189     : m_PssmInput(input), m_PssmInputFreqRatios(NULL)  in CPssmEngine()
197     : m_PssmInput(NULL), m_PssmInputFreqRatios(input)  in CPssmEngine()
204 CPssmEngine::CPssmEngine(IPssmInputCdd* input) : m_PssmInput(NULL),  in CPssmEngine()
287     if (m_PssmInput) {  in Run()
378     _ASSERT(m_PssmInput);  in x_CreatePssmFromMsa()
380     m_PssmInput->Process();  in x_CreatePssmFromMsa()
381     s_Validate(m_PssmInput);  in x_CreatePssmFromMsa()
386         PSICreatePssmWithDiagnostics(m_PssmInput->GetData(),  in x_CreatePssmFromMsa()
387                                      m_PssmInput->GetOptions(),  in x_CreatePssmFromMsa()
389                                      m_PssmInput->GetDiagnosticsRequest(),  in x_CreatePssmFromMsa()
400     retval = x_PSIMatrix2Asn1(pssm, m_PssmInput->GetMatrixName(),   in x_CreatePssmFromMsa()
401                               m_PssmInput->GetOptions(), diagnostics);  in x_CreatePssmFromMsa()
402     CRef<CBioseq> query = m_PssmInput->GetQueryForPssm();  in x_CreatePssmFromMsa()
588     return (m_PssmInput ?   in x_GetQuery()
589             m_PssmInput->GetQuery() : m_PssmInputFreqRatios->GetQuery());  in x_GetQuery()
595     return (m_PssmInput ?  in x_GetQueryLength()
596             m_PssmInput->GetQueryLength() :  in x_GetQueryLength()
603     return (m_PssmInput ?  in x_GetMatrixName()
604             m_PssmInput->GetMatrixName() :  in x_GetMatrixName()
611     return (m_PssmInput ?  in x_GetGapExistence()
612             m_PssmInput->GetGapExistence() :  in x_GetGapExistence()
619     return (m_PssmInput ?  in x_GetGapExtension()
620             m_PssmInput->GetGapExtension() :  in x_GetGapExtension()