SparseVectorWriter

Full name SMRUCC.genomics.Model.MotifGraph.ProteinStructure.FamilyCluster.SparseVectorWriter Assembly SMRUCC.genomics.Model.MotifGraph.ProteinStructure Members 12

stream-friendly (coordinate list) writer / reader for the per-sequence TF-IDF sparse vectors produced by the first pass of the streaming pipeline.

the on-disk layout is deliberately simple and append-friendly so that the first pass can keep a single opened BufferedStream and emit one row per sequence without ever holding the whole matrix in memory:

vectors.coo : tab-separated " <TAB> <TAB> " lines, grouped by row.
titles.idx : JSON array mapping -> original sequence title, written once at the end.
meta.json : number of rows / columns so the second pass knows the matrix shape.

01 Syntax

SMRUCC.genomics.Model.MotifGraph.ProteinStructure.FamilyCluster.SparseVectorWriter

02 Methods

Name	Overloads	Summary
.ctor	1	reader-only constructor (column count is loaded from meta when needed)
OpenForWrite	1	open the append stream for writing COO rows (call once before SparseVectorWriter.WriteRow()))
WriteRow	1	write one sequence as a set of COO triples; the row index is implied by call order.
ReadRows	1	stream the COO rows back in order, yielding (rowIndex, title, columnIndices, values) blocks.
CloseForWrite	1
LoadMeta	1
LoadTitleIndex	1

03 Properties

Name	Overloads	Summary
RowCount	1
ColumnCount	1

04 Fields

Name	Overloads	Summary
COO_FILE	1
TITLE_INDEX_FILE	1
META_FILE	1

05 Members

method .ctor #

#ctor(String)

reader-only constructor (column count is loaded from meta when needed)

method OpenForWrite #

OpenForWrite

open the append stream for writing COO rows (call once before SparseVectorWriter.WriteRow())

method WriteRow #

WriteRow(String, Int32(), Double())

write one sequence as a set of COO triples; the row index is implied by call order.

method ReadRows #

ReadRows

stream the COO rows back in order, yielding (rowIndex, title, columnIndices, values) blocks. the caller feeds each block into the next stage (SVD) so the whole matrix is never materialized at once.

field COO_FILE #

COO_FILE

field TITLE_INDEX_FILE #

TITLE_INDEX_FILE

field META_FILE #

META_FILE

property RowCount #

RowCount

property ColumnCount #

ColumnCount

method CloseForWrite #

CloseForWrite()

method LoadMeta #

LoadMeta(String)

method LoadTitleIndex #

LoadTitleIndex(String)