diamondcli/org.veupathdb.lib.cli.diamond.commands

Package-level declarations

Types

interface BlastN : DiamondCommandConfig, AdvancedGeneralOptionContainer, AdvancedClusteringAlignmentOptionContainer, AdvancedQueryOptionContainer, HiddenOptionContainer

interface BlastP : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, GeneralOutputHeaderOptionContainer, GeneralOutputOptionContainer, AlignerClusteringRealignOptionContainer, AlignerClusteringOptionContainer, AlignerGeneralOptionContainer, AlignerSensitivityOptionContainer, AlignerViewOptionContainer, OutputFormatOptionContainer, AdvancedGeneralOptionContainer, AdvancedClusteringAlignmentOptionContainer, AdvancedQueryOptionContainer, ViewAlignOptionContainer, HiddenOptionContainer

interface BlastX : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, GeneralOutputHeaderOptionContainer, GeneralOutputOptionContainer, AlignerClusteringRealignOptionContainer, AlignerClusteringOptionContainer, AlignerGeneralOptionContainer, AlignerSensitivityOptionContainer, AlignerViewOptionContainer, OutputFormatOptionContainer, AdvancedGeneralOptionContainer, AdvancedClusteringAlignmentOptionContainer, AdvancedQueryOptionContainer, ViewAlignOptionContainer, HiddenOptionContainer

interface Cluster : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, GeneralOutputHeaderOptionContainer, GeneralOutputOptionContainer, AlignerClusteringRealignOptionContainer, AlignerClusteringOptionContainer, ClusteringGeneralOptionContainer, ClusteringReassignOptionContainer, AdvancedGeneralOptionContainer, AdvancedClusteringAlignmentOptionContainer, HiddenOptionContainer

interface ClusterRealign : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, GeneralOutputHeaderOptionContainer, GeneralOutputOptionContainer, AlignerClusteringRealignOptionContainer, OutputFormatOptionContainer, ClusteringInputOptionContainer, HiddenOptionContainer

interface DBInfo : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, HiddenOptionContainer

interface DeepClustering : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, GeneralOutputHeaderOptionContainer, GeneralOutputOptionContainer, AlignerClusteringRealignOptionContainer, AlignerClusteringOptionContainer, ClusteringGeneralOptionContainer, ClusteringReassignOptionContainer, AdvancedGeneralOptionContainer, AdvancedClusteringAlignmentOptionContainer, HiddenOptionContainer

DiamondCommandConfig

sealed interface DiamondCommandConfig

interface GetSeq : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, GeneralOutputOptionContainer, HiddenOptionContainer

GreedyVortexCover

interface GreedyVortexCover : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, GeneralOutputHeaderOptionContainer, GeneralOutputOptionContainer, ClusteringReassignOptionContainer, HiddenOptionContainer

interface LinearCluster : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, GeneralOutputHeaderOptionContainer, GeneralOutputOptionContainer, AlignerClusteringRealignOptionContainer, AlignerClusteringOptionContainer, ClusteringGeneralOptionContainer, ClusteringReassignOptionContainer, AdvancedGeneralOptionContainer, AdvancedClusteringAlignmentOptionContainer, HiddenOptionContainer

interface MakeDB : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, AdvancedGeneralOptionContainer, HiddenOptionContainer

interface MakeIndex : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, AlignerSensitivityOptionContainer, HiddenOptionContainer

interface MergeDAA : DiamondCommandConfig, GeneralOptionContainer, GeneralOutputOptionContainer, HiddenOptionContainer

interface PrepDB : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, HiddenOptionContainer

ReassignClusters

interface ReassignClusters : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, GeneralOutputHeaderOptionContainer, GeneralOutputOptionContainer, AlignerClusteringRealignOptionContainer, AlignerClusteringOptionContainer, ClusteringReassignOptionContainer, ClusteringInputOptionContainer, AdvancedGeneralOptionContainer, AdvancedClusteringAlignmentOptionContainer, HiddenOptionContainer

RecomputeClustering

interface RecomputeClustering : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, GeneralOutputHeaderOptionContainer, GeneralOutputOptionContainer, AlignerClusteringRealignOptionContainer, AlignerClusteringOptionContainer, ClusteringGeneralOptionContainer, ClusteringReassignOptionContainer, ClusteringInputOptionContainer, AdvancedClusteringAlignmentOptionContainer, HiddenOptionContainer

interface View : DiamondCommandConfig, GeneralOptionContainer, GeneralDBOptionContainer, GeneralOutputHeaderOptionContainer, GeneralOutputOptionContainer, AlignerViewOptionContainer, OutputFormatOptionContainer, ViewAlignOptionContainer, HiddenOptionContainer