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API Docs / SMRUCC.genomics.Model.MotifGraph.ProteinStructure

SMRUCC.genomics.Model.MotifGraph.ProteinStructure 1.0.9762.7562.

Namespaces 6 Types 31 Members 156

01 Namespaces

SMRUCC.genomics.Model.MotifGraph.ProteinStructure

TypeSummary Members
CDHitFamilyExport 1
CreateMatrix Create sgt embedding matrix 2
FamilyExports 4
GenomeMetabolicEmbedding 1
KmerTFIDFVectorizer 1
MorganFingerprint help for make embedding a sequence to vector 0

SMRUCC.genomics.Model.MotifGraph.ProteinStructure.FamilyCluster

TypeSummary Members
ApproxKnnBuilder block-wise approximate nearest-neighbour builder for the streaming pipeline. 5
BlockLouvain community detection stage of the streaming pipeline. 5
ClusteringResult full result of the unsupervised protein family clustering pipeline. 18
KmerVocabulary Extracts kmer features from a protein sequence database and selects a top-N vocabulary used as the fixed dictionary for the TF-IDF vectorization step. 13
ProteinFamily a single protein family discovered by the unsupervised clustering pipeline 5
ProteinFamilyClustering unsupervised protein family clustering pipeline. 13
SparseVectorWriter stream-friendly (coordinate list) writer / reader for the per-sequence TF-IDF sparse vectors produced by the first pass of the streaming pipeline. 12
StreamingClustering streaming orchestrator for the unsupervised protein-family clustering pipeline. 9
SvdBlockReducer block-wise randomized SVD reducer for the streaming pipeline. 5

SMRUCC.genomics.Model.MotifGraph.ProteinStructure.FamilyCluster.KmerVocabulary

TypeSummary Members
SortMode how kmers are ranked before the top-N slice is taken 4

SMRUCC.genomics.Model.MotifGraph.ProteinStructure.Kmer

TypeSummary Members
KMerGraph k-mer graph 1

SMRUCC.genomics.Model.MotifGraph.ProteinStructure.Linclust

TypeSummary Members
CascadeFilter 1
Cluster 单个聚类簇 4
ClusterExporter 1
ClusterResult 聚类结果 4
FastPass 快速过滤结果 10
GreedyCover 1
KmerEntry 16 字节 k-mer 记录行 8
KmerGroup 一个 k-mer 组(共享同一 k-mer 的全部序列) 2
KmerTable 3
Linclust 3
LinclustOptions Linclust 运行配置 7
ReducedAlphabet 7
RollingHash 4

SMRUCC.genomics.Model.MotifGraph.ProteinStructure.Linclust.RollingHash

TypeSummary Members
KmerHash 单个 k-mer 的哈希结果:哈希值 + 在序列中的位置 2