnalyzer.java	14
server/catgenome/src/main/java/com/epam/catgenome/manager/index/SearchRequest.java	18
server/catgenome/src/main/java/com/epam/catgenome/manager/index/Filter.java	14
server/catgenome/src/main/java/com/epam/catgenome/manager/UpdateItemPathScheduledService.java	21
server/catgenome/src/main/java/com/epam/catgenome/manager/pathway/PathwayManager.java	490
server/catgenome/src/main/java/com/epam/catgenome/manager/pathway/PathwaySecurityService.java	51
server/catgenome/src/main/java/com/epam/catgenome/manager/aws/S3Manager.java	65
server/catgenome/src/main/java/com/epam/catgenome/manager/seg/SegFileManager.java	82
server/catgenome/src/main/java/com/epam/catgenome/manager/seg/SegManager.java	198
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server/catgenome/src/main/java/com/epam/catgenome/manager/seg/parser/SegFeature.java	7
server/catgenome/src/main/java/com/epam/catgenome/manager/seg/parser/NggbSegFeature.java	64
server/catgenome/src/main/java/com/epam/catgenome/manager/seg/SegSecurityService.java	30
server/catgenome/src/main/java/com/epam/catgenome/manager/FileManager.java	1503
server/catgenome/src/main/java/com/epam/catgenome/manager/heatmap/HeatmapSecurityService.java	65
server/catgenome/src/main/java/com/epam/catgenome/manager/heatmap/HeatmapManager.java	431
server/catgenome/src/main/java/com/epam/catgenome/manager/export/VcfExportFilterForm.java	10
server/catgenome/src/main/java/com/epam/catgenome/manager/export/GeneExportFilterForm.java	10
server/catgenome/src/main/java/com/epam/catgenome/manager/export/ExportField.java	6
server/catgenome/src/main/java/com/epam/catgenome/manager/export/ExportManager.java	147
server/catgenome/src/main/java/com/epam/catgenome/manager/export/ExcelExportUtils.java	60
server/catgenome/src/main/java/com/epam/catgenome/manager/export/VcfField.java	61
server/catgenome/src/main/java/com/epam/catgenome/manager/export/GeneField.java	51
server/catgenome/src/main/java/com/epam/catgenome/manager/export/ExportUtils.java	43
server/catgenome/src/main/java/com/epam/catgenome/manager/sequence/SequencesManager.java	214
server/catgenome/src/main/java/com/epam/catgenome/manager/genbank/NGBGenbankReader.java	73
server/catgenome/src/main/java/com/epam/catgenome/manager/genbank/GenbankManager.java	176
server/catgenome/src/main/java/com/epam/catgenome/manager/genbank/GenbankUtils.java	52
server/catgenome/src/main/java/com/epam/catgenome/manager/genbank/GeneType.java	75
server/catgenome/src/main/java/com/epam/catgenome/manager/metadata/MetadataManager.java	80
server/catgenome/src/main/java/com/epam/catgenome/manager/metadata/MetadataSecurityService.java	19
server/catgenome/src/main/java/com/epam/catgenome/manager/pdb/PdbFileField.java	15
server/catgenome/src/main/java/com/epam/catgenome/manager/pdb/PdbFileSecurityService.java	44
server/catgenome/src/main/java/com/epam/catgenome/manager/pdb/PdbFileManager.java	184
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/ReferenceSecurityService.java	127
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/io/FastaIndex.java	96
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/io/ChromosomeReferenceSequence.java	93
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/io/FastaUtils.java	164
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/io/NibDataReader.java	395
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/io/cytoband/CytobandReader.java	123
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/io/cytoband/CytobandRecord.java	24
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/io/FastaSequenceFile.java	87
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/io/NibDataWriter.java	194
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/ReferenceManager.java	482
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/ReferenceGenomeManager.java	347
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/MotifSearchManager.java	567
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/BookmarkManager.java	96
server/catgenome/src/main/java/com/epam/catgenome/manager/reference/CytobandManager.java	98
server/catgenome/src/main/java/com/epam/catgenome/manager/session/NGBSessionManager.java	60
server/catgenome/src/main/java/com/epam/catgenome/manager/session/NGBSessionSecurityService.java	42
server/catgenome/src/main/java/com/epam/catgenome/constant/MessagesConstants.java	220
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server/catgenome/src/main/java/com/epam/catgenome/exception/HistogramReadingException.java	8
server/catgenome/src/main/java/com/epam/catgenome/exception/ResponseException.java	9
server/catgenome/src/main/java/com/epam/catgenome/exception/DownloadingTimeoutException.java	9
server/catgenome/src/main/java/com/epam/catgenome/exception/CloudPipelineUnavailableException.java	9
server/catgenome/src/main/java/com/epam/catgenome/exception/S3ReadingException.java	6
server/catgenome/src/main/java/com/epam/catgenome/exception/NgbException.java	6
server/catgenome/src/main/java/com/epam/catgenome/exception/ExternalDbUnavailableException.java	9
server/catgenome/src/main/java/com/epam/catgenome/exception/FeatureFileReadingException.java	12
server/catgenome/src/main/java/com/epam/catgenome/exception/RegistrationException.java	9
server/catgenome/src/main/java/com/epam/catgenome/exception/UnsupportedGeneFileTypeException.java	7
server/catgenome/src/main/java/com/epam/catgenome/exception/AlignmentException.java	6
server/catgenome/src/main/java/com/epam/catgenome/exception/TMapException.java	6
server/catgenome/src/main/java/com/epam/catgenome/exception/FileParsingException.java	9
server/catgenome/src/main/java/com/epam/catgenome/exception/IndexException.java	9
server/catgenome/src/main/java/com/epam/catgenome/exception/SortingException.java	12
server/catgenome/src/main/java/com/epam/catgenome/exception/TargetGenesException.java	6
server/catgenome/src/main/java/com/epam/catgenome/exception/FeatureIndexException.java	14
server/catgenome/src/main/java/com/epam/catgenome/exception/Ga4ghResourceUnavailableException.java	6
server/catgenome/src/main/java/com/epam/catgenome/exception/HistogramWritingException.java	6
server/catgenome/src/main/java/com/epam/catgenome/exception/GeneReadingException.java	16
server/catgenome/src/main/java/com/epam/catgenome/exception/VcfReadingException.java	12
server/catgenome/src/main/java/com/epam/catgenome/exception/ReferenceReadingException.java	11
server/catgenome/src/main/java/com/epam/catgenome/exception/SamAlignmentException.java	6
server/catgenome/src/main/java/com/epam/catgenome/exception/TargetUpdateException.java	6
server/catgenome/src/main/java/com/epam/catgenome/exception/BlastRequestException.java	9
server/catgenome/src/main/java/com/epam/catgenome/exception/BedFileParsingException.java	9
server/catgenome/src/main/java/com/epam/catgenome/client/TokenInterceptor.java	18
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server/catgenome/src/main/java/com/epam/catgenome/client/cloud/pipeline/CloudPipelineApi.java	21
server/catgenome/src/main/java/com/epam/catgenome/client/blast/BlastApi.java	31
server/catgenome/src/main/java/com/epam/catgenome/client/blast/BlastApiBuilder.java	75
server/catgenome/src/main/java/com/epam/catgenome/client/CookieInterceptor.java	18
client/index.js	3
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export-templates/target-identification/src/model/types/structures.ts	32
export-templates/target-identification/src/model/types/total-counts.ts	29
export-templates/target-identification/src/model/types/bibliography.ts	8
export-templates/target-identification/src/model/types/known-drugs.ts	66
export-templates/target-identification/src/model/types/associated-diseases.ts	47
export-templates/target-identification/src/model/types/index.ts	50
export-templates/target-identification/src/model/types/comparative-genomics.ts	11
export-templates/target-identification/src/model/types/sequences.ts	20
export-templates/target-identification/src/model/utilities.ts	35
export-templates/target-identification/src/model/main.ts	127
export-templates/target-identification/src/model/sorted-data.ts	67
export-templates/target-identification/src/model/paged-data.ts	28
export-templates/target-identification/src/model/base/use-injected-data.ts	9
export-templates/target-identification/src/model/filtered-data.ts	263
export-templates/target-identification/src/style.css	33