Defined in file scoremat.asn
C++ class: CPssm

Pssm ::= SEQUENCE {

    -- Is the this a protein or nucleotide scoring matrix?
    isProtein       BOOLEAN DEFAULT TRUE,	

    -- PSSM identifier
    identifier      Object-id OPTIONAL,	

    -- The dimensions of the matrix are returned so the client can
    -- verify that all data was received.

    numRows         INTEGER,	-- number of rows
    numColumns      INTEGER,	-- number of columns

    -- row-labels is given to note the order of residue types so that it can
    -- be cross-checked between applications.
    -- If this field is not given, the matrix values are presented in 
    -- order of the alphabet ncbistdaa is used for protein, ncbi4na for nucl.
    -- for proteins the values returned correspond to 
    -- (-,-), (-,A), (-,B), (-,C) ... (A,-), (A,A), (A,B), (A,C) ...
    rowLabels       SEQUENCE OF VisibleString OPTIONAL,

    -- are matrices stored row by row?
    byRow           BOOLEAN DEFAULT FALSE, 

    -- PSSM representative sequence (master) 
    query           Seq-entry OPTIONAL,           

    -- both intermediateData and finalData can be provided, but at least one of
    -- them must be provided.
    -- N.B.: by default PSI-BLAST will return the PSSM in its PssmIntermediateData 
    -- representation. 

    -- Intermediate or final data for the PSSM
    intermediateData    PssmIntermediateData OPTIONAL,

    -- Final representation for the PSSM
    finalData           PssmFinalData OPTIONAL