blast_args.cpp

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/* $Id: blast_args.cpp 101043 2023-10-19 14:38:29Z camacho $
* ===========================================================================
*
*                            PUBLIC DOMAIN NOTICE
*               National Center for Biotechnology Information
*
*  This software/database is a "United States Government Work" under the
*  terms of the United States Copyright Act.  It was written as part of
*  the author's offical duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
*  to the public for use. The National Library of Medicine and the U.S.
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*
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*  and reliability of the software and data, the NLM and the U.S.
*  Government do not and cannot warrant the performance or results that
*  may be obtained by using this software or data. The NLM and the U.S.
*  Government disclaim all warranties, express or implied, including
*  warranties of performance, merchantability or fitness for any particular
*  purpose.
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*  Please cite the author in any work or product based on this material.
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/*****************************************************************************
 
File name: blast_args.cpp
 
Author: Jason Papadopoulos
 
******************************************************************************/
 
/** @file blast_args.cpp
 * convert blast-related command line
 * arguments into blast options
*/
#include <ncbi_pch.hpp>
#include <corelib/ncbi_system.hpp>
#include <algo/blast/api/version.hpp>
#include <algo/blast/blastinput/blast_args.hpp>
#include <algo/blast/api/blast_exception.hpp>
#include <algo/blast/api/blast_aux.hpp>
#include <algo/blast/api/objmgr_query_data.hpp> /* for CObjMgrQueryFactory */
#include <algo/blast/core/blast_nalookup.h>
#include <algo/blast/core/hspfilter_besthit.h>
#include <objects/scoremat/PssmWithParameters.hpp>
#include <util/format_guess.hpp>
#include <util/line_reader.hpp>
#include <objtools/blast/seqdb_reader/seqdb.hpp>
#include <algo/blast/blastinput/blast_input.hpp>    // for CInputException
#include <algo/winmask/seq_masker_istat_factory.hpp>    // for CSeqMaskerIstatFactory::DiscoverStatType
#include <connect/ncbi_connutil.h>
#include <objtools/align_format/align_format_util.hpp>
 
#include <algo/blast/api/msa_pssm_input.hpp>    // for CPsiBlastInputClustalW
#include <algo/blast/api/pssm_engine.hpp>       // for CPssmEngine
 
#include <objtools/blast/seqdb_reader/seqdbcommon.hpp>
#include <objtools/blast/seqdb_reader/tax4blastsqlite.hpp> // for taxid to their descendant taxids lookup
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(blast)
USING_SCOPE(objects);
USING_SCOPE(align_format);
 
void
IBlastCmdLineArgs::ExtractAlgorithmOptions(const CArgs& /* cmd_line_args */,
                                           CBlastOptions& /* options */)
{}
 
CProgramDescriptionArgs::CProgramDescriptionArgs(const string& program_name,
                                                 const string& program_desc)
    : m_ProgName(program_name), m_ProgDesc(program_desc)
{}
 
void
CProgramDescriptionArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    // program description
    arg_desc.SetUsageContext(m_ProgName, m_ProgDesc + " " +
                             CBlastVersion().Print());
}
 
CTaskCmdLineArgs::CTaskCmdLineArgs(const set<string>& supported_tasks,
                                   const string& default_task)
: m_SupportedTasks(supported_tasks), m_DefaultTask(default_task)
{
    _ASSERT( !m_SupportedTasks.empty() );
    if ( !m_DefaultTask.empty() ) {
        _ASSERT(m_SupportedTasks.find(m_DefaultTask) != m_SupportedTasks.end());
    }
}
 
void
CTaskCmdLineArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("General search options");
    if ( !m_DefaultTask.empty() ) {
        arg_desc.AddDefaultKey(kTask, "task_name", "Task to execute",
                               CArgDescriptions::eString, m_DefaultTask);
    } else {
        arg_desc.AddKey(kTask, "task_name", "Task to execute",
                        CArgDescriptions::eString);
    }
    arg_desc.SetConstraint(kTask, new CArgAllowStringSet(m_SupportedTasks));
    arg_desc.SetCurrentGroup("");
 
}
 
void
CTaskCmdLineArgs::ExtractAlgorithmOptions(const CArgs& /* cmd_line_args */,
                                          CBlastOptions& /* options */)
{
    // N.B.: handling of tasks occurs at the application level to ensure that
    // only relevant tasks are added (@sa CBlastnAppArgs)
}
 
CGenericSearchArgs::CGenericSearchArgs(EBlastProgramType program)
{
    // Only support blastn for now
    if (program == eBlastTypeBlastn) {
        m_QueryIsProtein = false;
        m_IsRpsBlast = false;
        m_ShowPercentIdentity= true;
        m_IsTblastx= false;
        m_IsIgBlast = false;
        m_SuppressSumStats = true;
        m_IsBlastn = true;
    }
    else {
         NCBI_THROW(CInputException, eInvalidInput, "Invalid program");
    }
}
 
void
CGenericSearchArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("General search options");
 
    // evalue cutoff
    if (!m_IsIgBlast) {
        string des = "Expectation value (E) threshold for saving hits. Default = 10";
        if(m_IsBlastn) {
            des += " (1000 for blastn-short)";
        }
        arg_desc.AddOptionalKey(kArgEvalue, "evalue", des, CArgDescriptions::eDouble);
    } else if (m_QueryIsProtein) {
        arg_desc.AddDefaultKey(kArgEvalue, "evalue",
                     "Expectation value (E) threshold for saving hits ",
                     CArgDescriptions::eDouble,
                     NStr::DoubleToString(1.0));
    } else {
        //igblastn
        arg_desc.AddDefaultKey(kArgEvalue, "evalue",
                     "Expectation value (E) threshold for saving hits ",
                     CArgDescriptions::eDouble,
                     NStr::DoubleToString(20.0));
    }
 
    // word size
    // Default values: blastn=11, megablast=28, others=3
    if(!m_IsRpsBlast) {
        const string description = m_QueryIsProtein
            ? "Word size for wordfinder algorithm"
            : "Word size for wordfinder algorithm (length of best perfect match)";
        arg_desc.AddOptionalKey(kArgWordSize, "int_value", description,
                                CArgDescriptions::eInteger);
        arg_desc.SetConstraint(kArgWordSize, m_QueryIsProtein
                               ? new CArgAllowValuesGreaterThanOrEqual(2)
                               : new CArgAllowValuesGreaterThanOrEqual(4));
    }
 
    if ( !m_IsRpsBlast && !m_IsTblastx) {
        // gap open penalty
        arg_desc.AddOptionalKey(kArgGapOpen, "open_penalty",
                                "Cost to open a gap",
                                CArgDescriptions::eInteger);
 
        // gap extend penalty
        arg_desc.AddOptionalKey(kArgGapExtend, "extend_penalty",
                               "Cost to extend a gap",
                               CArgDescriptions::eInteger);
    }
 
 
    if (m_ShowPercentIdentity && !m_IsIgBlast) {
        arg_desc.SetCurrentGroup("Restrict search or results");
        arg_desc.AddOptionalKey(kArgPercentIdentity, "float_value",
                                "Percent identity",
                                CArgDescriptions::eDouble);
        arg_desc.SetConstraint(kArgPercentIdentity,
                               new CArgAllow_Doubles(0.0, 100.0));
    }
 
    if (!m_IsIgBlast) {
        arg_desc.SetCurrentGroup("Restrict search or results");
        arg_desc.AddOptionalKey(kArgQueryCovHspPerc, "float_value",
                            "Percent query coverage per hsp",
                            CArgDescriptions::eDouble);
        arg_desc.SetConstraint(kArgQueryCovHspPerc,
                           new CArgAllow_Doubles(0.0, 100.0));
 
        arg_desc.AddOptionalKey(kArgMaxHSPsPerSubject, "int_value",
                           "Set maximum number of HSPs per subject sequence to save for each query",
                           CArgDescriptions::eInteger);
        arg_desc.SetConstraint(kArgMaxHSPsPerSubject,
                           new CArgAllowValuesGreaterThanOrEqual(1));
 
        arg_desc.SetCurrentGroup("Extension options");
        // ungapped X-drop
        // Default values: blastn=20, megablast=10, others=7
        arg_desc.AddOptionalKey(kArgUngappedXDropoff, "float_value",
                            "X-dropoff value (in bits) for ungapped extensions",
                            CArgDescriptions::eDouble);
        
        // Tblastx is ungapped only.
        if (!m_IsTblastx) {
         // initial gapped X-drop
         // Default values: blastn=30, megablast=20, tblastx=0, others=15
            arg_desc.AddOptionalKey(kArgGappedXDropoff, "float_value",
                 "X-dropoff value (in bits) for preliminary gapped extensions",
                 CArgDescriptions::eDouble);
 
         // final gapped X-drop
         // Default values: blastn/megablast=50, tblastx=0, others=25
            arg_desc.AddOptionalKey(kArgFinalGappedXDropoff, "float_value",
                         "X-dropoff value (in bits) for final gapped alignment",
                         CArgDescriptions::eDouble);
        }
    }
    arg_desc.SetCurrentGroup("Statistical options");
    // effective search space
    // Default value is the real size
    arg_desc.AddOptionalKey(kArgEffSearchSpace, "int_value",
                            "Effective length of the search space",
                            CArgDescriptions::eInt8);
    arg_desc.SetConstraint(kArgEffSearchSpace,
                           new CArgAllowValuesGreaterThanOrEqual(0));
 
    if (!m_SuppressSumStats) {
        arg_desc.AddOptionalKey(kArgSumStats, "bool_value",
                            "Use sum statistics",
                            CArgDescriptions::eBoolean);
    }
 
    arg_desc.SetCurrentGroup("");
}
 
void
CGenericSearchArgs::ExtractAlgorithmOptions(const CArgs& args,
                                            CBlastOptions& opt)
{
    if (args.Exist(kArgEvalue) && args[kArgEvalue]) {
        opt.SetEvalueThreshold(args[kArgEvalue].AsDouble());
    }
 
    int gap_open=0, gap_extend=0;
    if (args.Exist(kArgMatrixName) && args[kArgMatrixName])
         BLAST_GetProteinGapExistenceExtendParams
             (args[kArgMatrixName].AsString().c_str(), &gap_open, &gap_extend);
 
    if (args.Exist(kArgGapOpen) && args[kArgGapOpen]) {
        opt.SetGapOpeningCost(args[kArgGapOpen].AsInteger());
    }
    else if (args.Exist(kArgMatrixName) && args[kArgMatrixName]) {
        opt.SetGapOpeningCost(gap_open);
    }
 
    if (args.Exist(kArgGapExtend) && args[kArgGapExtend]) {
        opt.SetGapExtensionCost(args[kArgGapExtend].AsInteger());
    }
    else if (args.Exist(kArgMatrixName) && args[kArgMatrixName]) {
        opt.SetGapExtensionCost(gap_extend);
    }
 
    if (args.Exist(kArgUngappedXDropoff) && args[kArgUngappedXDropoff]) {
        opt.SetXDropoff(args[kArgUngappedXDropoff].AsDouble());
    }
 
    if (args.Exist(kArgGappedXDropoff) && args[kArgGappedXDropoff]) {
        opt.SetGapXDropoff(args[kArgGappedXDropoff].AsDouble());
    }
 
    if (args.Exist(kArgFinalGappedXDropoff) && args[kArgFinalGappedXDropoff]) {
        opt.SetGapXDropoffFinal(args[kArgFinalGappedXDropoff].AsDouble());
    }
 
    if ( args.Exist(kArgWordSize) && args[kArgWordSize]) {
        if (m_QueryIsProtein && args[kArgWordSize].AsInteger() > 4){
           opt.SetLookupTableType(eCompressedAaLookupTable);
           opt.SetWordThreshold(19.3);
           if (args[kArgWordSize].AsInteger() > 5) {
               opt.SetWordThreshold(21.0);
           }
           if (args[kArgWordSize].AsInteger() > 6) {
               opt.SetWordThreshold(20.25);
           }
        }
        opt.SetWordSize(args[kArgWordSize].AsInteger());
 
    }
 
    if (args.Exist(kArgEffSearchSpace) && args[kArgEffSearchSpace]) {
        CNcbiEnvironment env;
        env.Set("OLD_FSC", "true");
        opt.SetEffectiveSearchSpace(args[kArgEffSearchSpace].AsInt8());
    }
 
    if (args.Exist(kArgPercentIdentity) && args[kArgPercentIdentity]) {
        opt.SetPercentIdentity(args[kArgPercentIdentity].AsDouble());
    }
 
    if (args.Exist(kArgQueryCovHspPerc) && args[kArgQueryCovHspPerc]) {
        opt.SetQueryCovHspPerc(args[kArgQueryCovHspPerc].AsDouble());
    }
 
    if (args.Exist(kArgMaxHSPsPerSubject) && args[kArgMaxHSPsPerSubject]) {
        opt.SetMaxHspsPerSubject(args[kArgMaxHSPsPerSubject].AsInteger());
    }
 
    if (args.Exist(kArgSumStats) && args[kArgSumStats]) {
        opt.SetSumStatisticsMode(args[kArgSumStats].AsBoolean());
    }
}
 
void
CFilteringArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("Query filtering options");
 
    if (m_QueryIsProtein) {
        arg_desc.AddDefaultKey(kArgSegFiltering, "SEG_options",
                        "Filter query sequence with SEG "
                        "(Format: '" + kDfltArgApplyFiltering + "', " +
                        "'window locut hicut', or '" + kDfltArgNoFiltering +
                        "' to disable)",
                        CArgDescriptions::eString, m_FilterByDefault
                        ? kDfltArgSegFiltering : kDfltArgNoFiltering);
        arg_desc.AddDefaultKey(kArgLookupTableMaskingOnly, "soft_masking",
                        "Apply filtering locations as soft masks",
                        CArgDescriptions::eBoolean,
                        kDfltArgLookupTableMaskingOnlyProt);
    } else {
        arg_desc.AddOptionalKey(kArgDustFiltering, "DUST_options",
                        "Filter query sequence with DUST "
                        "(Format: '" + kDfltArgApplyFiltering + "', " +
                        "'level window linker', or '" + kDfltArgNoFiltering +
                        "' to disable) Default = '20 64 1' ('" + kDfltArgNoFiltering + "' for blastn-short)",
                        CArgDescriptions::eString);
        arg_desc.AddOptionalKey(kArgFilteringDb, "filtering_database",
                "BLAST database containing filtering elements (i.e.: repeats)",
                CArgDescriptions::eString);
 
        arg_desc.AddOptionalKey(kArgWindowMaskerTaxId, "window_masker_taxid",
                "Enable WindowMasker filtering using a Taxonomic ID",
                CArgDescriptions::eInteger);
 
        arg_desc.AddOptionalKey(kArgWindowMaskerDatabase, "window_masker_db",
                "Enable WindowMasker filtering using this repeats database.",
                CArgDescriptions::eString);
 
        arg_desc.AddDefaultKey(kArgLookupTableMaskingOnly, "soft_masking",
                        "Apply filtering locations as soft masks",
                        CArgDescriptions::eBoolean,
                        kDfltArgLookupTableMaskingOnlyNucl);
    }
 
    arg_desc.SetCurrentGroup("");
}
 
void
CFilteringArgs::x_TokenizeFilteringArgs(const string& filtering_args,
                                        vector<string>& output) const
{
    output.clear();
    NStr::Split(filtering_args, " ", output);
    if (output.size() != 3) {
        NCBI_THROW(CInputException, eInvalidInput,
                   "Invalid number of arguments to filtering option");
    }
}
 
void
CFilteringArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt)
{
    if (args[kArgLookupTableMaskingOnly]) {
        opt.SetMaskAtHash(args[kArgLookupTableMaskingOnly].AsBoolean());
    }
 
    vector<string> tokens;
 
    try {
        if (m_QueryIsProtein && args[kArgSegFiltering]) {
            const string& seg_opts = args[kArgSegFiltering].AsString();
            if (seg_opts == kDfltArgNoFiltering) {
                opt.SetSegFiltering(false);
            } else if (seg_opts == kDfltArgApplyFiltering) {
                opt.SetSegFiltering(true);
            } else {
                x_TokenizeFilteringArgs(seg_opts, tokens);
                opt.SetSegFilteringWindow(NStr::StringToInt(tokens[0]));
                opt.SetSegFilteringLocut(NStr::StringToDouble(tokens[1]));
                opt.SetSegFilteringHicut(NStr::StringToDouble(tokens[2]));
            }
        }
 
        if ( !m_QueryIsProtein && args[kArgDustFiltering]) {
            const string& dust_opts = args[kArgDustFiltering].AsString();
            if (dust_opts == kDfltArgNoFiltering) {
                opt.SetDustFiltering(false);
            } else if (dust_opts == kDfltArgApplyFiltering) {
                opt.SetDustFiltering(true);
            } else {
                x_TokenizeFilteringArgs(dust_opts, tokens);
                opt.SetDustFilteringLevel(NStr::StringToInt(tokens[0]));
                opt.SetDustFilteringWindow(NStr::StringToInt(tokens[1]));
                opt.SetDustFilteringLinker(NStr::StringToInt(tokens[2]));
            }
        }
    } catch (const CStringException& e) {
        if (e.GetErrCode() == CStringException::eConvert) {
            NCBI_THROW(CInputException, eInvalidInput,
                       "Invalid input for filtering parameters");
        }
    }
 
    int filter_dbs = 0;
 
    if (args.Exist(kArgFilteringDb) && args[kArgFilteringDb]) {
        opt.SetRepeatFilteringDB(args[kArgFilteringDb].AsString().c_str());
        filter_dbs++;
    }
 
    if (args.Exist(kArgWindowMaskerTaxId) &&
        args[kArgWindowMaskerTaxId]) {
 
        opt.SetWindowMaskerTaxId
            (args[kArgWindowMaskerTaxId].AsInteger());
 
        filter_dbs++;
    }
 
    if (args.Exist(kArgWindowMaskerDatabase) &&
        args[kArgWindowMaskerDatabase]) {
        const string& stat_file = args[kArgWindowMaskerDatabase].AsString();
        const CSeqMaskerIstatFactory::EStatType type =
            CSeqMaskerIstatFactory::DiscoverStatType(stat_file);
        if (type != CSeqMaskerIstatFactory::eOBinary &&
            type != CSeqMaskerIstatFactory::eBinary) {
            string msg("Only optimized binary windowmasker stat files are supported");
            NCBI_THROW(CInputException, eInvalidInput, msg);
        }
 
        opt.SetWindowMaskerDatabase(stat_file.c_str());
        filter_dbs++;
    }
 
    if (filter_dbs > 1) {
        string msg =
            string("Please specify at most one of ") + kArgFilteringDb + ", " +
            kArgWindowMaskerTaxId + ", or " + kArgWindowMaskerDatabase + ".";
 
        NCBI_THROW(CInputException, eInvalidInput, msg);
    }
}
 
void
CWindowSizeArg::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("Extension options");
    // 2-hit wordfinder window size
    arg_desc.AddOptionalKey(kArgWindowSize, "int_value",
                            "Multiple hits window size, use 0 to specify "
                            "1-hit algorithm",
                            CArgDescriptions::eInteger);
    arg_desc.SetConstraint(kArgWindowSize,
                           new CArgAllowValuesGreaterThanOrEqual(0));
    arg_desc.SetCurrentGroup("");
}
 
void
CWindowSizeArg::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt)
{
    if (args[kArgWindowSize]) {
        opt.SetWindowSize(args[kArgWindowSize].AsInteger());
    } else {
        int window = -1;
        BLAST_GetSuggestedWindowSize(opt.GetProgramType(),
                                     opt.GetMatrixName(),
                                     &window);
        if (window != -1) {
            opt.SetWindowSize(window);
        }
    }
}
 
void
COffDiagonalRangeArg::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("Extension options");
    // 2-hit wordfinder off diagonal range
    arg_desc.AddDefaultKey(kArgOffDiagonalRange, "int_value",
                            "Number of off-diagonals to search for the 2nd hit, "
                            "use 0 to turn off",
                            CArgDescriptions::eInteger,
                            NStr::IntToString(kDfltOffDiagonalRange));
    arg_desc.SetConstraint(kArgOffDiagonalRange,
                           new CArgAllowValuesGreaterThanOrEqual(0));
    arg_desc.SetCurrentGroup("");
}
 
void
COffDiagonalRangeArg::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt)
{
    if (args[kArgOffDiagonalRange]) {
        opt.SetOffDiagonalRange(args[kArgOffDiagonalRange].AsInteger());
    } else {
        opt.SetOffDiagonalRange(0);
    }
}
 
// Options specific to rmblastn -RMH-
void
CRMBlastNArg::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("General search options");
 
    arg_desc.AddDefaultKey(kArgMatrixName, "matrix_name",
                           "Scoring matrix name",
                           CArgDescriptions::eString,
                           string(""));
 
    arg_desc.AddFlag(kArgComplexityAdj,
                     "Use complexity adjusted scoring",
                     true);
 
 
    arg_desc.AddDefaultKey(kArgMaskLevel, "int_value",
                            "Masklevel - percentage overlap allowed per "
                            "query domain [0-101]",
                            CArgDescriptions::eInteger,
                            kDfltArgMaskLevel);
    arg_desc.SetConstraint(kArgMaskLevel,
                           new CArgAllowValuesLessThanOrEqual(101));
 
    arg_desc.SetCurrentGroup("");
}
 
// Options specific to rmblastn -RMH-
void
CRMBlastNArg::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt)
{
    if (args[kArgMatrixName]) {
        opt.SetMatrixName(args[kArgMatrixName].AsString().c_str());
    }
 
    opt.SetComplexityAdjMode( args[kArgComplexityAdj] );
 
    if (args[kArgMaskLevel]) {
        opt.SetMaskLevel(args[kArgMaskLevel].AsInteger());
    }
 
    if (args[kArgMinRawGappedScore]) {
        opt.SetCutoffScore(args[kArgMinRawGappedScore].AsInteger());
    }else if (args[kArgUngappedXDropoff]) {
        opt.SetCutoffScore(args[kArgUngappedXDropoff].AsInteger());
    }
}
 
void
CWordThresholdArg::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("General search options");
    // lookup table word score threshold
    arg_desc.AddOptionalKey(kArgWordScoreThreshold, "float_value",
                 "Minimum word score such that the word is added to the "
                 "BLAST lookup table",
                 CArgDescriptions::eDouble);
    arg_desc.SetConstraint(kArgWordScoreThreshold,
                           new CArgAllowValuesGreaterThanOrEqual(0));
    arg_desc.SetCurrentGroup("");
}
 
static bool
s_IsDefaultWordThreshold(EProgram program, double threshold)
{
    int word_threshold = static_cast<int>(threshold);
    bool retval = true;
    if (program == eBlastp &&
        word_threshold != BLAST_WORD_THRESHOLD_BLASTP) {
        retval = false;
    } else if (program == eBlastx &&
        word_threshold != BLAST_WORD_THRESHOLD_BLASTX) {
        retval = false;
    } else if (program == eTblastn &&
               word_threshold != BLAST_WORD_THRESHOLD_TBLASTN) {
        retval = false;
    }
    return retval;
}
 
void
CWordThresholdArg::ExtractAlgorithmOptions(const CArgs& args,
                                           CBlastOptions& opt)
{
    if (args[kArgWordScoreThreshold]) {
        opt.SetWordThreshold(args[kArgWordScoreThreshold].AsDouble());
    } else if (s_IsDefaultWordThreshold(opt.GetProgram(),
                                        opt.GetWordThreshold())) {
        double threshold = -1;
        BLAST_GetSuggestedThreshold(opt.GetProgramType(),
                                    opt.GetMatrixName(),
                                    &threshold);
        if (threshold != -1) {
            opt.SetWordThreshold(threshold);
        }
    }
}
 
void
CMatrixNameArg::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("General search options");
    arg_desc.AddOptionalKey(kArgMatrixName, "matrix_name",
                           "Scoring matrix name (normally BLOSUM62)",
                           CArgDescriptions::eString);
    arg_desc.SetCurrentGroup("");
}
 
void
CMatrixNameArg::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& opt)
{
    if (args[kArgMatrixName]) {
        opt.SetMatrixName(args[kArgMatrixName].AsString().c_str());
    }
}
 
void
CNuclArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    // TLM arg_desc.SetCurrentGroup("Nucleotide scoring options");
 
    arg_desc.SetCurrentGroup("General search options");
    // blastn mismatch penalty
    arg_desc.AddOptionalKey(kArgMismatch, "penalty",
                           "Penalty for a nucleotide mismatch",
                           CArgDescriptions::eInteger);
    arg_desc.SetConstraint(kArgMismatch,
                           new CArgAllowValuesLessThanOrEqual(0));
 
    // blastn match reward
    arg_desc.AddOptionalKey(kArgMatch, "reward",
                           "Reward for a nucleotide match",
                           CArgDescriptions::eInteger);
    arg_desc.SetConstraint(kArgMatch,
                           new CArgAllowValuesGreaterThanOrEqual(0));
 
 
    arg_desc.SetCurrentGroup("Extension options");
    arg_desc.AddFlag(kArgNoGreedyExtension,
                     "Use non-greedy dynamic programming extension",
                     true);
 
    arg_desc.SetCurrentGroup("");
}
 
void
CNuclArgs::ExtractAlgorithmOptions(const CArgs& cmd_line_args,
                                   CBlastOptions& options)
{
    if (cmd_line_args.Exist(kArgMismatch) && cmd_line_args[kArgMismatch]) {
        options.SetMismatchPenalty(cmd_line_args[kArgMismatch].AsInteger());
    }
    if (cmd_line_args.Exist(kArgMatch) && cmd_line_args[kArgMatch]) {
        options.SetMatchReward(cmd_line_args[kArgMatch].AsInteger());
    }
 
    if (cmd_line_args.Exist(kArgNoGreedyExtension) &&
        cmd_line_args[kArgNoGreedyExtension]) {
        options.SetGapExtnAlgorithm(eDynProgScoreOnly);
        options.SetGapTracebackAlgorithm(eDynProgTbck);
    }
}
 
const string CDiscontiguousMegablastArgs::kTemplType_Coding("coding");
const string CDiscontiguousMegablastArgs::kTemplType_Optimal("optimal");
const string
CDiscontiguousMegablastArgs::kTemplType_CodingAndOptimal("coding_and_optimal");
 
void
CDiscontiguousMegablastArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("Extension options");
    // FIXME: this can be applied to any program, but since it was only offered
    // in megablast, we're putting it here
    arg_desc.AddOptionalKey(kArgMinRawGappedScore, "int_value",
                            "Minimum raw gapped score to keep an alignment "
                            "in the preliminary gapped and traceback stages",
                            CArgDescriptions::eInteger);
 
    arg_desc.SetCurrentGroup("Discontiguous MegaBLAST options");
 
    arg_desc.AddOptionalKey(kArgDMBTemplateType, "type",
                 "Discontiguous MegaBLAST template type",
                 CArgDescriptions::eString);
    arg_desc.SetConstraint(kArgDMBTemplateType, &(*new CArgAllow_Strings,
                                                  kTemplType_Coding,
                                                  kTemplType_Optimal,
                                                  kTemplType_CodingAndOptimal));
    arg_desc.SetDependency(kArgDMBTemplateType,
                           CArgDescriptions::eRequires,
                           kArgDMBTemplateLength);
 
    arg_desc.AddOptionalKey(kArgDMBTemplateLength, "int_value",
                 "Discontiguous MegaBLAST template length",
                 CArgDescriptions::eInteger);
    set<int> allowed_values;
    allowed_values.insert(16);
    allowed_values.insert(18);
    allowed_values.insert(21);
    arg_desc.SetConstraint(kArgDMBTemplateLength,
                           new CArgAllowIntegerSet(allowed_values));
    arg_desc.SetDependency(kArgDMBTemplateLength,
                           CArgDescriptions::eRequires,
                           kArgDMBTemplateType);
 
    arg_desc.SetCurrentGroup("");
}
 
void
CDiscontiguousMegablastArgs::ExtractAlgorithmOptions(const CArgs& args,
                                                     CBlastOptions& options)
{
    if (args[kArgMinRawGappedScore]) {
        options.SetCutoffScore(args[kArgMinRawGappedScore].AsInteger());
    }
 
    if (args[kArgDMBTemplateType]) {
        const string& type = args[kArgDMBTemplateType].AsString();
        EDiscWordType temp_type = eMBWordCoding;
 
        if (type == kTemplType_Coding) {
            temp_type = eMBWordCoding;
        } else if (type == kTemplType_Optimal) {
            temp_type = eMBWordOptimal;
        } else if (type == kTemplType_CodingAndOptimal) {
            temp_type = eMBWordTwoTemplates;
        } else {
            abort();
        }
        options.SetMBTemplateType(static_cast<unsigned char>(temp_type));
    }
 
    if (args[kArgDMBTemplateLength]) {
        unsigned char tlen =
            static_cast<unsigned char>(args[kArgDMBTemplateLength].AsInteger());
        options.SetMBTemplateLength(tlen);
    }
 
    // FIXME: should the window size be adjusted if this is set?
}
 
void
CCompositionBasedStatsArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("General search options");
    // composition based statistics, keep in sync with ECompoAdjustModes
    // documentation in composition_constants.h
 
    string zero_opt = !m_ZeroOptDescr.empty() ?
        (string)"    0 or F or f: " + m_ZeroOptDescr + "\n" :
        "    0 or F or f: No composition-based statistics\n";
 
    string one_opt_insrt = m_Is2and3Supported ? "" : " or T or t";
 
    string more_opts = m_Is2and3Supported ?
        "    2 or T or t : Composition-based score adjustment as in "
        "Bioinformatics 21:902-911,\n"
        "    2005, conditioned on sequence properties\n"
        "    3: Composition-based score adjustment as in "
        "Bioinformatics 21:902-911,\n"
        "    2005, unconditionally\n" : "";
 
    string legend = (string)"Use composition-based statistics:\n"
        "    D or d: default (equivalent to " + m_DefaultOpt + " )\n"
        + zero_opt
        + "    1" + one_opt_insrt + ": Composition-based statistics "
        "as in NAR 29:2994-3005, 2001\n"
        + more_opts;
 
    arg_desc.AddDefaultKey(kArgCompBasedStats, "compo", legend,
                           CArgDescriptions::eString, m_DefaultOpt);
 
 
    arg_desc.SetCurrentGroup("Miscellaneous options");
    // Use Smith-Waterman algorithm in traceback stage
    // FIXME: available only for gapped blastp/tblastn, and with
    // composition-based statistics
    arg_desc.AddFlag(kArgUseSWTraceback,
                     "Compute locally optimal Smith-Waterman alignments?",
                     true);
    arg_desc.SetCurrentGroup("");
}
 
/**
 * @brief Auxiliary function to set the composition based statistics and smith
 * waterman options
 *
 * @param opt BLAST options object [in|out]
 * @param comp_stat_string command line value for composition based statistics
 * [in]
 * @param smith_waterman_value command line value for determining the use of
 * the smith-waterman algorithm [in]
 * @param ungapped pointer to the value which determines whether the search
 * should be ungapped or not. It is NULL if ungapped searches are not
 * applicable
 * @param is_deltablast is program deltablast [in]
 */
static void
s_SetCompositionBasedStats(CBlastOptions& opt,
                           const string& comp_stat_string,
                           bool smith_waterman_value,
                           bool* ungapped)
{
    const EProgram program = opt.GetProgram();
    if (program == eBlastp || program == eTblastn ||
        program == ePSIBlast || program == ePSITblastn ||
        program == eRPSBlast || program == eRPSTblastn ||
        program == eBlastx  ||  program == eDeltaBlast) {
 
        ECompoAdjustModes compo_mode = eNoCompositionBasedStats;
 
        switch (comp_stat_string[0]) {
            case '0': case 'F': case 'f':
                compo_mode = eNoCompositionBasedStats;
                break;
            case '1':
                compo_mode = eCompositionBasedStats;
                break;
            case 'D': case 'd':
                if ((program == eRPSBlast) || (program == eRPSTblastn)) {
                    compo_mode = eNoCompositionBasedStats;
                }
                else if (program == eDeltaBlast) {
                    compo_mode = eCompositionBasedStats;
                }
                else {
                    compo_mode = eCompositionMatrixAdjust;
                }
                break;
            case '2':
                compo_mode = eCompositionMatrixAdjust;
                break;
            case '3':
                compo_mode = eCompoForceFullMatrixAdjust;
                break;
            case 'T': case 't':
                compo_mode = (program == eRPSBlast || program == eRPSTblastn || program == eDeltaBlast) ?
                    eCompositionBasedStats : eCompositionMatrixAdjust;
                break;
        }
 
        if(program == ePSITblastn) {
            compo_mode = eNoCompositionBasedStats;
        }
 
        if (ungapped && *ungapped && compo_mode != eNoCompositionBasedStats) {
            NCBI_THROW(CInputException, eInvalidInput,
                       "Composition-adjusted searched are not supported with "
                       "an ungapped search, please add -comp_based_stats F or "
                       "do a gapped search");
        }
 
        opt.SetCompositionBasedStats(compo_mode);
        if (program == eBlastp &&
            compo_mode != eNoCompositionBasedStats &&
            tolower(comp_stat_string[1]) == 'u') {
            opt.SetUnifiedP(1);
        }
        opt.SetSmithWatermanMode(smith_waterman_value);
    }
}
 
void
CCompositionBasedStatsArgs::ExtractAlgorithmOptions(const CArgs& args,
                                                    CBlastOptions& opt)
{
    if (args[kArgCompBasedStats]) {
        unique_ptr<bool> ungapped(args.Exist(kArgUngapped)
            ? new bool(args[kArgUngapped]) : 0);
        s_SetCompositionBasedStats(opt,
                                   args[kArgCompBasedStats].AsString(),
                                   args[kArgUseSWTraceback],
                                   ungapped.get());
    }
 
}
 
void
CGappedArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    // perform gapped search
#if 0
    arg_desc.AddOptionalKey(ARG_GAPPED, "gapped",
                 "Perform gapped alignment (default T, but "
                 "not available for tblastx)",
                 CArgDescriptions::eBoolean,
                 CArgDescriptions::fOptionalSeparator);
    arg_desc.AddAlias("-gapped", ARG_GAPPED);
#endif
    arg_desc.SetCurrentGroup("Extension options");
    arg_desc.AddFlag(kArgUngapped, "Perform ungapped alignment only?", true);
    arg_desc.SetCurrentGroup("");
}
 
void
CGappedArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& options)
{
#if 0
    if (args[ARG_GAPPED] && options.GetProgram() != eTblastx) {
        options.SetGappedMode(args[ARG_GAPPED].AsBoolean());
    }
#endif
    options.SetGappedMode( !args[kArgUngapped] );
}
 
void
CLargestIntronSizeArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("General search options");
    // largest intron length
    arg_desc.AddDefaultKey(kArgMaxIntronLength, "length",
                    "Length of the largest intron allowed in a translated "
                    "nucleotide sequence when linking multiple distinct "
                    "alignments",
                    CArgDescriptions::eInteger,
                    NStr::IntToString(kDfltArgMaxIntronLength));
    arg_desc.SetConstraint(kArgMaxIntronLength,
                           new CArgAllowValuesGreaterThanOrEqual(0));
    arg_desc.SetCurrentGroup("");
}
 
void
CLargestIntronSizeArgs::ExtractAlgorithmOptions(const CArgs& args,
                                                CBlastOptions& opt)
{
    if ( !args[kArgMaxIntronLength] ) {
        return;
    }
 
    // sum statistics are defauled to be on unless a cmdline option is set
    opt.SetLongestIntronLength(args[kArgMaxIntronLength].AsInteger());
 
}
 
void
CFrameShiftArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("General search options");
    // applicable in blastx/tblastn, off by default
    arg_desc.AddOptionalKey(kArgFrameShiftPenalty, "frameshift",
                            "Frame shift penalty (for use with out-of-frame "
                            "gapped alignment in blastx or tblastn, default "
                            "ignored)",
                            CArgDescriptions::eInteger);
    arg_desc.SetConstraint(kArgFrameShiftPenalty,
                           new CArgAllowValuesGreaterThanOrEqual(1));
    arg_desc.SetDependency(kArgFrameShiftPenalty, CArgDescriptions::eExcludes,kArgUngapped);
    arg_desc.SetCurrentGroup("");
}
 
void
CFrameShiftArgs::ExtractAlgorithmOptions(const CArgs& args,
                                         CBlastOptions& opt)
{
    if (args[kArgFrameShiftPenalty]) {
        if (args[kArgCompBasedStats]) {
            string cbs = args[kArgCompBasedStats].AsString();
 
            if ((cbs[0] != '0' )&& (cbs[0] != 'F')  &&  (cbs[0] != 'f')) {
                NCBI_THROW(CInputException, eInvalidInput,
                       "Composition-adjusted searches are not supported with "
                       "Out-Of-Frame option, please add -comp_based_stats F ");
            }
        }
 
        opt.SetOutOfFrameMode();
        opt.SetFrameShiftPenalty(args[kArgFrameShiftPenalty].AsInteger());
    }
}
 
/// Auxiliary class to validate the genetic code input
class CArgAllowGeneticCodeInteger : public CArgAllow
{
protected:
     /// Overloaded method from CArgAllow
     virtual bool Verify(const string& value) const {
         static int gcs[] = {1,2,3,4,5,6,9,10,11,12,13,14,15,16,21,22,23,24,25,26,27,28,29,30,31,33};
         static const set<int> genetic_codes(gcs, gcs+sizeof(gcs)/sizeof(*gcs));
         const int val = NStr::StringToInt(value);
         return (genetic_codes.find(val) != genetic_codes.end());
     }
 
     /// Overloaded method from CArgAllow
     virtual string GetUsage(void) const {
         return "values between: 1-6, 9-16, 21-31, 33";
     }
};
 
void
CGeneticCodeArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    if (m_Target == eQuery) {
        arg_desc.SetCurrentGroup("Input query options");
        // query genetic code
        arg_desc.AddDefaultKey(kArgQueryGeneticCode, "int_value",
                               "Genetic code to use to translate query (see https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes for details)\n",
                               CArgDescriptions::eInteger,
                               NStr::IntToString(BLAST_GENETIC_CODE));
        arg_desc.SetConstraint(kArgQueryGeneticCode,
                               new CArgAllowGeneticCodeInteger());
    } else {
        arg_desc.SetCurrentGroup("General search options");
        // DB genetic code
        arg_desc.AddDefaultKey(kArgDbGeneticCode, "int_value",
                               "Genetic code to use to translate "
                               "database/subjects (see user manual for details)\n",
                               CArgDescriptions::eInteger,
                               NStr::IntToString(BLAST_GENETIC_CODE));
        arg_desc.SetConstraint(kArgDbGeneticCode,
                               new CArgAllowGeneticCodeInteger());
 
    }
    arg_desc.SetCurrentGroup("");
}
 
void
CGeneticCodeArgs::ExtractAlgorithmOptions(const CArgs& args,
                                          CBlastOptions& opt)
{
    const EProgram program = opt.GetProgram();
 
    if (m_Target == eQuery && args[kArgQueryGeneticCode]) {
        opt.SetQueryGeneticCode(args[kArgQueryGeneticCode].AsInteger());
    }
 
    if (m_Target == eDatabase && args[kArgDbGeneticCode] &&
        (program == eTblastn || program == eTblastx) ) {
        opt.SetDbGeneticCode(args[kArgDbGeneticCode].AsInteger());
    }
}
 
void
CGapTriggerArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("Extension options");
 
    const double default_value = m_QueryIsProtein
        ? BLAST_GAP_TRIGGER_PROT : BLAST_GAP_TRIGGER_NUCL;
    arg_desc.AddDefaultKey(kArgGapTrigger, "float_value",
                           "Number of bits to trigger gapping",
                           CArgDescriptions::eDouble,
                           NStr::DoubleToString(default_value));
    arg_desc.SetCurrentGroup("");
}
 
void
CGapTriggerArgs::ExtractAlgorithmOptions(const CArgs& args,
                                         CBlastOptions& opt)
{
    if (args[kArgGapTrigger]) {
        opt.SetGapTrigger(args[kArgGapTrigger].AsDouble());
    }
}
 
void
CPssmEngineArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("PSSM engine options");
 
    // Pseudo count
    arg_desc.AddDefaultKey(kArgPSIPseudocount, "pseudocount",
                           "Pseudo-count value used when constructing PSSM",
                           CArgDescriptions::eInteger,
                           NStr::IntToString(PSI_PSEUDO_COUNT_CONST));
 
    if (m_IsDeltaBlast) {
        arg_desc.AddDefaultKey(kArgDomainInclusionEThreshold, "ethresh",
                               "E-value inclusion threshold for alignments "
                               "with conserved domains",
                               CArgDescriptions::eDouble,
                               NStr::DoubleToString(DELTA_INCLUSION_ETHRESH));
    }
 
    // Evalue inclusion threshold
    arg_desc.AddDefaultKey(kArgPSIInclusionEThreshold, "ethresh",
                   "E-value inclusion threshold for pairwise alignments",
                   CArgDescriptions::eDouble,
                   NStr::DoubleToString(PSI_INCLUSION_ETHRESH));
 
    arg_desc.SetCurrentGroup("");
}
 
void
CPssmEngineArgs::ExtractAlgorithmOptions(const CArgs& args,
                                         CBlastOptions& opt)
{
    if (args[kArgPSIPseudocount]) {
        opt.SetPseudoCount(args[kArgPSIPseudocount].AsInteger());
    }
 
    if (args[kArgPSIInclusionEThreshold]) {
        opt.SetInclusionThreshold(args[kArgPSIInclusionEThreshold].AsDouble());
    }
 
    if (args.Exist(kArgDomainInclusionEThreshold)
        && args[kArgDomainInclusionEThreshold]) {
 
        opt.SetDomainInclusionThreshold(
                             args[kArgDomainInclusionEThreshold].AsDouble());
    }
}
 
void
CPsiBlastArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
 
    if (m_DbTarget == eNucleotideDb) {
        arg_desc.SetCurrentGroup("PSI-TBLASTN options");
 
        // PSI-tblastn checkpoint
        arg_desc.AddOptionalKey(kArgPSIInputChkPntFile, "psi_chkpt_file",
                                "PSI-TBLASTN checkpoint file",
                                CArgDescriptions::eInputFile);
        arg_desc.SetDependency(kArgPSIInputChkPntFile,
                                CArgDescriptions::eExcludes,
                                kArgRemote);
    } else {
        arg_desc.SetCurrentGroup("PSI-BLAST options");
 
        // Number of iterations
        arg_desc.AddDefaultKey(kArgPSINumIterations, "int_value",
                               "Number of iterations to perform (0 means run "
                               "until convergence)", CArgDescriptions::eInteger,
                               NStr::IntToString(kDfltArgPSINumIterations));
        arg_desc.SetConstraint(kArgPSINumIterations,
                               new CArgAllowValuesGreaterThanOrEqual(0));
        arg_desc.SetDependency(kArgPSINumIterations,
                               CArgDescriptions::eExcludes,
                               kArgRemote);
        // checkpoint file
        arg_desc.AddOptionalKey(kArgPSIOutputChkPntFile, "checkpoint_file",
 
                                "File name to store checkpoint file",
                                CArgDescriptions::eOutputFile);
        // ASCII matrix file
        arg_desc.AddOptionalKey(kArgAsciiPssmOutputFile, "ascii_mtx_file",
                                "File name to store ASCII version of PSSM",
                                CArgDescriptions::eOutputFile);
 
        arg_desc.AddFlag(kArgSaveLastPssm, "Save PSSM after the last database "
                         "search");
        arg_desc.AddFlag(kArgSaveAllPssms, "Save PSSM after each iteration "
                         "(file name is given in -save_pssm or "
                         "-save_ascii_pssm options)");
 
        if (!m_IsDeltaBlast) {
            vector<string> msa_exclusions;
            msa_exclusions.push_back(kArgPSIInputChkPntFile);
            msa_exclusions.push_back(kArgQuery);
            msa_exclusions.push_back(kArgQueryLocation);
            // pattern and MSA is not supported
            msa_exclusions.push_back(kArgPHIPatternFile);
            arg_desc.SetCurrentGroup("");
            arg_desc.SetCurrentGroup("");
 
            // MSA restart file
            arg_desc.SetCurrentGroup("PSSM engine options");
            arg_desc.AddOptionalKey(kArgMSAInputFile, "align_restart",
                                    "File name of multiple sequence alignment to "
                                    "restart PSI-BLAST",
                                    CArgDescriptions::eInputFile);
            ITERATE(vector<string>, exclusion, msa_exclusions) {
                arg_desc.SetDependency(kArgMSAInputFile,
                                       CArgDescriptions::eExcludes,
                                       *exclusion);
            }
 
            arg_desc.AddOptionalKey(kArgMSAMasterIndex, "index",
                                    "Ordinal number (1-based index) of the sequence"
                                    " to use as a master in the multiple sequence "
                                    "alignment. If not provided, the first sequence"
                                    " in the multiple sequence alignment will be "
                                    "used", CArgDescriptions::eInteger);
            arg_desc.SetConstraint(kArgMSAMasterIndex,
                                   new CArgAllowValuesGreaterThanOrEqual(1));
            ITERATE(vector<string>, exclusion, msa_exclusions) {
                arg_desc.SetDependency(kArgMSAMasterIndex,
                                       CArgDescriptions::eExcludes,
                                       *exclusion);
            }
            arg_desc.SetDependency(kArgMSAMasterIndex,
                                   CArgDescriptions::eRequires,
                                   kArgMSAInputFile);
            arg_desc.SetDependency(kArgMSAMasterIndex,
                                   CArgDescriptions::eExcludes,
                                   kArgIgnoreMsaMaster);
 
            arg_desc.AddFlag(kArgIgnoreMsaMaster,
                             "Ignore the master sequence when creating PSSM", true);
 
            vector<string> ignore_pssm_master_exclusions;
            ignore_pssm_master_exclusions.push_back(kArgMSAMasterIndex);
            ignore_pssm_master_exclusions.push_back(kArgPSIInputChkPntFile);
            ignore_pssm_master_exclusions.push_back(kArgQuery);
            ignore_pssm_master_exclusions.push_back(kArgQueryLocation);
            ITERATE(vector<string>, exclusion, msa_exclusions) {
                arg_desc.SetDependency(kArgIgnoreMsaMaster,
                                       CArgDescriptions::eExcludes,
                                       *exclusion);
            }
            arg_desc.SetDependency(kArgIgnoreMsaMaster,
                                   CArgDescriptions::eRequires,
                                   kArgMSAInputFile);
 
            // PSI-BLAST checkpoint
            arg_desc.AddOptionalKey(kArgPSIInputChkPntFile, "psi_chkpt_file",
                                    "PSI-BLAST checkpoint file",
                                    CArgDescriptions::eInputFile);
            arg_desc.SetDependency(kArgPSIInputChkPntFile,
                                   CArgDescriptions::eExcludes,
                                   kArgRemote);
        }
    }
 
    if (!m_IsDeltaBlast) {
        arg_desc.SetDependency(kArgPSIInputChkPntFile,
                               CArgDescriptions::eExcludes,
                               kArgQuery);
        arg_desc.SetDependency(kArgPSIInputChkPntFile,
                               CArgDescriptions::eExcludes,
                               kArgQueryLocation);
    }
    arg_desc.SetCurrentGroup("");
}
 
CRef<CPssmWithParameters>
CPsiBlastArgs::x_CreatePssmFromMsa(CNcbiIstream& input_stream,
                                   CBlastOptions& opt, bool save_ascii_pssm,
                                   unsigned int msa_master_idx,
                                   bool ignore_pssm_tmplt_seq)
{
    // FIXME get these from CBlastOptions
    CPSIBlastOptions psiblast_opts;
    PSIBlastOptionsNew(&psiblast_opts);
    psiblast_opts->nsg_compatibility_mode = ignore_pssm_tmplt_seq;
 
    CPSIDiagnosticsRequest diags(PSIDiagnosticsRequestNewEx(save_ascii_pssm));
    CPsiBlastInputClustalW pssm_input(input_stream, *psiblast_opts,
                                      opt.GetMatrixName(), diags, NULL, 0,
                                      opt.GetGapOpeningCost(),
                                      opt.GetGapExtensionCost(),
                                      msa_master_idx);
    CPssmEngine pssm_engine(&pssm_input);
    return pssm_engine.Run();
}
 
void
CPsiBlastArgs::ExtractAlgorithmOptions(const CArgs& args,
                                       CBlastOptions& opt)
{
    if (m_DbTarget == eProteinDb) {
        if (args[kArgPSINumIterations]) {
            if(m_NumIterations == 1)
                m_NumIterations = args[kArgPSINumIterations].AsInteger();
        }
 
        if (args.Exist(kArgSaveLastPssm) && args[kArgSaveLastPssm] &&
            (!args.Exist(kArgPSIOutputChkPntFile) ||
             !args[kArgPSIOutputChkPntFile]) &&
            (!args.Exist(kArgAsciiPssmOutputFile) ||
             !args[kArgAsciiPssmOutputFile])) {
 
            NCBI_THROW(CInputException, eInvalidInput, kArgSaveLastPssm +
                       " option requires " + kArgPSIOutputChkPntFile + " or " +
                       kArgAsciiPssmOutputFile);
        }
 
        if (args.Exist(kArgSaveAllPssms) && args[kArgSaveAllPssms] &&
            (!args.Exist(kArgPSIOutputChkPntFile) ||
             !args[kArgPSIOutputChkPntFile]) &&
            (!args.Exist(kArgAsciiPssmOutputFile) ||
             !args[kArgAsciiPssmOutputFile])) {
 
            NCBI_THROW(CInputException, eInvalidInput, kArgSaveAllPssms +
                       " option requires " + kArgPSIOutputChkPntFile + " or " +
                       kArgAsciiPssmOutputFile);
        }
 
        const bool kSaveAllPssms
            = args.Exist(kArgSaveAllPssms) && args[kArgSaveAllPssms];
        if (args.Exist(kArgPSIOutputChkPntFile) &&
            args[kArgPSIOutputChkPntFile]) {
            m_CheckPointOutput.Reset
                (new CAutoOutputFileReset
                 (args[kArgPSIOutputChkPntFile].AsString(), kSaveAllPssms));
        }
        const bool kSaveAsciiPssm = args[kArgAsciiPssmOutputFile];
        if (kSaveAsciiPssm) {
            m_AsciiMatrixOutput.Reset
                (new CAutoOutputFileReset
                 (args[kArgAsciiPssmOutputFile].AsString(), kSaveAllPssms));
        }
        if (args.Exist(kArgMSAInputFile) && args[kArgMSAInputFile]) {
            CNcbiIstream& in = args[kArgMSAInputFile].AsInputFile();
            unsigned int msa_master_idx = 0;
            if (args[kArgMSAMasterIndex]) {
                msa_master_idx = args[kArgMSAMasterIndex].AsInteger() - 1;
            }
            m_Pssm = x_CreatePssmFromMsa(in, opt, kSaveAsciiPssm,
                                         msa_master_idx,
                                         args[kArgIgnoreMsaMaster]);
        }
        if (!m_IsDeltaBlast) {
            opt.SetIgnoreMsaMaster(args[kArgIgnoreMsaMaster]);
        }
 
        if (args.Exist(kArgSaveLastPssm) && args[kArgSaveLastPssm]) {
            m_SaveLastPssm = true;
        }
    }
 
    if (args.Exist(kArgPSIInputChkPntFile) && args[kArgPSIInputChkPntFile]) {
        CNcbiIstream& in = args[kArgPSIInputChkPntFile].AsInputFile();
        _ASSERT(m_Pssm.Empty());
        m_Pssm.Reset(new CPssmWithParameters);
        try {
            switch (CFormatGuess().Format(in)) {
            case CFormatGuess::eBinaryASN:
                in >> MSerial_AsnBinary >> *m_Pssm;
                break;
            case CFormatGuess::eTextASN:
                in >> MSerial_AsnText >> *m_Pssm;
                break;
            case CFormatGuess::eXml:
                in >> MSerial_Xml >> *m_Pssm;
                break;
            default:
                NCBI_THROW(CInputException, eInvalidInput,
                           "Unsupported format for PSSM");
            }
        } catch (const CSerialException&) {
            string msg("Unrecognized format for PSSM in ");
            msg += args[kArgPSIInputChkPntFile].AsString() + " (must be ";
            msg += "PssmWithParameters)";
            NCBI_THROW(CInputException, eInvalidInput, msg);
        }
        _ASSERT(m_Pssm.NotEmpty());
    }
}
 
void
CPhiBlastArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("PHI-BLAST options");
 
    arg_desc.AddOptionalKey(kArgPHIPatternFile, "file",
                            "File name containing pattern to search",
                            CArgDescriptions::eInputFile);
    arg_desc.SetDependency(kArgPHIPatternFile,
                           CArgDescriptions::eExcludes,
                           kArgPSIInputChkPntFile);
 
    arg_desc.SetCurrentGroup("");
}
 
void
CPhiBlastArgs::ExtractAlgorithmOptions(const CArgs& args,
                                       CBlastOptions& opt)
{
    if (args.Exist(kArgPHIPatternFile) && args[kArgPHIPatternFile]) {
        CNcbiIstream& in = args[kArgPHIPatternFile].AsInputFile();
        in.clear();
        in.seekg(0);
        char buffer[4096];
        string line;
        string pattern;
        string name;
        while (in.getline(buffer, 4096)) {
           line = buffer;
           string ltype = line.substr(0, 2);
           if (ltype == "ID")
             name = line.substr(4);
           else if (ltype == "PA")
             pattern = line.substr(4);
        }
        if (!pattern.empty())
            opt.SetPHIPattern(pattern.c_str(),
               (Blast_QueryIsNucleotide(opt.GetProgramType())
               ? true : false));
        else
            NCBI_THROW(CInputException, eInvalidInput,
                       "PHI pattern not read");
    }
}
 
void
CKBlastpArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
   arg_desc.SetCurrentGroup("KBLASTP options");
   arg_desc.AddDefaultKey(kArgJDistance, "threshold", "Jaccard Distance",
            CArgDescriptions::eDouble, kDfltArgJDistance);
   arg_desc.AddDefaultKey(kArgMinHits, "minhits", "minimal number of LSH matches",
            CArgDescriptions::eInteger, kDfltArgMinHits);
   arg_desc.AddDefaultKey(kArgCandidateSeqs, "candidates", "Number of candidate sequences to process with BLAST",
            CArgDescriptions::eInteger, kDfltArgCandidateSeqs);
}
 
void
CKBlastpArgs::ExtractAlgorithmOptions(const CArgs& args,
                                         CBlastOptions& opt)
{
    if (args.Exist(kArgJDistance))
        m_JDistance = args[kArgJDistance].AsDouble();
    if (args.Exist(kArgMinHits))
        m_MinHits = args[kArgMinHits].AsInteger();
    if (args.Exist(kArgCandidateSeqs))
        m_CandidateSeqs = args[kArgCandidateSeqs].AsInteger();
}
 
 
void
CDeltaBlastArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("DELTA-BLAST options");
 
    arg_desc.AddDefaultKey(kArgRpsDb, "database_name", "BLAST domain "
                           "database name", CArgDescriptions::eString,
                           kDfltArgRpsDb);
 
    arg_desc.AddFlag(kArgShowDomainHits, "Show domain hits");
    arg_desc.SetDependency(kArgShowDomainHits, CArgDescriptions::eExcludes,
                           kArgRemote);
    arg_desc.SetDependency(kArgShowDomainHits, CArgDescriptions::eExcludes,
                           kArgSubject);
}
 
void
CDeltaBlastArgs::ExtractAlgorithmOptions(const CArgs& args,
                                         CBlastOptions& opt)
{
    m_DomainDb.Reset(new CSearchDatabase(args[kArgRpsDb].AsString(),
                                         CSearchDatabase::eBlastDbIsProtein));
 
    if (args.Exist(kArgShowDomainHits)) {
        m_ShowDomainHits = args[kArgShowDomainHits];
    }
}
 
void
CMappingArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
 
    arg_desc.SetCurrentGroup("Mapping options");
    arg_desc.AddDefaultKey(kArgScore, "num", "Cutoff score for accepting "
                           "alignments. Can be expressed as a number or a "
                           "function of read length: "
                           "L,b,a for a * length + b.\n"
                           "Zero means that the cutoff score will be equal to:\n"
                           "read length,      if read length <= 20,\n"
                           "20,               if read length <= 30,\n"
                           "read length - 10, if read length <= 50,\n"
                           "40,               otherwise.",
                           CArgDescriptions::eString, "0");
    arg_desc.AddOptionalKey(kArgMaxEditDist, "num", "Cutoff edit distance for "
                            "accepting an alignment\nDefault = unlimited",
                            CArgDescriptions::eInteger);
    arg_desc.AddDefaultKey(kArgSplice, "TF", "Search for spliced alignments",
                           CArgDescriptions::eBoolean, "true");
    arg_desc.AddDefaultKey(kArgRefType, "type", "Type of the reference: "
                           "genome or transcriptome",
                           CArgDescriptions::eString, "genome");
    arg_desc.SetConstraint(kArgRefType,
                        &(*new CArgAllow_Strings, "genome", "transcriptome"));
 
    arg_desc.SetCurrentGroup("Query filtering options");
    arg_desc.AddDefaultKey(kArgLimitLookup, "TF", "Remove word seeds with "
                           "high frequency in the searched database",
                           CArgDescriptions::eBoolean, "true");
    arg_desc.AddDefaultKey(kArgMaxDbWordCount, "num", "Words that appear more "
                           "than this number of times in the database will be"
                           " masked in the lookup table",
                           CArgDescriptions::eInteger,
                           NStr::IntToString(MAX_DB_WORD_COUNT_MAPPER));
    arg_desc.SetConstraint(kArgMaxDbWordCount,
                           new CArgAllowValuesBetween(2, 255, true));
    arg_desc.AddDefaultKey(kArgLookupStride, "num", "Number of words to skip "
                "after collecting one while creating a lookup table",
                 CArgDescriptions::eInteger, "0");
 
    arg_desc.SetCurrentGroup("");
}
 
 
void
CMappingArgs::ExtractAlgorithmOptions(const CArgs& args,
                                      CBlastOptions& opt)
{
    if (args.Exist(kArgScore) && args[kArgScore]) {
 
        string s = args[kArgScore].AsString();
        // score cutoff may be defined as a liner function of query length:
        // L,0.0,0.6 ...
        if (s[0] == 'L') {
            list<string> tokens;
            NStr::Split(s, ",", tokens);
            vector<double> coeffs;
            if (tokens.size() < 3) {
                NCBI_THROW(CInputException, eInvalidInput,
                           (string)"Incorrectly formatted score function: " +
                           s + ". It should be of the form 'L,b,a' for ax + b,"
                           "a, b must be numbers");
            }
            auto it = tokens.begin();
            ++it;
            try {
                for (; it != tokens.end(); ++it) {
                    coeffs.push_back(NStr::StringToDouble(*it));
                }
            }
            catch (CException& e) {
                NCBI_THROW(CInputException, eInvalidInput,
                           (string)"Incorrectly formatted score function: " +
                           s + ". It should be of the form 'L,b,a' for ax + b,"
                           " a, b must be real numbers");
            }
            opt.SetCutoffScoreCoeffs(coeffs);
        }
        else {
            // ... or a numerical constant
            try {
                opt.SetCutoffScore(NStr::StringToInt(s));
            }
            catch (CException&) {
                NCBI_THROW(CInputException, eInvalidInput,
                           (string)"Incorrectly formatted score threshold: " +
                           s + ". It must be either an integer or a linear "
                           "function in the form: L,b,a for ax + b, a and b "
                           "must be real numbers");
            }
        }
    }
 
    if (args.Exist(kArgMaxEditDist) && args[kArgMaxEditDist]) {
        opt.SetMaxEditDistance(args[kArgMaxEditDist].AsInteger());
    }
 
    if (args.Exist(kArgSplice) && args[kArgSplice]) {
        opt.SetSpliceAlignments(args[kArgSplice].AsBoolean());
    }
 
    string ref_type = "genome";
    if (args.Exist(kArgRefType) && args[kArgRefType]) {
        ref_type = args[kArgRefType].AsString();
    }
 
    if (args.Exist(kArgLimitLookup) && args[kArgLimitLookup]) {
        opt.SetLookupDbFilter(args[kArgLimitLookup].AsBoolean());
    }
    else {
        opt.SetLookupDbFilter(ref_type == "genome");
    }
 
    if (args.Exist(kArgMaxDbWordCount) && args[kArgMaxDbWordCount]) {
        opt.SetMaxDbWordCount(args[kArgMaxDbWordCount].AsInteger());
    }
 
    if (args.Exist(kArgLookupStride) && args[kArgLookupStride]) {
        opt.SetLookupTableStride(args[kArgLookupStride].AsInteger());
    }
}
 
 
void
CIgBlastArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("Ig-BLAST options");
    const static char suffix[] = "VDJ";
    const static int df_num_align[3] = {3,3,3};
    int num_genes = (m_IsProtein) ? 1 : 3;
 
 
    for (int gene=0; gene<num_genes; ++gene) {
        // Subject sequence input
        /* TODO disabled for now
        string arg_sub = kArgGLSubject;
        arg_sub.push_back(suffix[gene]);
        arg_desc.AddOptionalKey(arg_sub , "filename",
                            "Germline subject sequence to align",
                            CArgDescriptions::eInputFile);
        */
        // Germline database file name
        string arg_db = kArgGLDatabase;
        arg_db.push_back(suffix[gene]);
        arg_desc.AddOptionalKey(arg_db, "germline_database_name",
                            "Germline database name",
                            CArgDescriptions::eString);
        //arg_desc.SetDependency(arg_db, CArgDescriptions::eExcludes, arg_sub);
        // Number of alignments to show
        string arg_na = kArgGLNumAlign;
        arg_na.push_back(suffix[gene]);
        arg_desc.AddDefaultKey(arg_na, "int_value",
                            "Number of Germline sequences to show alignments for",
                            CArgDescriptions::eInteger,
                            NStr::IntToString(df_num_align[gene]));
        //arg_desc.SetConstraint(arg_na,
        //                   new CArgAllowValuesBetween(0, 4));
        // Seqidlist
        arg_desc.AddOptionalKey(arg_db + "_seqidlist", "filename",
                            "Restrict search of germline database to list of SeqIds's",
                            CArgDescriptions::eString);
    }
 
    if (!m_IsProtein) {
        arg_desc.AddDefaultKey(kArgCRegionNumAlign, "int_value",
                               "Number of Germline sequences to show alignments for",
                               CArgDescriptions::eInteger, "2");
        
        arg_desc.AddOptionalKey(kArgCRegionDatabase, "constant_region_database_name",
                            "C region database name",
                            CArgDescriptions::eString);
        
        arg_desc.AddOptionalKey(kArgCustomInternalData, "filename",
                            "custom internal data file for V region annotation",
                            CArgDescriptions::eString);
 
        arg_desc.AddOptionalKey(kArgDFrameDefinitionFile, "filename",
                                "D gene frame definition file",
                                CArgDescriptions::eString);
 
        arg_desc.AddOptionalKey(kArgGLChainType, "filename",
                            "File containing the coding frame start positions for sequences in germline J database",
                            CArgDescriptions::eString);
 
        arg_desc.AddOptionalKey(kArgMinDMatch, "min_D_match",
                                "Required minimal consecutive nucleotide base matches for D genes ",
                                CArgDescriptions::eInteger);
        arg_desc.SetConstraint(kArgMinDMatch,
                               new CArgAllowValuesGreaterThanOrEqual(5));
 
        arg_desc.AddDefaultKey(kArgVPenalty, "V_penalty",
                                "Penalty for a nucleotide mismatch in V gene",
                                CArgDescriptions::eInteger, "-1");
        arg_desc.SetConstraint(kArgVPenalty,
                               new CArgAllowValuesBetween(-4, 0));
 
 
        arg_desc.AddDefaultKey(kArgDPenalty, "D_penalty",
                                "Penalty for a nucleotide mismatch in D gene",
                                CArgDescriptions::eInteger, "-2");
 
        arg_desc.SetConstraint(kArgDPenalty,
                               new CArgAllowValuesBetween(-5, 0));
 
        arg_desc.AddDefaultKey(kArgJPenalty, "J_penalty",
                                "Penalty for a nucleotide mismatch in J gene",
                                CArgDescriptions::eInteger, "-2");
 
        arg_desc.SetConstraint(kArgJPenalty,
                               new CArgAllowValuesBetween(-4, 0));
 
        arg_desc.AddDefaultKey(kArgNumClonotype, "num_clonotype",
                                "Number of top clonotypes to show ",
                               CArgDescriptions::eInteger, "100");
        arg_desc.SetConstraint(kArgNumClonotype,
                               new CArgAllowValuesGreaterThanOrEqual(0));
 
        arg_desc.AddOptionalKey(kArgClonotypeFile, "clonotype_out",
                                "Output file name for clonotype info",
                               CArgDescriptions::eOutputFile);
 
        arg_desc.AddFlag(kArgDetectOverlap, "Allow V(D)J genes to overlap.  This option is active only when D_penalty and J_penalty are set to -4 and -3, respectively", true);
 
 
    }
 
    arg_desc.AddDefaultKey(kArgGLOrigin, "germline_origin",
                           "The organism for your query sequence. Supported organisms include human, mouse, rat, rabbit and rhesus_monkey for Ig and human and mouse for TCR. Custom organism is also supported but you need to supply your own germline annotations (see IgBLAST web site for details)",
                           CArgDescriptions::eString, "human");
    
    arg_desc.AddDefaultKey(kArgGLDomainSystem, "domain_system",
                           "Domain system to be used for segment annotation",
                           CArgDescriptions::eString, "imgt");
    arg_desc.SetConstraint(kArgGLDomainSystem, &(*new CArgAllow_Strings, "kabat", "imgt"));
 
    arg_desc.AddDefaultKey(kArgIgSeqType, "sequence_type",
                            "Specify Ig or T cell receptor sequence",
                            CArgDescriptions::eString, "Ig");
    arg_desc.SetConstraint(kArgIgSeqType, &(*new CArgAllow_Strings, "Ig", "TCR"));
 
 
    arg_desc.AddFlag(kArgGLFocusV, "Should the search only be for V segment (effective only for non-germline database search using -db option)?", true);
 
    arg_desc.AddFlag(kArgExtendAlign5end, "Extend V gene alignment at 5' end", true);
 
    arg_desc.AddFlag(kArgExtendAlign3end, "Extend J gene alignment at 3' end", true);
 
    arg_desc.AddDefaultKey(kArgMinVLength, "Min_V_Length",
                           "Minimal required V gene length",
                           CArgDescriptions::eInteger, "9");
 
    arg_desc.SetConstraint(kArgMinVLength,
                           new CArgAllowValuesGreaterThanOrEqual(9));
 
    if (! m_IsProtein) {
        arg_desc.AddDefaultKey(kArgMinJLength, "Min_J_Length",
                               "Minimal required J gene length",
                               CArgDescriptions::eInteger, "0");
 
        arg_desc.SetConstraint(kArgMinJLength,
                               new CArgAllowValuesGreaterThanOrEqual(0));
    }
 
    if (! m_IsProtein) {
        arg_desc.AddFlag(kArgTranslate, "Show translated alignments", true);
    }
 
    arg_desc.SetCurrentGroup("");
}
 
static string s_RegisterOMDataLoader(CRef<CSeqDB> db_handle)
{    // the blast formatter requires that the database coexist in
    // the same scope with the query sequences
    CRef<CObjectManager> om = CObjectManager::GetInstance();
    CBlastDbDataLoader::RegisterInObjectManager(*om, db_handle, true,
                        CObjectManager::eDefault,
                        CBlastDatabaseArgs::kSubjectsDataLoaderPriority);
    CBlastDbDataLoader::SBlastDbParam param(db_handle);
    string retval(CBlastDbDataLoader::GetLoaderNameFromArgs(param));
    _TRACE("Registering " << retval << " at priority " <<
           (int)CBlastDatabaseArgs::kSubjectsDataLoaderPriority);
    return retval;
}
 
void
CIgBlastArgs::ExtractAlgorithmOptions(const CArgs& args,
                                      CBlastOptions& opts)
{
    string paths[3];
    CNcbiEnvironment env;
    paths[0] = CDirEntry::NormalizePath(CDir::GetCwd(), eFollowLinks);
    paths[1] = CDirEntry::NormalizePath(env.Get("IGDATA"), eFollowLinks);
    CNcbiApplication* app = CNcbiApplication::Instance();
    if (app) {
        const CNcbiRegistry& registry = app->GetConfig();
        paths[2] = CDirEntry::NormalizePath(registry.Get("BLAST","IGDATA"), eFollowLinks);
    } else {
#if defined(NCBI_OS_DARWIN)
       paths[2] = "/usr/local/ncbi/igblast/data";
#else
       paths[2] = paths[0];
#endif
    }
 
    m_IgOptions.Reset(new CIgBlastOptions());
 
    CBlastDatabaseArgs::EMoleculeType mol_type = Blast_SubjectIsNucleotide(opts.GetProgramType())
        ? CSearchDatabase::eBlastDbIsNucleotide
        : CSearchDatabase::eBlastDbIsProtein;
 
    m_IgOptions->m_IsProtein = (mol_type == CSearchDatabase::eBlastDbIsProtein);
    m_IgOptions->m_Origin = args[kArgGLOrigin].AsString();
    m_IgOptions->m_DomainSystem = args[kArgGLDomainSystem].AsString();
    m_IgOptions->m_FocusV = args.Exist(kArgGLFocusV) ? args[kArgGLFocusV] : false;
    m_IgOptions->m_ExtendAlign5end = args.Exist(kArgExtendAlign5end) ? args[kArgExtendAlign5end] : false;
    m_IgOptions->m_ExtendAlign3end = args.Exist(kArgExtendAlign3end) ? args[kArgExtendAlign3end] : false;
    m_IgOptions->m_DetectOverlap = args.Exist(kArgDetectOverlap) ? args[kArgDetectOverlap] : false;
    m_IgOptions->m_MinVLength = args[kArgMinVLength].AsInteger();
    if (args.Exist(kArgMinJLength) && args[kArgMinJLength]) {
        m_IgOptions->m_MinJLength = args[kArgMinJLength].AsInteger();
    } else {
        m_IgOptions->m_MinJLength = 0;
    }
    m_IgOptions->m_Translate = args.Exist(kArgTranslate) ? args[kArgTranslate] : false;
    m_IgOptions->m_CustomInternalData = NcbiEmptyString;
    m_IgOptions->m_DFrameFileName = NcbiEmptyString;
 
    if (!m_IsProtein) {
        string aux_file = (args.Exist(kArgGLChainType) && args[kArgGLChainType])
                             ? args[kArgGLChainType].AsString()
                             : m_IgOptions->m_Origin + "_gl.aux";
        m_IgOptions->m_AuxFilename = aux_file;
        for (int i=0; i<3; i++) {
            string aux_path = CDirEntry::ConcatPath(paths[i], aux_file);
            CDirEntry entry(aux_path);
            if (entry.Exists() && entry.IsFile()) {
                m_IgOptions->m_AuxFilename = aux_path;
                break;
            }
        }
 
        if (args.Exist(kArgCustomInternalData) && args[kArgCustomInternalData]) {
            m_IgOptions->m_CustomInternalData = args[kArgCustomInternalData].AsString();
        } 
        
        if (args.Exist(kArgDFrameDefinitionFile) && args[kArgDFrameDefinitionFile]) {
            m_IgOptions->m_DFrameFileName = args[kArgDFrameDefinitionFile].AsString();
        } 
    }
 
    _ASSERT(m_IsProtein == m_IgOptions->m_IsProtein);
 
    m_Scope.Reset(new CScope(*CObjectManager::GetInstance()));
 
    // default germline database name for annotation
    for (int i=0; i<3; i++) {
        string int_data = CDirEntry::ConcatPath(paths[i], "internal_data");
        CDirEntry entry(int_data);
        if (entry.Exists() && entry.IsDir()) {
            m_IgOptions->m_IgDataPath = int_data;
            break;
        }
    }
 
    m_IgOptions->m_SequenceType = "Ig";
    if (args.Exist(kArgIgSeqType) && args[kArgIgSeqType]) {
        m_IgOptions->m_SequenceType = args[kArgIgSeqType].AsString();
    }
 
    string df_db_name = CDirEntry::ConcatPath(
                        CDirEntry::ConcatPath(m_IgOptions->m_IgDataPath,
                           m_IgOptions->m_Origin), m_IgOptions->m_Origin +
                        ((m_IgOptions->m_SequenceType == "TCR")?"_TR":"") + "_V");
    CRef<CSearchDatabase> db(new CSearchDatabase(df_db_name, mol_type));
    m_IgOptions->m_Db[3].Reset(new CLocalDbAdapter(*db));
    try {
        db->GetSeqDb();
    } catch(...) {
        NCBI_THROW(CInputException, eInvalidInput,
           "Germline annotation database " + df_db_name + " could not be found in [internal_data] directory");
    }
 
    m_IgOptions->m_Min_D_match = 5;
    if (args.Exist(kArgMinDMatch) && args[kArgMinDMatch]) {
        m_IgOptions->m_Min_D_match = args[kArgMinDMatch].AsInteger();
    }
 
   if (args.Exist(kArgVPenalty) && args[kArgVPenalty]) {
        m_IgOptions->m_V_penalty = args[kArgVPenalty].AsInteger();
   }
 
    if (args.Exist(kArgDPenalty) && args[kArgDPenalty]) {
        m_IgOptions->m_D_penalty = args[kArgDPenalty].AsInteger();
    }
 
    if (args.Exist(kArgJPenalty) && args[kArgJPenalty]) {
        m_IgOptions->m_J_penalty = args[kArgJPenalty].AsInteger();
    }
 
    CRef<CBlastOptionsHandle> opts_hndl;
    if (m_IgOptions->m_IsProtein) {
        opts_hndl.Reset(CBlastOptionsFactory::Create(eBlastp));
    } else {
        opts_hndl.Reset(CBlastOptionsFactory::Create(eBlastn));
    }
 
 
    const static char suffix[] = "VDJ";
    int num_genes = (m_IsProtein) ? 1: 3;
    for (int gene=0; gene< num_genes; ++gene) {
        string arg_sub = kArgGLSubject;
        string arg_db  = kArgGLDatabase;
        string arg_na  = kArgGLNumAlign;
 
        arg_sub.push_back(suffix[gene]);
        arg_db.push_back(suffix[gene]);
        arg_na.push_back(suffix[gene]);
 
        m_IgOptions->m_NumAlign[gene] = args[arg_na].AsInteger();
 
        if (args.Exist(arg_sub) && args[arg_sub]) {
            CNcbiIstream& subj_input_stream = args[arg_sub].AsInputFile();
            TSeqRange subj_range;
 
            const bool parse_deflines = args.Exist(kArgParseDeflines)
            ? bool(args[kArgParseDeflines])
                : kDfltArgParseDeflines;
            const bool use_lcase_masks = args.Exist(kArgUseLCaseMasking)
            ? bool(args[kArgUseLCaseMasking])
                : kDfltArgUseLCaseMasking;
            CRef<blast::CBlastQueryVector> subjects;
            CRef<CScope> scope = ReadSequencesToBlast(subj_input_stream,
                                       m_IgOptions->m_IsProtein,
                                       subj_range, parse_deflines,
                                       use_lcase_masks, subjects);
            m_Scope->AddScope(*scope,
                        CBlastDatabaseArgs::kSubjectsDataLoaderPriority);
            CRef<IQueryFactory> sub_seqs(
                                new blast::CObjMgr_QueryFactory(*subjects));
            m_IgOptions->m_Db[gene].Reset(new CLocalDbAdapter(
                                       sub_seqs, opts_hndl));
        } else {
            string gl_db_name = m_IgOptions->m_Origin + "_gl_";
            gl_db_name.push_back(suffix[gene]);
            string db_name = (args.Exist(arg_db) && args[arg_db])
                       ?  args[arg_db].AsString() :  gl_db_name;
            db.Reset(new CSearchDatabase(db_name, mol_type));
 
            if (args.Exist(arg_db + "_seqidlist") && args[arg_db + "_seqidlist"]) {
                string fn(SeqDB_ResolveDbPath(args[arg_db + "_seqidlist"].AsString()));
                db->SetGiList(CRef<CSeqDBGiList> (new CSeqDBFileGiList(fn,
                             CSeqDBFileGiList::eSiList)));
            }
 
            m_IgOptions->m_Db[gene].Reset(new CLocalDbAdapter(*db));
            m_Scope->AddDataLoader(s_RegisterOMDataLoader(db->GetSeqDb()));
        }
    }
 
    if (args.Exist(kArgCRegionDatabase) && args[kArgCRegionDatabase]) {
        m_IgOptions->m_NumAlign[3] = args[kArgCRegionNumAlign].AsInteger();
        db.Reset(new CSearchDatabase(args[kArgCRegionDatabase].AsString(), mol_type));
        m_IgOptions->m_Db[4].Reset(new CLocalDbAdapter(*db));
        m_Scope->AddDataLoader(s_RegisterOMDataLoader(db->GetSeqDb()));
    } else {
        m_IgOptions->m_Db[4].Reset(0);
    }
}
 
void
CQueryOptionsArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
 
    arg_desc.SetCurrentGroup("Query filtering options");
    // lowercase masking
    arg_desc.AddFlag(kArgUseLCaseMasking,
         "Use lower case filtering in query and subject sequence(s)?", true);
 
    arg_desc.SetCurrentGroup("Input query options");
    // query location
    arg_desc.AddOptionalKey(kArgQueryLocation, "range",
                            "Location on the query sequence in 1-based offsets "
                            "(Format: start-stop)",
                            CArgDescriptions::eString);
 
    if ( !m_QueryCannotBeNucl) {
        // search strands
        arg_desc.AddDefaultKey(kArgStrand, "strand",
                     "Query strand(s) to search against database/subject",
                               CArgDescriptions::eString, kDfltArgStrand);
        arg_desc.SetConstraint(kArgStrand, &(*new CArgAllow_Strings,
                                             kDfltArgStrand, "plus", "minus"));
    }
 
    arg_desc.SetCurrentGroup("Miscellaneous options");
    arg_desc.AddFlag(kArgParseDeflines,
                 "Should the query and subject defline(s) be parsed?", true);
 
    arg_desc.SetCurrentGroup("");
}
 
void
CQueryOptionsArgs::ExtractAlgorithmOptions(const CArgs& args,
                                           CBlastOptions& opt)
{
    // Get the strand
    {
        m_Strand = eNa_strand_unknown;
 
        if (!Blast_QueryIsProtein(opt.GetProgramType())) {
 
            if (args.Exist(kArgStrand) && args[kArgStrand]) {
                const string& kStrand = args[kArgStrand].AsString();
                if (kStrand == "both") {
                    m_Strand = eNa_strand_both;
                } else if (kStrand == "plus") {
                    m_Strand = eNa_strand_plus;
                } else if (kStrand == "minus") {
                    m_Strand = eNa_strand_minus;
                } else {
                    abort();
                }
            }
            else {
                m_Strand = eNa_strand_both;
            }
        }
    }
 
    // set the sequence range
    if (args.Exist(kArgQueryLocation) && args[kArgQueryLocation]) {
        m_Range = ParseSequenceRange(args[kArgQueryLocation].AsString(),
                                     "Invalid specification of query location");
    }
 
    m_UseLCaseMask = args.Exist(kArgUseLCaseMasking) &&
        static_cast<bool>(args[kArgUseLCaseMasking]);
    m_ParseDeflines = args.Exist(kArgParseDeflines) &&
        static_cast<bool>(args[kArgParseDeflines]);
}
 
void
CMapperQueryOptionsArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
 
    arg_desc.SetCurrentGroup("Query filtering options");
    // lowercase masking
    arg_desc.AddFlag(kArgUseLCaseMasking,
                     "Use lower case filtering in subject sequence(s)?", true);
    arg_desc.AddDefaultKey(kArgQualityFilter, "TF", "Reject low quality "
                           "sequences ", CArgDescriptions::eBoolean, "true");
 
    arg_desc.SetCurrentGroup("Input query options");
    arg_desc.AddDefaultKey(kArgInputFormat, "format", "Input format for "
                           "sequences", CArgDescriptions::eString, "fasta");
    arg_desc.SetConstraint(kArgInputFormat, &(*new CArgAllow_Strings,
                                              "fasta", "fastc", "fastq",
                                              "asn1", "asn1b"));
    arg_desc.AddFlag(kArgPaired, "Input query sequences are paired", true);
    arg_desc.AddOptionalKey(kArgQueryMate, "infile", "FASTA file with "
                            "mates for query sequences (if given in "
                            "another file)", CArgDescriptions::eInputFile);
    arg_desc.SetDependency(kArgQueryMate, CArgDescriptions::eRequires,
                           kArgQuery);
 
    arg_desc.AddOptionalKey(kArgSraAccession, "accession",
                            "Comma-separated SRA accessions",
                            CArgDescriptions::eString);
    arg_desc.SetDependency(kArgSraAccession, CArgDescriptions::eExcludes,
                           kArgQuery);
    arg_desc.SetDependency(kArgSraAccession, CArgDescriptions::eExcludes,
                          kArgInputFormat);
 
    arg_desc.AddOptionalKey(kArgSraAccessionBatch, "file",
                            "File with a list of SRA accessions, one per line",
                            CArgDescriptions::eInputFile);
    arg_desc.SetDependency(kArgSraAccessionBatch, CArgDescriptions::eExcludes,
                           kArgSraAccession);
    arg_desc.SetDependency(kArgSraAccessionBatch, CArgDescriptions::eExcludes,
                           kArgQuery);
    arg_desc.SetDependency(kArgSraAccessionBatch, CArgDescriptions::eExcludes,
                           kArgInputFormat);
 
    arg_desc.SetCurrentGroup("Miscellaneous options");
    arg_desc.AddDefaultKey(kArgParseDeflines, "TF", "Should the query and "
                           "subject defline(s) be parsed?",
                           CArgDescriptions::eBoolean, "true");
 
    arg_desc.AddFlag(kArgEnableSraCache, "Enable SRA caching in local files");
    arg_desc.SetDependency(kArgEnableSraCache, CArgDescriptions::eRequires,
                           kArgSraAccession);
 
 
    arg_desc.SetCurrentGroup("");
}
 
void
CMapperQueryOptionsArgs::ExtractAlgorithmOptions(const CArgs& args,
                                                 CBlastOptions& opt)
{
    CQueryOptionsArgs::ExtractAlgorithmOptions(args, opt);
 
    if (args.Exist(kArgPaired) && args[kArgPaired]) {
        opt.SetPaired(true);
        m_IsPaired = true;
    }
 
    if (args.Exist(kArgInputFormat) && args[kArgInputFormat]) {
        if (args[kArgInputFormat].AsString() == "fasta") {
            m_InputFormat = eFasta;
        }
        else if (args[kArgInputFormat].AsString() == "fastc") {
            m_InputFormat = eFastc;
        }
        else if (args[kArgInputFormat].AsString() == "fastq") {
            m_InputFormat = eFastq;
        }
        else if (args[kArgInputFormat].AsString() == "asn1") {
            m_InputFormat = eASN1text;
        }
        else if (args[kArgInputFormat].AsString() == "asn1b") {
            m_InputFormat = eASN1bin;
        }
        else {
            NCBI_THROW(CInputException, eInvalidInput,
                       "Unexpected input format: " +
                       args[kArgInputFormat].AsString());
        }
    }
 
    if (m_InputFormat == eFastc) {
        // FASTC format always has pairs in a single file
        opt.SetPaired(true);
        m_IsPaired = true;
    }
 
    if (args.Exist(kArgQualityFilter) && args[kArgQualityFilter]) {
        opt.SetReadQualityFiltering(args[kArgQualityFilter].AsBoolean());
    }
 
    if (args.Exist(kArgQueryMate) && args[kArgQueryMate]) {
        // create a decompress stream is the file is compressed
        // (the primary query file is handeled by CStdCmdLieArgs object)
        if (NStr::EndsWith(args[kArgQueryMate].AsString(), ".gz",
                           NStr::eNocase)) {
            m_DecompressIStream.reset(new CDecompressIStream(
                                            args[kArgQueryMate].AsInputFile(),
                                            CDecompressIStream::eGZipFile));
            m_MateInputStream = m_DecompressIStream.get();
        }
        else {
            m_MateInputStream = &args[kArgQueryMate].AsInputFile();
        }
 
        // queries have pairs in the mate stream
        opt.SetPaired(true);
        m_IsPaired = true;
    }
 
    if ((args.Exist(kArgSraAccession) && args[kArgSraAccession]) ||
        (args.Exist(kArgSraAccessionBatch) && args[kArgSraAccessionBatch])) {
 
        if (args[kArgSraAccession]) {
            // accessions given in the command-line
            NStr::Split((CTempString)args[kArgSraAccession].AsString(), ",",
                        m_SraAccessions);
        }
        else {
            // accessions given in a file
            while (!args[kArgSraAccessionBatch].AsInputFile().eof()) {
                string line;
                args[kArgSraAccessionBatch].AsInputFile() >> line;
                if (!line.empty()) {
                    m_SraAccessions.push_back(line);
                }
            }
        }
 
        if (m_SraAccessions.empty()) {
            NCBI_THROW(CInputException, eInvalidInput,
                       "No SRA accessions provided");
        }
 
        m_InputFormat = eSra;
        // assume SRA input is paired, that information for each read is in
        // SRA database, this option will trigger checking for pairs
        opt.SetPaired(true);
        m_IsPaired = true;
    }
 
    if (args.Exist(kArgEnableSraCache) && args[kArgEnableSraCache]) {
        m_EnableSraCache = true;
    }
}
 
 
 
CBlastDatabaseArgs::CBlastDatabaseArgs(bool request_mol_type /* = false */,
                                       bool is_rpsblast /* = false */,
                                       bool is_igblast  /* = false */,
                                       bool is_mapper   /* = false */,
                                       bool is_kblast   /* = false */)
    : m_RequestMoleculeType(request_mol_type),
      m_IsRpsBlast(is_rpsblast),
      m_IsIgBlast(is_igblast),
      m_IsProtein(true),
      m_IsMapper(is_mapper),
      m_IsKBlast(is_kblast),
      m_SupportsDatabaseMasking(false),
      m_SupportIPGFiltering(false)
{}
 
bool
CBlastDatabaseArgs::HasBeenSet(const CArgs& args)
{
    if ( (args.Exist(kArgDb) && args[kArgDb].HasValue()) ||
         (args.Exist(kArgSubject) && args[kArgSubject].HasValue()) ) {
        return true;
    }
    return false;
}
 
void
CBlastDatabaseArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("General search options");
    // database filename
    if (m_IsIgBlast){ 
        arg_desc.AddOptionalKey(kArgDb, "database_name", "Optional additional database name",
                                CArgDescriptions::eString);
    } else {
        arg_desc.AddOptionalKey(kArgDb, "database_name", "BLAST database name",
                                CArgDescriptions::eString);
    }
 
    arg_desc.SetCurrentGroup("");
 
    if (m_RequestMoleculeType) {
        arg_desc.AddKey(kArgDbType, "database_type",
                        "BLAST database molecule type",
                        CArgDescriptions::eString);
        arg_desc.SetConstraint(kArgDbType,
                               &(*new CArgAllow_Strings, "prot", "nucl"));
    }
 
    vector<string> database_args;
    database_args.push_back(kArgDb);
    database_args.push_back(kArgGiList);
    database_args.push_back(kArgSeqIdList);
    database_args.push_back(kArgNegativeGiList);
    database_args.push_back(kArgNegativeSeqidList);
    database_args.push_back(kArgTaxIdList);
    database_args.push_back(kArgTaxIdListFile);
    database_args.push_back(kArgNegativeTaxIdList);
    database_args.push_back(kArgNegativeTaxIdListFile);
    database_args.push_back(kArgNoTaxIdExpansion);
    if (m_SupportIPGFiltering) {
        database_args.push_back(kArgIpgList);
        database_args.push_back(kArgNegativeIpgList);
    }
    if (m_SupportsDatabaseMasking) {
        database_args.push_back(kArgDbSoftMask);
        database_args.push_back(kArgDbHardMask);
    }
 
    // DB size
    if (!m_IsMapper) {
        arg_desc.SetCurrentGroup("Statistical options");
        arg_desc.AddOptionalKey(kArgDbSize, "num_letters",
                                "Effective length of the database ",
                                CArgDescriptions::eInt8);
    }
 
    arg_desc.SetCurrentGroup("Restrict search or results");
    // GI list
    if (!m_IsRpsBlast && !m_IsIgBlast) {
        arg_desc.AddOptionalKey(kArgGiList, "filename",
                                "Restrict search of database to list of GIs",
                                CArgDescriptions::eString);
        // SeqId list
        arg_desc.AddOptionalKey(kArgSeqIdList, "filename",
                                "Restrict search of database to list of SeqIDs",
                                CArgDescriptions::eString);
        // Negative GI list
        arg_desc.AddOptionalKey(kArgNegativeGiList, "filename",
                                "Restrict search of database to everything"
                                " except the specified GIs",
                                CArgDescriptions::eString);
 
        // Negative SeqId list
        arg_desc.AddOptionalKey(kArgNegativeSeqidList, "filename",
                                "Restrict search of database to everything"
                                " except the specified SeqIDs",
                                CArgDescriptions::eString);
 
        // Tax ID list
        arg_desc.AddOptionalKey(kArgTaxIdList, "taxids",
                                "Restrict search of database to include only "
                                "the specified taxonomy IDs and their descendants "
                                "(multiple IDs delimited by ',')",
                                CArgDescriptions::eString);
        arg_desc.AddOptionalKey(kArgNegativeTaxIdList, "taxids",
                                "Restrict search of database to everything "
                                "except the specified taxonomy IDs and their descendants "
                                "(multiple IDs delimited by ',')",
                                CArgDescriptions::eString);
        // Tax ID list file
        arg_desc.AddOptionalKey(kArgTaxIdListFile, "filename",
                                "Restrict search of database to include only "
                                "the specified taxonomy IDs and their descendants ",
                                CArgDescriptions::eString);
        arg_desc.AddOptionalKey(kArgNegativeTaxIdListFile, "filename",
                                "Restrict search of database to everything "
                                "except the specified taxonomy IDs and their descendants ",
                                CArgDescriptions::eString);
    // Disable Tax ID resoution to the descendants
        arg_desc.AddFlag(kArgNoTaxIdExpansion, "Do not expand the taxonomy IDs provided to their descendant taxonomy IDs ", true);
    arg_desc.SetDependency(kArgNoTaxIdExpansion,CArgDescriptions::eExcludes, kArgSubject );
    arg_desc.SetDependency(kArgNoTaxIdExpansion,CArgDescriptions::eExcludes, kArgSubjectLocation );
    arg_desc.SetDependency(kArgNoTaxIdExpansion,CArgDescriptions::eExcludes, kArgWindowMaskerTaxId);
    arg_desc.SetDependency(kArgNoTaxIdExpansion,CArgDescriptions::eExcludes, kArgGiList );
    arg_desc.SetDependency(kArgNoTaxIdExpansion,CArgDescriptions::eExcludes, kArgSeqIdList );
    arg_desc.SetDependency(kArgNoTaxIdExpansion,CArgDescriptions::eExcludes, kArgNegativeGiList );
    arg_desc.SetDependency(kArgNoTaxIdExpansion,CArgDescriptions::eExcludes, kArgNegativeSeqidList );
 
        if (m_SupportIPGFiltering) {
            arg_desc.AddOptionalKey(kArgIpgList, "filename",
                                "Restrict search of database to list of IPGs",
                                CArgDescriptions::eString);
 
            // Negative IPG list
            arg_desc.AddOptionalKey(kArgNegativeIpgList, "filename",
                                "Restrict search of database to everything"
                                " except the specified IPGs",
                                CArgDescriptions::eString);
        }
        // N.B.: all restricting options are mutually exclusive
        const vector<string> kBlastDBFilteringOptions = {
            kArgGiList, 
            kArgSeqIdList, 
            kArgTaxIdList,
            kArgTaxIdListFile,
 
            kArgNegativeGiList, 
            kArgNegativeSeqidList,
            kArgNegativeTaxIdList,
            kArgNegativeTaxIdListFile,
        };
        for (size_t i = 0; i < kBlastDBFilteringOptions.size(); i++) {
            for (size_t j = i+1; j < kBlastDBFilteringOptions.size(); j++) {
                arg_desc.SetDependency(kBlastDBFilteringOptions[i], CArgDescriptions::eExcludes, 
                                       kBlastDBFilteringOptions[j]);
            }
        }
 
        // For now, disable pairing -remote with either -gilist or
        // -negative_gilist as this is not implemented in the BLAST server
        for (const string& s: kBlastDBFilteringOptions) {
            arg_desc.SetDependency(kArgRemote, CArgDescriptions::eExcludes, s);
        }
    }
 
    // Entrez Query
    if (!m_IsMapper) {
        arg_desc.AddOptionalKey(kArgEntrezQuery, "entrez_query",
                                "Restrict search with the given Entrez query",
                                CArgDescriptions::eString);
 
        // Entrez query currently requires the -remote option
        arg_desc.SetDependency(kArgEntrezQuery, CArgDescriptions::eRequires,
                               kArgRemote);
    }
 
 
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION  > 550)) && \
     (!defined(NCBI_COMPILER_MIPSPRO)) )
    // Masking of database
    if (m_SupportsDatabaseMasking) {
        arg_desc.AddOptionalKey(kArgDbSoftMask,
                "filtering_algorithm",
                "Filtering algorithm ID to apply to the BLAST database as soft "
                "masking",
                CArgDescriptions::eString);
        arg_desc.SetDependency(kArgDbSoftMask, CArgDescriptions::eExcludes,
                           kArgDbHardMask);
 
        arg_desc.AddOptionalKey(kArgDbHardMask,
                "filtering_algorithm",
                "Filtering algorithm ID to apply to the BLAST database as hard "
                "masking",
                CArgDescriptions::eString);
    }
#endif
 
    // There is no RPS-BLAST 2 sequences
    if ( !m_IsRpsBlast && !m_IsKBlast && !m_IsIgBlast) {
        arg_desc.SetCurrentGroup("BLAST-2-Sequences options");
        // subject sequence input (for bl2seq)
        arg_desc.AddOptionalKey(kArgSubject, "subject_input_file",
                                "Subject sequence(s) to search",
                                CArgDescriptions::eInputFile);
        ITERATE(vector<string>, dbarg, database_args) {
            arg_desc.SetDependency(kArgSubject, CArgDescriptions::eExcludes,
                                   *dbarg);
        }
 
        // subject location
        arg_desc.AddOptionalKey(kArgSubjectLocation, "range",
                        "Location on the subject sequence in 1-based offsets "
                        "(Format: start-stop)",
                        CArgDescriptions::eString);
        ITERATE(vector<string>, dbarg, database_args) {
            arg_desc.SetDependency(kArgSubjectLocation,
                                   CArgDescriptions::eExcludes,
                                   *dbarg);
        }
        // Because Blast4-subject does not support Seq-locs, specifying a
        // subject range does not work for remote searches
        arg_desc.SetDependency(kArgSubjectLocation,
                               CArgDescriptions::eExcludes, kArgRemote);
    }
 
    arg_desc.SetCurrentGroup("");
}
 
 
 
//
// Get taid(s) from user provided string or file, optionally resolve taxid to it's descendant if isTargetOnly == false
// logic to add/resolve is next:
// --------------------------------------------------------------------------------------
// isTargetOnly  |   decsendant(s) found |  
// --------------------------------------------------------------------------------------
// TRUE          |    N/A                |  add user's taxids, no lookup for decsendant
// FALSE         |    TRUE               |  add user's taxid AND add only found descendant(s)                 
// --------------------------------------------------------------------------------------
//
static void s_GetTaxIDList(const string & in, bool isFile, bool isNegativeList, CRef<CSearchDatabase> & sdb, bool isTargetOnly )
{
    vector<string> ids;
    if (isFile) {
        string filename(SeqDB_ResolveDbPath(in));
        if(filename == kEmptyStr) {
            NCBI_THROW(CInputException, eInvalidInput, "File is not acessible: "+ in );
        }
        CNcbiIfstream instream(filename.c_str());
        CStreamLineReader reader(instream);        
 
        while (!reader.AtEOF()) {
            reader.ReadLine();
            ids.push_back(reader.GetCurrentLine());
        }
    } else {
        NStr::Split(in, ",", ids, NStr::fSplit_Tokenize);
    }
    unique_ptr<ITaxonomy4Blast> tb;
    if( !isTargetOnly ) {
        try{
            tb.reset(new CTaxonomy4BlastSQLite());
        }
        catch(CException &){
            LOG_POST(Warning << "The -taxids command line option requires additional data files. Please see the section 'Taxonomic filtering for BLAST databases' in https://www.ncbi.nlm.nih.gov/books/NBK569839/ for details.");
        }
    }
    set<TTaxId> tax_ids;
    for (auto id : ids) {
        try {
            if (NStr::IsBlank(id)) {
                continue;
            }
            auto taxid = NStr::StringToNumeric<TTaxId>(id, NStr::fAllowLeadingSpaces | NStr::fAllowTrailingSpaces);
            if( isTargetOnly ) {
                tax_ids.insert(taxid);
            } else if (tb) {
                tax_ids.insert(taxid);
                vector<int> desc;
                tb->GetLeafNodeTaxids(taxid, desc);
                for (auto i: desc)
                    tax_ids.insert( static_cast<TTaxId>(i) );
            }
        } catch(CException &){
            NCBI_THROW(CInputException, eInvalidInput, "Invalid taxidlist file ");
        }
    }
 
    CRef<CSeqDBGiList> taxid_list(new CSeqDBGiList());
    taxid_list->AddTaxIds(tax_ids);
    if(isNegativeList) {
        sdb->SetNegativeGiList(taxid_list.GetPointer());
    }
    else {
        sdb->SetGiList(taxid_list.GetPointer());
    }
 
}
 
 
void
CBlastDatabaseArgs::ExtractAlgorithmOptions(const CArgs& args,
                                            CBlastOptions& opts)
{
    EMoleculeType mol_type = Blast_SubjectIsNucleotide(opts.GetProgramType())
        ? CSearchDatabase::eBlastDbIsNucleotide
        : CSearchDatabase::eBlastDbIsProtein;
    m_IsProtein = (mol_type == CSearchDatabase::eBlastDbIsProtein);
 
    if (args.Exist(kArgDb) && args[kArgDb]) {
    std::string local_dblist = NStr::TruncateSpaces( args[kArgDb].AsString() ); 
 
        m_SearchDb.Reset(new CSearchDatabase( local_dblist, 
                                             mol_type));
        
        if (args.Exist(kArgGiList) && args[kArgGiList]) {
            string fn(SeqDB_ResolveDbPath(args[kArgGiList].AsString()));
            m_SearchDb->SetGiList(CRef<CSeqDBGiList> (new CSeqDBFileGiList(fn)));
 
        } else if (args.Exist(kArgNegativeGiList) && args[kArgNegativeGiList]) {
            string fn(SeqDB_ResolveDbPath(args[kArgNegativeGiList].AsString()));
            m_SearchDb->SetNegativeGiList(CRef<CSeqDBGiList> (new CSeqDBFileGiList(fn)));
 
        } else if (args.Exist(kArgSeqIdList) && args[kArgSeqIdList]) {
            string fn(SeqDB_ResolveDbPath(args[kArgSeqIdList].AsString()));
            m_SearchDb->SetGiList(CRef<CSeqDBGiList> (new CSeqDBFileGiList(fn,
                             CSeqDBFileGiList::eSiList)));
        } else if (args.Exist(kArgNegativeSeqidList) && args[kArgNegativeSeqidList]) {
            string fn(SeqDB_ResolveDbPath(args[kArgNegativeSeqidList].AsString()));
            m_SearchDb->SetNegativeGiList(CRef<CSeqDBGiList> (new CSeqDBFileGiList(fn,CSeqDBFileGiList::eSiList)));
        } else if (args.Exist(kArgTaxIdList) && args[kArgTaxIdList]) {
            s_GetTaxIDList(args[kArgTaxIdList].AsString(), false, false, m_SearchDb,args[kArgNoTaxIdExpansion].AsBoolean());
 
        } else if (args.Exist(kArgTaxIdListFile) && args[kArgTaxIdListFile]) {
            s_GetTaxIDList(args[kArgTaxIdListFile].AsString(), true, false, m_SearchDb, args[kArgNoTaxIdExpansion].AsBoolean());
 
        } else if (args.Exist(kArgNegativeTaxIdList) && args[kArgNegativeTaxIdList]) {
            s_GetTaxIDList(args[kArgNegativeTaxIdList].AsString(), false, true, m_SearchDb, args[kArgNoTaxIdExpansion].AsBoolean());
 
        } else if (args.Exist(kArgNegativeTaxIdListFile) && args[kArgNegativeTaxIdListFile]) {
            s_GetTaxIDList(args[kArgNegativeTaxIdListFile].AsString(), true, true, m_SearchDb,args[kArgNoTaxIdExpansion].AsBoolean());
 
        } else if (args.Exist(kArgIpgList) && args[kArgIpgList]) {
            string fn(SeqDB_ResolveDbPath(args[kArgIpgList].AsString()));
            m_SearchDb->SetGiList(CRef<CSeqDBGiList> (new CSeqDBFileGiList(fn, CSeqDBFileGiList::ePigList)));
        }  else if (args.Exist(kArgNegativeIpgList) && args[kArgNegativeIpgList]) {
            string fn(SeqDB_ResolveDbPath(args[kArgNegativeIpgList].AsString()));
            m_SearchDb->SetNegativeGiList(CRef<CSeqDBGiList> (new CSeqDBFileGiList(fn, CSeqDBFileGiList::ePigList)));
 
        }
 
        if (args.Exist(kArgEntrezQuery) && args[kArgEntrezQuery])
            m_SearchDb->SetEntrezQueryLimitation(args[kArgEntrezQuery].AsString());
 
#if ((!defined(NCBI_COMPILER_WORKSHOP) || (NCBI_COMPILER_VERSION  > 550)) && \
     (!defined(NCBI_COMPILER_MIPSPRO)) )
        if (args.Exist(kArgDbSoftMask) && args[kArgDbSoftMask]) {
            m_SearchDb->SetFilteringAlgorithm(args[kArgDbSoftMask].AsString(), eSoftSubjMasking);
        } else if (args.Exist(kArgDbHardMask) && args[kArgDbHardMask]) {
            m_SearchDb->SetFilteringAlgorithm(args[kArgDbHardMask].AsString(), eHardSubjMasking);
        }
#endif
    } else if (args.Exist(kArgSubject) && args[kArgSubject]) {
 
        CNcbiIstream* subj_input_stream = NULL;
        unique_ptr<CDecompressIStream> decompress_stream;
        if (m_IsMapper &&
            NStr::EndsWith(args[kArgSubject].AsString(), ".gz", NStr::eNocase)) {
            decompress_stream.reset(
                        new CDecompressIStream(args[kArgSubject].AsInputFile(),
                        CDecompressIStream::eGZipFile));
            subj_input_stream = decompress_stream.get();
        }
        else {
            subj_input_stream = &args[kArgSubject].AsInputFile();
        }
 
        TSeqRange subj_range;
        if (args.Exist(kArgSubjectLocation) && args[kArgSubjectLocation]) {
            subj_range =
                ParseSequenceRange(args[kArgSubjectLocation].AsString(),
                            "Invalid specification of subject location");
        }
 
        const bool parse_deflines = args.Exist(kArgParseDeflines)
            ? args[kArgParseDeflines].AsBoolean()
            : kDfltArgParseDeflines;
        const bool use_lcase_masks = args.Exist(kArgUseLCaseMasking)
        ? bool(args[kArgUseLCaseMasking])
            : kDfltArgUseLCaseMasking;
        CRef<blast::CBlastQueryVector> subjects;
        m_Scope = ReadSequencesToBlast(*subj_input_stream, IsProtein(),
                                       subj_range, parse_deflines,
                                       use_lcase_masks, subjects, m_IsMapper);
        m_Subjects.Reset(new blast::CObjMgr_QueryFactory(*subjects));
 
    } else if (!m_IsIgBlast){
        // IgBlast permits use of germline database
        NCBI_THROW(CInputException, eInvalidInput,
           "Either a BLAST database or subject sequence(s) must be specified");
    }
 
    if (opts.GetEffectiveSearchSpace() != 0) {
        // no need to set any other options, as this trumps them
        return;
    }
 
    if (args.Exist(kArgDbSize) && args[kArgDbSize]) {
        opts.SetDbLength(args[kArgDbSize].AsInt8());
    }
 
}
 
void
CFormattingArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("Formatting options");
 
    string kOutputFormatDescription = string(
    "alignment view options:\n"
    "  0 = Pairwise,\n"
    "  1 = Query-anchored showing identities,\n"
    "  2 = Query-anchored no identities,\n"
    "  3 = Flat query-anchored showing identities,\n"
    "  4 = Flat query-anchored no identities,\n"
    "  5 = BLAST XML,\n"
    "  6 = Tabular,\n"
    "  7 = Tabular with comment lines,\n"
    "  8 = Seqalign (Text ASN.1),\n"
    "  9 = Seqalign (Binary ASN.1),\n"
    " 10 = Comma-separated values,\n"
    " 11 = BLAST archive (ASN.1),\n"
    " 12 = Seqalign (JSON),\n"
    " 13 = Multiple-file BLAST JSON,\n"
    " 14 = Multiple-file BLAST XML2,\n"
    " 15 = Single-file BLAST JSON,\n"
    " 16 = Single-file BLAST XML2");
 
    if(m_FormatFlags & eIsSAM) {
        kOutputFormatDescription += ",\n 17 = Sequence Alignment/Map (SAM)";
    }
    kOutputFormatDescription += ",\n 18 = Organism Report\n\n";
    if(m_FormatFlags & eIsSAM) {
        kOutputFormatDescription +=
                "Options 6, 7, 10 and 17 "
                "can be additionally configured to produce\n"
                "a custom format specified by space delimited format specifiers,\n"
                "or in the case of options 6, 7, and 10, by a token specified\n"
                "by the delim keyword. E.g.: \"17 delim=@ qacc sacc score\".\n"
                "The delim keyword must appear after the numeric output format\n"
                "specification.\n"
                "The supported format specifiers for options 6, 7 and 10 are:\n";
    }
    else {
        kOutputFormatDescription +=
                "Options 6, 7 and 10 "
                "can be additionally configured to produce\n"
                "a custom format specified by space delimited format specifiers,\n"
                "or by a token specified by the delim keyword.\n"
                " E.g.: \"10 delim=@ qacc sacc score\".\n"                
                "The delim keyword must appear after the numeric output format\n"
                "specification.\n"
                "The supported format specifiers are:\n";
    }
    
    kOutputFormatDescription += DescribeTabularOutputFormatSpecifiers() +  string("\n");
 
    if(m_FormatFlags & eIsSAM) {
        kOutputFormatDescription +=
                "The supported format specifier for option 17 is:\n" +
                DescribeSAMOutputFormatSpecifiers();
    }
 
 
    int dft_outfmt = kDfltArgOutputFormat;
 
    // Igblast shows extra column of gaps
    if (m_IsIgBlast) {
        kOutputFormatDescription = string(
    "alignment view options:\n"
    "  3 = Flat query-anchored, show identities,\n"
    "  4 = Flat query-anchored, no identities,\n"
    "  7 = Tabular with comment lines\n"
    "  19 = Rearrangement summary report (AIRR format)\n\n"
    "Options 7 can be additionally configured to produce\n"
    "a custom format specified by space delimited format specifiers.\n"
    "The supported format specifiers are:\n") +
        DescribeTabularOutputFormatSpecifiers(true) +
        string("\n");
        dft_outfmt = 3;
    }
 
    // alignment view
    arg_desc.AddDefaultKey(kArgOutputFormat, "format",
                           kOutputFormatDescription,
                           CArgDescriptions::eString,
                           NStr::IntToString(dft_outfmt));
 
    // show GIs in deflines
    arg_desc.AddFlag(kArgShowGIs, "Show NCBI GIs in deflines?", true);
 
    // number of one-line descriptions to display
    arg_desc.AddOptionalKey(kArgNumDescriptions, "int_value",
                 "Number of database sequences to show one-line "
                 "descriptions for\n"
                 "Not applicable for outfmt > 4\n"
                 "Default = `"+ NStr::IntToString(m_DfltNumDescriptions)+ "'",
                 CArgDescriptions::eInteger);
    arg_desc.SetConstraint(kArgNumDescriptions,
                           new CArgAllowValuesGreaterThanOrEqual(0));
 
    // number of alignments per DB sequence
    arg_desc.AddOptionalKey(kArgNumAlignments, "int_value",
                 "Number of database sequences to show alignments for\n"
                 "Default = `" + NStr::IntToString(m_DfltNumAlignments) + "'",
                 CArgDescriptions::eInteger );
    arg_desc.SetConstraint(kArgNumAlignments,
                           new CArgAllowValuesGreaterThanOrEqual(0));
 
    arg_desc.AddOptionalKey(kArgLineLength, "line_length",
                            "Line length for formatting alignments\n"
                            "Not applicable for outfmt > 4\n"
                            "Default = `"+ NStr::NumericToString(align_format::kDfltLineLength) + "'",
                            CArgDescriptions::eInteger);
    arg_desc.SetConstraint(kArgLineLength,
                           new CArgAllowValuesGreaterThanOrEqual(1));
 
    if(!m_IsIgBlast){
        // Produce HTML?
        arg_desc.AddFlag(kArgProduceHtml, "Produce HTML output?", true);
        
    
        arg_desc.AddOptionalKey(kArgSortHits, "sort_hits",
                           "Sorting option for hits:\n"
                           "alignment view options:\n"
                           "  0 = Sort by evalue,\n"
                           "  1 = Sort by bit score,\n" 
                           "  2 = Sort by total score,\n" 
                           "  3 = Sort by percent identity,\n" 
                           "  4 = Sort by query coverage\n"        
                           "Not applicable for outfmt > 4\n",
                           CArgDescriptions::eInteger);
        arg_desc.SetConstraint(kArgSortHits,
                           new CArgAllowValuesBetween(CAlignFormatUtil::eEvalue,
                                                      CAlignFormatUtil::eQueryCoverage,
                                                      true));                           
    
        arg_desc.AddOptionalKey(kArgSortHSPs, "sort_hsps",
                           "Sorting option for hps:\n"
                           "  0 = Sort by hsp evalue,\n"
                           "  1 = Sort by hsp score,\n"                            
                           "  2 = Sort by hsp query start,\n"
                           "  3 = Sort by hsp percent identity,\n" 
                           "  4 = Sort by hsp subject start\n"                           
                           "Not applicable for outfmt != 0\n",
                           CArgDescriptions::eInteger); 
        arg_desc.SetConstraint(kArgSortHSPs,
                           new CArgAllowValuesBetween(CAlignFormatUtil::eHspEvalue,
                                                      CAlignFormatUtil::eSubjectStart,
                                                      true));                                                                
        /// Hit list size, listed here for convenience only
        arg_desc.SetCurrentGroup("Restrict search or results");
        arg_desc.AddOptionalKey(kArgMaxTargetSequences, "num_sequences",
                            "Maximum number of aligned sequences to keep \n"
                            "(value of 5 or more is recommended)\n"
                            "Default = `" + NStr::IntToString(BLAST_HITLIST_SIZE) + "'",
                            CArgDescriptions::eInteger);
        arg_desc.SetConstraint(kArgMaxTargetSequences,
                           new CArgAllowValuesGreaterThanOrEqual(1));
        arg_desc.SetDependency(kArgMaxTargetSequences,
                           CArgDescriptions::eExcludes,
                           kArgNumDescriptions);
        arg_desc.SetDependency(kArgMaxTargetSequences,
                           CArgDescriptions::eExcludes,
                           kArgNumAlignments);
    }
    arg_desc.SetCurrentGroup("");
}
 
bool
CFormattingArgs::ArchiveFormatRequested(const CArgs& args) const
{
    EOutputFormat output_fmt;
    string ignore1, ignore2;
    ParseFormattingString(args, output_fmt, ignore1, ignore2);
    return (output_fmt == eArchiveFormat ? true : false);
}
 
 
static void s_ValidateCustomDelim(string custom_fmt_spec,string customDelim)
{
    bool error = false;
    string checkfield;
    custom_fmt_spec = NStr::TruncateSpaces(custom_fmt_spec);
    if(custom_fmt_spec.empty()) return;
 
    //Check if delim is already used
    const string kFieldsWithSemicolSeparator = "sallseqid staxids sscinames scomnames sblastnames sskingdoms";//sep = ";"
    const string kFramesField = "frames"; //sep = "/"
    const string kAllTitlesField ="salltitles"; //sep = "<>""    
 
    if(customDelim == ";") {
        vector <string> tokens;
        NStr::Split(kFieldsWithSemicolSeparator," ", tokens);   
        for(size_t i = 0; i < tokens.size(); i++)   {
            if(NStr::Find(custom_fmt_spec,tokens[i]) != NPOS) {
                checkfield = tokens[i];
                error = true;                
                break;
            }
        }
    }
    else {
        if(customDelim == "/") {
            checkfield = kFramesField;
        }
        else if(customDelim == "<>") {
            checkfield = kAllTitlesField;
        }
        if(!checkfield.empty() && NStr::Find(custom_fmt_spec,checkfield) != NPOS) {
            error = true;
        }
    }
    
    if(error) {                
        string msg("Your custom record separator (" + customDelim + ") is also used by the format specifier (" + checkfield +
                                                                ") to separate multiple entries. Please use a different record separator (delim keyword).");
        NCBI_THROW(CInputException, eInvalidInput, msg);                                                                
    }
}
 
void
CFormattingArgs::ParseFormattingString(const CArgs& args,
                                       EOutputFormat& fmt_type,
                                       string& custom_fmt_spec,
                                       string& custom_delim) const
{
    custom_fmt_spec.clear();
    if (args[kArgOutputFormat]) {
        string fmt_choice =
            NStr::TruncateSpaces(args[kArgOutputFormat].AsString());
        string::size_type pos;                            
        if ( (pos = fmt_choice.find_first_of(' ')) != string::npos) {
            custom_fmt_spec.assign(fmt_choice, pos+1,
                                   fmt_choice.size()-(pos+1));
            fmt_choice.erase(pos);
        }       
        if(!custom_fmt_spec.empty()) {            
            if(NStr::StartsWith(custom_fmt_spec, "delim")) {                
                vector <string> tokens;
                NStr::Split(custom_fmt_spec," ",tokens);
                if(tokens.size() > 0) {
                    string tag;
                    bool isValid = NStr::SplitInTwo(tokens[0],"=",tag,custom_delim);
                    if(!isValid) {
                        string msg("Delimiter format is invalid. Valid format is delim=<delimiter value>");
                        NCBI_THROW(CInputException, eInvalidInput, msg);
                    }                    
                    else {
                        custom_fmt_spec = NStr::Replace(custom_fmt_spec,tokens[0],"");                                                
                    }                  
                }                 
            }                        
        }        
        int val = 0;
        try { val = NStr::StringToInt(fmt_choice); }
        catch (const CStringException&) {   // probably a conversion error
            CNcbiOstrstream os;
            os << "'" << fmt_choice << "' is not a valid output format";
            string msg = CNcbiOstrstreamToString(os);
            NCBI_THROW(CInputException, eInvalidInput, msg);
        }
        if (val < 0 || val >= static_cast<int>(eEndValue)) {
            string msg("Formatting choice is out of range");
            throw std::out_of_range(msg);
        }
        if (m_IsIgBlast && (val != 3 && val != 4 && val != 7 && val != eAirrRearrangement)) {
            string msg("Formatting choice is not valid");
            throw std::out_of_range(msg);
        }
        fmt_type = static_cast<EOutputFormat>(val);
        if ( !(fmt_type == eTabular ||
               fmt_type == eTabularWithComments ||
               fmt_type == eCommaSeparatedValues ||
               fmt_type == eSAM) ) {
               custom_fmt_spec.clear();
        }
    }    
}
 
 
void
CFormattingArgs::ExtractAlgorithmOptions(const CArgs& args,
                                         CBlastOptions& opt)
{
    ParseFormattingString(args, m_OutputFormat, m_CustomOutputFormatSpec,m_CustomDelim);
    if((m_OutputFormat == eSAM) && !(m_FormatFlags & eIsSAM) ){
            NCBI_THROW(CInputException, eInvalidInput,
                                    "SAM format is only applicable to blastn" );
    }
    if((m_OutputFormat == eAirrRearrangement) && !(m_FormatFlags & eIsAirrRearrangement) ){
        NCBI_THROW(CInputException, eInvalidInput,
                   "AIRR rearrangement format is only applicable to igblastn" );
    }
    if (m_OutputFormat == eFasta) {
        NCBI_THROW(CInputException, eInvalidInput,
                   "FASTA output format is only applicable to magicblast");
    }
    s_ValidateCustomDelim(m_CustomOutputFormatSpec,m_CustomDelim);
    m_ShowGis = static_cast<bool>(args[kArgShowGIs]);
    if(m_IsIgBlast){
        m_Html = false;
    } else {
        m_Html = static_cast<bool>(args[kArgProduceHtml]);
    }
    // Default hitlist size 500, value can be changed if import search strategy is used
    int hitlist_size = opt.GetHitlistSize();
 
    // To preserve hitlist size in import search strategy > 500,
    // we need to increase the  num_ descriptions and num_alignemtns
    if(hitlist_size > BLAST_HITLIST_SIZE )
    {
        if((!args.Exist(kArgNumDescriptions) || !args[kArgNumDescriptions]) &&
           (!args.Exist(kArgNumAlignments) || !args[kArgNumAlignments]) &&
           (m_OutputFormat <= eFlatQueryAnchoredNoIdentities)) {
            m_NumDescriptions = hitlist_size;
            m_NumAlignments = hitlist_size/ 2;
            return;
        }
    }
 
    if(m_OutputFormat <= eFlatQueryAnchoredNoIdentities) {
 
 
         m_NumDescriptions = m_DfltNumDescriptions;
         m_NumAlignments = m_DfltNumAlignments;
 
         if (args.Exist(kArgNumDescriptions) && args[kArgNumDescriptions]) {
            m_NumDescriptions = args[kArgNumDescriptions].AsInteger();
         }
 
         if (args.Exist(kArgNumAlignments) && args[kArgNumAlignments]) {
            m_NumAlignments = args[kArgNumAlignments].AsInteger();
        }
 
         if (args.Exist(kArgMaxTargetSequences) && args[kArgMaxTargetSequences]) {
            m_NumDescriptions = args[kArgMaxTargetSequences].AsInteger();
            m_NumAlignments = args[kArgMaxTargetSequences].AsInteger();
            hitlist_size = m_NumAlignments;
         }
 
        // The If clause is for handling import_search_strategy hitlist size < 500
        // We want to preserve the hitlist size in iss if no formatting input is entered in cmdline
        // If formmating option(s) is entered than the iss hitlist size is overridden.
         // FIXME: does this work with import search strategies?
         if ((args.Exist(kArgNumDescriptions) && args[kArgNumDescriptions]) ||
             (args.Exist(kArgNumAlignments) && args[kArgNumAlignments])) {
            hitlist_size = max(m_NumDescriptions, m_NumAlignments);
        }
 
        if (args[kArgLineLength]) {
            m_LineLength = args[kArgLineLength].AsInteger();
        }
        if(args.Exist(kArgSortHits) && args[kArgSortHits])
        {
            m_HitsSortOption = args[kArgSortHits].AsInteger();
        }
    }
    else
    {
        if (args.Exist(kArgNumDescriptions) && args[kArgNumDescriptions]) {
         ERR_POST(Warning << "The parameter -num_descriptions is ignored for "
                             "output formats > 4 . Use -max_target_seqs "
                             "to control output");
        }
 
        if (args[kArgLineLength]) {
         ERR_POST(Warning << "The parameter -line_length is not applicable for "
                             "output formats > 4 .");
        }
 
        if (args.Exist(kArgMaxTargetSequences) && args[kArgMaxTargetSequences]) {
            hitlist_size = args[kArgMaxTargetSequences].AsInteger();
        }
        else if (args.Exist(kArgNumAlignments) && args[kArgNumAlignments]) {
            hitlist_size = args[kArgNumAlignments].AsInteger();
        }
 
        m_NumDescriptions = hitlist_size;
        m_NumAlignments = hitlist_size;
 
        if(args.Exist(kArgSortHits) && args[kArgSortHits]) {            
            ERR_POST(Warning << "The parameter -sorthits is ignored for output formats > 4.");                    
        }
    }   
    
    if(hitlist_size < 5){
        ERR_POST(Warning << "Examining 5 or more matches is recommended");
    }
    opt.SetHitlistSize(hitlist_size);
 
    if(args.Exist(kArgSortHSPs) && args[kArgSortHSPs]) 
    {
        int hspsSortOption = args[kArgSortHSPs].AsInteger();
        if(m_OutputFormat == ePairwise) {        
            m_HspsSortOption = hspsSortOption;
        }        
        else {
            ERR_POST(Warning << "The parameter -sorthsps is ignored for output formats != 0.");
        }
    }
    return;
}
 
 
void
CMapperFormattingArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("Formatting options");
    string kOutputFormatDescription = string(
                                             "alignment view options:\n"
                                             "sam = SAM format,\n"
                                             "tabular = Tabular format,\n"
                                             "asn = text ASN.1\n");
 
    string kUnalignedOutputFormatDescription = string(
                                    "format for reporting unaligned reads:\n"
                                    "sam = SAM format,\n"
                                    "tabular = Tabular format,\n"
                                    "fasta = sequences in FASTA format\n"
                                    "Default = same as ") +
                                    align_format::kArgOutputFormat;
 
    arg_desc.AddDefaultKey(align_format::kArgOutputFormat, "format",
                           kOutputFormatDescription,
                           CArgDescriptions::eString,
                           "sam");
 
    set<string> allowed_formats = {"sam", "tabular", "asn"};
    arg_desc.SetConstraint(align_format::kArgOutputFormat,
                           new CArgAllowStringSet(allowed_formats));
 
    arg_desc.AddOptionalKey(kArgUnalignedFormat, "format",
                            kUnalignedOutputFormatDescription,
                            CArgDescriptions::eString);
 
    set<string> allowed_unaligned_formats = {"sam", "tabular", "fasta"};
    arg_desc.SetConstraint(kArgUnalignedFormat,
                           new CArgAllowStringSet(allowed_unaligned_formats));
 
    arg_desc.SetDependency(kArgUnalignedFormat, CArgDescriptions::eRequires,
                           kArgUnalignedOutput);
 
 
    arg_desc.AddFlag(kArgPrintMdTag, "Include MD tag in SAM report");
    arg_desc.AddFlag(kArgNoReadIdTrim, "Do not trim '.1', '/1', '.2', " \
                     "or '/2' at the end of read ids for SAM format and" \
                     "paired runs");
 
    arg_desc.AddFlag(kArgNoUnaligned, "Do not report unaligned reads");
 
    arg_desc.AddFlag(kArgNoDiscordant,
            "Suppress discordant alignments for paired reads");
 
    arg_desc.AddOptionalKey(kArgUserTag, "tag",
                            "A user tag to add to each alignment",
                            CArgDescriptions::eString);
 
    arg_desc.SetCurrentGroup("");
}
 
void CMapperFormattingArgs::ExtractAlgorithmOptions(const CArgs& args,
                                                    CBlastOptions& opt)
{
    if (args.Exist(align_format::kArgOutputFormat)) {
        string fmt_choice = args[align_format::kArgOutputFormat].AsString();
        if (fmt_choice == "sam") {
            m_OutputFormat = eSAM;
        }
        else if (fmt_choice == "tabular") {
            m_OutputFormat = eTabular;
        }
        else if (fmt_choice == "asn") {
            m_OutputFormat = eAsnText;
        }
        else {
            CNcbiOstrstream os;
            os << "'" << fmt_choice << "' is not a valid output format";
            string msg = CNcbiOstrstreamToString(os);
            NCBI_THROW(CInputException, eInvalidInput, msg);
        }
 
        m_UnalignedOutputFormat = m_OutputFormat;
    }
 
    if (args.Exist(kArgUnalignedFormat) && args[kArgUnalignedFormat]) {
        string fmt_choice = args[kArgUnalignedFormat].AsString();
        if (fmt_choice == "sam") {
            m_UnalignedOutputFormat = eSAM;
        }
        else if (fmt_choice == "tabular") {
            m_UnalignedOutputFormat = eTabular;
        }
        else if (fmt_choice == "fasta") {
            m_UnalignedOutputFormat = eFasta;
        }
        else {
            CNcbiOstrstream os;
            os << "'" << fmt_choice
               << "' is not a valid output format for unaligned reads";
            string msg = CNcbiOstrstreamToString(os);
            NCBI_THROW(CInputException, eInvalidInput, msg);
        }
    }
 
    m_ShowGis = true;
    m_Html = false;
 
    if (args.Exist(kArgNoReadIdTrim) && args[kArgNoReadIdTrim]) {
        m_TrimReadIds = false;
    }
 
    if (args.Exist(kArgNoUnaligned) && args[kArgNoUnaligned]) {
        m_PrintUnaligned = false;
    }
 
    if (args.Exist(kArgNoDiscordant) && args[kArgNoDiscordant]) {
        m_NoDiscordant = true;
    }
 
    if (args.Exist(kArgFwdRev) && args[kArgFwdRev]) {
        m_FwdRev = true;
    }
 
    if (args.Exist(kArgRevFwd) && args[kArgRevFwd]) {
        m_RevFwd = true;
    }
 
    if (args.Exist(kArgFwdOnly) && args[kArgFwdOnly]) {
        m_FwdOnly = true;
    }
 
    if (args.Exist(kArgRevOnly) && args[kArgRevOnly]) {
        m_RevOnly = true;
    }
 
    if (args.Exist(kArgOnlyStrandSpecific) && args[kArgOnlyStrandSpecific]) {
        m_OnlyStrandSpecific = true;
    }
 
    if (args.Exist(kArgPrintMdTag) && args[kArgPrintMdTag]) {
        m_PrintMdTag = true;
    }
 
   // only the fast tabular format is able to show merged HSPs with
    // common query bases
    if (m_OutputFormat != eTabular) {
        // FIXME: This is a hack. Merging should be done by the formatter,
        // but is currently done by HSP stream writer. This is an easy
        // switch until merging is implemented properly.
        CNcbiEnvironment().Set("MAPPER_NO_OVERLAPPED_HSP_MERGE", "1");
    }
 
    if (args.Exist(kArgUserTag) && args[kArgUserTag]) {
        NStr::Replace(args[kArgUserTag].AsString(), "\\t", "\t", m_UserTag);
    }
}
 
void
CMTArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    // number of threads
    arg_desc.SetCurrentGroup("Miscellaneous options");
#ifdef NCBI_THREADS
    const int kMinValue = static_cast<int>(CThreadable::kMinNumThreads);
    const int kMaxValue = static_cast<int>(CSystemInfo::GetCpuCount());
    const int kDfltValue = m_NumThreads != CThreadable::kMinNumThreads
        ? std::min<int>(static_cast<int>(m_NumThreads), kMaxValue) : kMinValue;
 
    arg_desc.AddDefaultKey(kArgNumThreads, "int_value",
                           "Number of threads (CPUs) to use in the BLAST search",
                           CArgDescriptions::eInteger,
                           NStr::IntToString(kDfltValue));
    arg_desc.SetConstraint(kArgNumThreads,
                           new CArgAllowValuesGreaterThanOrEqual(kMinValue));
    arg_desc.SetDependency(kArgNumThreads,
                           CArgDescriptions::eExcludes,
                           kArgRemote);
 
    if (m_MTMode >= 0) {
        arg_desc.AddDefaultKey(kArgMTMode, "int_value",
                               "Multi-thread mode to use in BLAST search:\n "
                               "0 auto split by database or queries \n "
                               "1 split by queries\n "
                               "2 split by database",
                               CArgDescriptions::eInteger,
                               NStr::IntToString(0));
        arg_desc.SetConstraint(kArgMTMode,
                               new CArgAllowValuesBetween(0, 2, true));
        arg_desc.SetDependency(kArgMTMode,
                               CArgDescriptions::eRequires,
                               kArgNumThreads);
    }
    /*
    arg_desc.SetDependency(kArgNumThreads,
                           CArgDescriptions::eExcludes,
                           kArgUseIndex);
    */
#endif
    arg_desc.SetCurrentGroup("");
}
 
CMTArgs::CMTArgs(const CArgs& args)
{
    x_ExtractAlgorithmOptions(args);
}
 
 
void
CMTArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& /* opts */)
{
    x_ExtractAlgorithmOptions(args);
}
void
CMTArgs::x_ExtractAlgorithmOptions(const CArgs& args)
{
    const int kMaxValue = static_cast<int>(CSystemInfo::GetCpuCount());
 
    if (args.Exist(kArgNumThreads) &&
        args[kArgNumThreads].HasValue()) {  // could be cancelled by the exclusion in CRemoteArgs
 
        // use the minimum of the two: user requested number of threads and
        // number of available CPUs for number of threads
        int num_threads = args[kArgNumThreads].AsInteger();
        if (num_threads > kMaxValue) {
            m_NumThreads = kMaxValue;
 
            ERR_POST(Warning << (string)"Number of threads was reduced to " +
                     NStr::IntToString((unsigned int)m_NumThreads) +
                     " to match the number of available CPUs");
        }
        else {
            m_NumThreads = num_threads;
        }
 
        // This is temporarily ignored (per SB-635)
        if (args.Exist(kArgSubject) && args[kArgSubject].HasValue() &&
            m_NumThreads != CThreadable::kMinNumThreads) {
            m_NumThreads = CThreadable::kMinNumThreads;
            string opt = kArgNumThreads;
            if (args.Exist(kArgMTMode) &&
               (args[kArgMTMode].AsInteger() == CMTArgs::eSplitByQueries)) {
                m_MTMode = CMTArgs::eSplitByDB;
                opt += " and " + kArgMTMode;
            }
            ERR_POST(Warning << "'" << opt << "' is currently "
                     << "ignored when '" << kArgSubject << "' is specified.");
            return;
        }
    }
    if (args.Exist(kArgMTMode) && args[kArgMTMode].HasValue()) {
        m_MTMode = (EMTMode) args[kArgMTMode].AsInteger();
    }
 
}
 
void
CRemoteArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("Miscellaneous options");
    arg_desc.AddFlag(kArgRemote, "Execute search remotely?", true);
 
    arg_desc.SetCurrentGroup("");
}
 
void
CRemoteArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& /* opts */)
{
    if (args.Exist(kArgRemote)) {
        m_IsRemote = static_cast<bool>(args[kArgRemote]);
    }
}
 
void
CDebugArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
#if _BLAST_DEBUG
    arg_desc.SetCurrentGroup("Miscellaneous options");
    arg_desc.AddFlag("verbose", "Produce verbose output (show BLAST options)",
                     true);
    arg_desc.AddFlag("remote_verbose",
                     "Produce verbose output for remote searches", true);
    arg_desc.AddFlag("use_test_remote_service",
                     "Send remote requests to test servers", true);
    arg_desc.SetCurrentGroup("");
#endif /* _BLAST_DEBUG */
}
 
void
CDebugArgs::ExtractAlgorithmOptions(const CArgs& args, CBlastOptions& /* opts */)
{
#if _BLAST_DEBUG
    m_DebugOutput = static_cast<bool>(args["verbose"]);
    m_RmtDebugOutput = static_cast<bool>(args["remote_verbose"]);
    if (args["use_test_remote_service"]) {
        IRWRegistry& reg = CNcbiApplication::Instance()->GetConfig();
        reg.Set("BLAST4", DEF_CONN_REG_SECTION "_" REG_CONN_SERVICE_NAME,
                "blast4_test");
    }
#endif /* _BLAST_DEBUG */
}
 
void
CHspFilteringArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    // culling limit
    arg_desc.SetCurrentGroup("Restrict search or results");
    arg_desc.AddOptionalKey(kArgCullingLimit, "int_value",
                     "If the query range of a hit is enveloped by that of at "
                     "least this many higher-scoring hits, delete the hit",
                     CArgDescriptions::eInteger);
    arg_desc.SetConstraint(kArgCullingLimit,
    // best hit algorithm arguments
               new CArgAllowValuesGreaterThanOrEqual(kDfltArgCullingLimit));
 
    arg_desc.AddOptionalKey(kArgBestHitOverhang, "float_value",
                            "Best Hit algorithm overhang value "
                            "(recommended value: " +
                            NStr::DoubleToString(kDfltArgBestHitOverhang) +
                            ")",
                            CArgDescriptions::eDouble);
    arg_desc.SetConstraint(kArgBestHitOverhang,
                           new CArgAllowValuesBetween(kBestHit_OverhangMin,
                                                      kBestHit_OverhangMax));
    arg_desc.SetDependency(kArgBestHitOverhang,
                           CArgDescriptions::eExcludes,
                           kArgCullingLimit);
 
    arg_desc.AddOptionalKey(kArgBestHitScoreEdge, "float_value",
                            "Best Hit algorithm score edge value "
                            "(recommended value: " +
                            NStr::DoubleToString(kDfltArgBestHitScoreEdge) +
                            ")",
                            CArgDescriptions::eDouble);
    arg_desc.SetConstraint(kArgBestHitScoreEdge,
                           new CArgAllowValuesBetween(kBestHit_ScoreEdgeMin,
                                                      kBestHit_ScoreEdgeMax));
    arg_desc.SetDependency(kArgBestHitScoreEdge,
                           CArgDescriptions::eExcludes,
                           kArgCullingLimit);
    arg_desc.AddFlag(kArgSubjectBestHit, "Turn on best hit per subject sequence", true);
 
    arg_desc.SetCurrentGroup("");
}
 
void
CHspFilteringArgs::ExtractAlgorithmOptions(const CArgs& args,
                                      CBlastOptions& opts)
{
    if (args[kArgCullingLimit]) {
        opts.SetCullingLimit(args[kArgCullingLimit].AsInteger());
    }
    if (args[kArgBestHitOverhang]) {
        opts.SetBestHitOverhang(args[kArgBestHitOverhang].AsDouble());
    }
    if (args[kArgBestHitScoreEdge]) {
        opts.SetBestHitScoreEdge(args[kArgBestHitScoreEdge].AsDouble());
    }
    if (args[kArgSubjectBestHit]) {
        opts.SetSubjectBestHit();
    }
}
 
void
CMbIndexArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("General search options");
    arg_desc.AddDefaultKey(
            kArgUseIndex, "boolean",
            "Use MegaBLAST database index",
            CArgDescriptions::eBoolean, NStr::BoolToString(kDfltArgUseIndex));
    arg_desc.AddOptionalKey(
            kArgIndexName, "string",
            "MegaBLAST database index name (deprecated; use only for old style indices)",
            CArgDescriptions::eString );
    arg_desc.SetCurrentGroup( "" );
}
 
bool
CMbIndexArgs::HasBeenSet(const CArgs& args)
{
    if ( (args.Exist(kArgUseIndex) && args[kArgUseIndex].HasValue()) ||
         (args.Exist(kArgIndexName) && args[kArgIndexName].HasValue()) ) {
        return true;
    }
    return false;
}
 
void
CMbIndexArgs::ExtractAlgorithmOptions(const CArgs& args,
                                      CBlastOptions& opts)
{
    // MB Index does not apply to Blast2Sequences
    if( args.Exist( kArgUseIndex ) &&
        !(args.Exist( kArgSubject ) && args[kArgSubject])) {
 
        bool use_index   = true;
        bool force_index = false;
        bool old_style_index = false;
 
        if( args[kArgUseIndex] ) {
            if( args[kArgUseIndex].AsBoolean() ) force_index = true;
            else use_index = false;
        }
 
        if( args.Exist( kTask ) && args[kTask] &&
                args[kTask].AsString() != "megablast" ) {
            use_index = false;
        }
 
        if( use_index ) {
            string index_name;
 
            if( args.Exist( kArgIndexName ) && args[kArgIndexName] ) {
                index_name = args[kArgIndexName].AsString();
                old_style_index = true;
            }
            else if( args.Exist( kArgDb ) && args[kArgDb] ) {
                index_name = args[kArgDb].AsString();
            }
            else {
                NCBI_THROW(CInputException, eInvalidInput,
                        "Can not deduce database index name" );
            }
 
            opts.SetUseIndex( true, index_name, force_index, old_style_index );
        }
    }
}
 
void
CStdCmdLineArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("Input query options");
 
    // query filename
    arg_desc.AddDefaultKey(kArgQuery, "input_file",
                     "Input file name",
                     CArgDescriptions::eInputFile, kDfltArgQuery);
    // for now it's either -query or -sra
    if( m_SRAaccessionEnabled ) {
        arg_desc.AddOptionalKey(kArgSraAccession, "accession",
                            "Comma-separated SRA accessions",
                            CArgDescriptions::eString);
    arg_desc.SetDependency(kArgSraAccession,
            CArgDescriptions::eExcludes,
            kArgQuery);
    }
 
    arg_desc.SetCurrentGroup("General search options");
 
    // report output file
    arg_desc.AddDefaultKey(kArgOutput, "output_file",
                   "Output file name",
                   CArgDescriptions::eOutputFile, "-");
    arg_desc.SetConstraint(kArgOutput, new CArgAllowMaximumFileNameLength());
 
    if (m_GzipEnabled) {
        arg_desc.AddFlag(kArgOutputGzip, "Output will be compressed");
    }
 
    arg_desc.SetCurrentGroup("");
}
 
void
CStdCmdLineArgs::ExtractAlgorithmOptions(const CArgs& args,
                                         CBlastOptions& /* opt */)
{
    if (args.Exist(kArgQuery) && args[kArgQuery].HasValue() &&
        m_InputStream == NULL) {
 
        if (m_GzipEnabled &&
            NStr::EndsWith(args[kArgQuery].AsString(), ".gz", NStr::eNocase)) {
            m_DecompressIStream.reset(new CDecompressIStream(
                                               args[kArgQuery].AsInputFile(),
                                               CDecompressIStream::eGZipFile));
            m_InputStream = m_DecompressIStream.get();
        }
        else {
            m_InputStream = &args[kArgQuery].AsInputFile();
        }
    }
 
    if (args.Exist(kArgOutputGzip) && args[kArgOutputGzip]) {
        m_CompressOStream.reset(new CCompressOStream(
                                              args[kArgOutput].AsOutputFile(),
                                              CCompressOStream::eGZipFile));
        m_OutputStream = m_CompressOStream.get();
    }
    else {
        m_OutputStream = &args[kArgOutput].AsOutputFile();
    }
 
    // stream for unaligned reads in magicblast
    if (args.Exist(kArgUnalignedOutput) && args[kArgUnalignedOutput]) {
        if (args.Exist(kArgOutputGzip) && args[kArgOutputGzip]) {
            m_UnalignedCompressOStream.reset(new CCompressOStream(
                                   args[kArgUnalignedOutput].AsOutputFile(),
                                   CCompressOStream::eGZipFile));
            m_UnalignedOutputStream = m_UnalignedCompressOStream.get();
        }
        else {
            m_UnalignedOutputStream = &args[kArgUnalignedOutput].AsOutputFile();
        }
    }
}
 
CNcbiIstream&
CStdCmdLineArgs::GetInputStream() const
{
    // programmer must ensure the ExtractAlgorithmOptions method is called
    // before this method is invoked
    if ( !m_InputStream ) {
        abort();
    }
    return *m_InputStream;
}
 
CNcbiOstream&
CStdCmdLineArgs::GetOutputStream() const
{
    // programmer must ensure the ExtractAlgorithmOptions method is called
    // before this method is invoked
    _ASSERT(m_OutputStream);
    return *m_OutputStream;
}
 
void
CStdCmdLineArgs::SetInputStream(CRef<CTmpFile> input_file)
{
    m_QueryTmpInputFile = input_file;
    m_InputStream = &input_file->AsInputFile(CTmpFile::eIfExists_Throw);
}
 
void
CSearchStrategyArgs::SetArgumentDescriptions(CArgDescriptions& arg_desc)
{
    arg_desc.SetCurrentGroup("Search strategy options");
 
    arg_desc.AddOptionalKey(kArgInputSearchStrategy,
                            "filename",
                            "Search strategy to use",
                            CArgDescriptions::eInputFile);
    arg_desc.AddOptionalKey(kArgOutputSearchStrategy,
                            "filename",
                            "File name to record the search strategy used",
                            CArgDescriptions::eOutputFile);
    arg_desc.SetDependency(kArgInputSearchStrategy,
                           CArgDescriptions::eExcludes,
                           kArgOutputSearchStrategy);
 
    arg_desc.SetCurrentGroup("");
}
 
void
CSearchStrategyArgs::ExtractAlgorithmOptions(const CArgs& /* cmd_line_args */,
                                             CBlastOptions& /* options */)
{
}
 
CNcbiIstream*
CSearchStrategyArgs::GetImportStream(const CArgs& args) const
{
    CNcbiIstream* retval = NULL;
    if (args.Exist(kArgInputSearchStrategy) &&
        args[kArgInputSearchStrategy].HasValue()) {
        retval = &args[kArgInputSearchStrategy].AsInputFile();
    }
    return retval;
}
 
CNcbiOstream*
CSearchStrategyArgs::GetExportStream(const CArgs& args) const
{
    CNcbiOstream* retval = NULL;
    if (args.Exist(kArgOutputSearchStrategy) &&
        args[kArgOutputSearchStrategy].HasValue()) {
        retval = &args[kArgOutputSearchStrategy].AsOutputFile();
    }
    return retval;
}
 
CBlastAppArgs::CBlastAppArgs()
{
    m_SearchStrategyArgs.Reset(new CSearchStrategyArgs);
    m_Args.push_back(CRef<IBlastCmdLineArgs>(&*m_SearchStrategyArgs));
    m_IsUngapped = false;
}
 
CArgDescriptions*
CBlastAppArgs::SetCommandLine()
{
    return SetUpCommandLineArguments(m_Args);
}
 
CRef<CBlastOptionsHandle>
CBlastAppArgs::SetOptions(const CArgs& args)
{
    // We're recovering from a saved strategy or combining
    // CBlastOptions/CBlastOptionsHandle with command line options (in GBench,
    // see GB-1116), so we need to still extract
    // certain options from the command line, include overriding query
    // and/or database
    if (m_OptsHandle.NotEmpty()) {
        CBlastOptions& opts = m_OptsHandle->SetOptions();
        //opts.DebugDumpText(cerr, "OptionsBeforeLoop", 1);
        const bool mbidxargs_set = CMbIndexArgs::HasBeenSet(args);
        const bool dbargs_set = CBlastDatabaseArgs::HasBeenSet(args);
        NON_CONST_ITERATE(TBlastCmdLineArgs, arg, m_Args) {
            if (dynamic_cast<CMbIndexArgs*>(&**arg)) {
                if (mbidxargs_set)
                    (*arg)->ExtractAlgorithmOptions(args, opts);
            } else if (dynamic_cast<CBlastDatabaseArgs*>(&**arg)) {
                if (dbargs_set)
                    m_BlastDbArgs->ExtractAlgorithmOptions(args, opts);
            } else {
                (*arg)->ExtractAlgorithmOptions(args, opts);
            }
        }
        m_IsUngapped = !opts.GetGappedMode();
        try { m_OptsHandle->Validate(); }
        catch (const CBlastException& e) {
            NCBI_THROW(CInputException, eInvalidInput, e.GetMsg());
        }
        //opts.DebugDumpText(cerr, "OptionsAfterLoop", 1);
        return m_OptsHandle;
    }
 
    CBlastOptions::EAPILocality locality =
        (args.Exist(kArgRemote) && args[kArgRemote])
        ? CBlastOptions::eRemote
        : CBlastOptions::eLocal;
 
    // This is needed as a CRemoteBlast object and its options are instantiated
    // to create the search strategy
    if (GetExportSearchStrategyStream(args) ||
           m_FormattingArgs->ArchiveFormatRequested(args)) {
        locality = CBlastOptions::eBoth;
    }
 
    CRef<CBlastOptionsHandle> retval(x_CreateOptionsHandle(locality, args));
    CBlastOptions& opts = retval->SetOptions();
    NON_CONST_ITERATE(TBlastCmdLineArgs, arg, m_Args) {
        (*arg)->ExtractAlgorithmOptions(args, opts);
    }
 
    m_IsUngapped = !opts.GetGappedMode();
    try { retval->Validate(); }
    catch (const CBlastException& e) {
        NCBI_THROW(CInputException, eInvalidInput, e.GetMsg());
    }
    return retval;
}
 
void CBlastAppArgs::SetTask(const string& task)
{
#if _BLAST_DEBUG
    ThrowIfInvalidTask(task);
#endif
    m_Task.assign(task);
}
 
/// Get the input stream
CNcbiIstream& CBlastAppArgs::GetInputStream() {
    return m_StdCmdLineArgs->GetInputStream();
}
/// Get the output stream
CNcbiOstream& CBlastAppArgs::GetOutputStream() {
    return m_StdCmdLineArgs->GetOutputStream();
}
 
CArgDescriptions*
SetUpCommandLineArguments(TBlastCmdLineArgs& args)
{
    unique_ptr<CArgDescriptions> retval(new CArgDescriptions);
 
    // Create the groups so that the ordering is established
    retval->SetCurrentGroup("Input query options");
    retval->SetCurrentGroup("General search options");
    retval->SetCurrentGroup("BLAST database options");
    retval->SetCurrentGroup("BLAST-2-Sequences options");
    retval->SetCurrentGroup("Formatting options");
    retval->SetCurrentGroup("Query filtering options");
    retval->SetCurrentGroup("Restrict search or results");
    retval->SetCurrentGroup("Discontiguous MegaBLAST options");
    retval->SetCurrentGroup("Statistical options");
    retval->SetCurrentGroup("Search strategy options");
    retval->SetCurrentGroup("Extension options");
    retval->SetCurrentGroup("");
 
 
    NON_CONST_ITERATE(TBlastCmdLineArgs, arg, args) {
        (*arg)->SetArgumentDescriptions(*retval);
    }
    return retval.release();
}
 
CRef<CBlastOptionsHandle>
CBlastAppArgs::x_CreateOptionsHandleWithTask
    (CBlastOptions::EAPILocality locality, const string& task)
{
    _ASSERT(!task.empty());
    CRef<CBlastOptionsHandle> retval;
    SetTask(task);
    retval.Reset(CBlastOptionsFactory::CreateTask(GetTask(), locality));
    _ASSERT(retval.NotEmpty());
    return retval;
}
 
void
CBlastAppArgs::x_IssueWarningsForIgnoredOptions(const CArgs& args)
{
    set<string> can_override;
    can_override.insert(kArgQuery);
    can_override.insert(kArgQueryLocation);
    can_override.insert(kArgSubject);
    can_override.insert(kArgSubjectLocation);
    can_override.insert(kArgUseLCaseMasking);
    can_override.insert(kArgDb);
    can_override.insert(kArgDbSize);
    can_override.insert(kArgEntrezQuery);
    can_override.insert(kArgDbSoftMask);
    can_override.insert(kArgDbHardMask);
    can_override.insert(kArgUseIndex);
    can_override.insert(kArgIndexName);
    can_override.insert(kArgStrand);
    can_override.insert(kArgParseDeflines);
    can_override.insert(kArgOutput);
    can_override.insert(kArgOutputFormat);
    can_override.insert(kArgNumDescriptions);
    can_override.insert(kArgNumAlignments);
    can_override.insert(kArgMaxTargetSequences);
    can_override.insert(kArgRemote);
    can_override.insert(kArgNumThreads);
    can_override.insert(kArgInputSearchStrategy);
    can_override.insert(kArgRemote);
    can_override.insert("remote_verbose");
    can_override.insert("verbose");
 
    // this stores the arguments (and their defaults) that cannot be overriden
    map<string, string> has_defaults;
    EBlastProgramType prog = m_OptsHandle->GetOptions().GetProgramType();
    has_defaults[kArgCompBasedStats] =
            Blast_ProgramIsRpsBlast(prog) ? kDfltArgCompBasedStatsDelta:kDfltArgCompBasedStats;
    // FIX the line below for igblast, and add igblast options
    has_defaults[kArgEvalue] = NStr::DoubleToString(BLAST_EXPECT_VALUE);
    has_defaults[kTask] = m_Task;
    has_defaults[kArgOldStyleIndex] = kDfltArgOldStyleIndex;
 
    if (Blast_QueryIsProtein(prog)) {
        if (NStr::Find(m_Task, "blastp") != NPOS ||
            NStr::Find(m_Task, "psiblast") != NPOS) {
            has_defaults[kArgSegFiltering] = kDfltArgNoFiltering;
        } else {
            has_defaults[kArgSegFiltering] = kDfltArgSegFiltering;
        }
        has_defaults[kArgLookupTableMaskingOnly] =
            kDfltArgLookupTableMaskingOnlyProt;
        has_defaults[kArgGapTrigger] =
            NStr::IntToString((int)BLAST_GAP_TRIGGER_PROT);
    } else {
        has_defaults[kArgDustFiltering] = kDfltArgDustFiltering;
        has_defaults[kArgLookupTableMaskingOnly] =
            kDfltArgLookupTableMaskingOnlyNucl;
        has_defaults[kArgGapTrigger] =
            NStr::IntToString((int)BLAST_GAP_TRIGGER_NUCL);
    }
    has_defaults[kArgOffDiagonalRange] =
        NStr::IntToString(kDfltOffDiagonalRange);
    has_defaults[kArgMaskLevel] = kDfltArgMaskLevel;
    has_defaults[kArgMaxIntronLength] =
        NStr::IntToString(kDfltArgMaxIntronLength);
    has_defaults[kArgQueryGeneticCode] = NStr::IntToString((int)BLAST_GENETIC_CODE);
    has_defaults[kArgDbGeneticCode] = NStr::IntToString((int)BLAST_GENETIC_CODE);
    // pssm engine/psiblast default options
    has_defaults[kArgPSIPseudocount] =
        NStr::IntToString(PSI_PSEUDO_COUNT_CONST);
    has_defaults[kArgPSIInclusionEThreshold] =
        NStr::DoubleToString(PSI_INCLUSION_ETHRESH);
    has_defaults[kArgPSINumIterations] =
        NStr::IntToString(kDfltArgPSINumIterations);
 
    // get arguments, remove the supported ones and warn about those that
    // cannot be overridden.
    typedef vector< CRef<CArgValue> > TArgs;
    TArgs arguments = args.GetAll();
    ITERATE(TArgs, a, arguments) {
        const string& arg_name = (*a)->GetName();
        const string& arg_value = (*a)->AsString();
        // if it has a default value, ignore it if it's not different from the
        // default, otherwise, issue a warning
        if (has_defaults.find(arg_name) != has_defaults.end()) {
            if (has_defaults[arg_name] == arg_value) {
                continue;
            } else {
                if (arg_name == kTask && arg_value == "megablast") {
                    // No need to issue warning here, as it's OK to change this
                    continue;
                }
                ERR_POST(Warning << arg_name << " cannot be overridden when "
                         "using a search strategy");
            }
        }
        // if the argument cannot be overridden, issue a warning
        if (can_override.find(arg_name) == can_override.end()) {
            ERR_POST(Warning << arg_name << " cannot be overridden when "
                     "using a search strategy");
        }
    }
}
 
CRef<CBlastOptionsHandle>
CBlastAppArgs::SetOptionsForSavedStrategy(const CArgs& args)
{
    if(m_OptsHandle.Empty())
    {
        NCBI_THROW(CInputException, eInvalidInput, "Empty Blast Options Handle");
    }
 
    // We're recovering from a saved strategy, so we need to still extract
    // certain options from the command line, include overriding query
    // and/or database
    CBlastOptions& opts = m_OptsHandle->SetOptions();
    // invoke ExtractAlgorithmOptions on certain argument classes, i.e.: those
    // that should have their arguments overriden
    m_QueryOptsArgs->ExtractAlgorithmOptions(args, opts);
    m_StdCmdLineArgs->ExtractAlgorithmOptions(args, opts);
    m_RemoteArgs->ExtractAlgorithmOptions(args, opts);
    m_DebugArgs->ExtractAlgorithmOptions(args, opts);
    m_FormattingArgs->ExtractAlgorithmOptions(args, opts);
    m_MTArgs->ExtractAlgorithmOptions(args, opts);
    if (CBlastDatabaseArgs::HasBeenSet(args)) {
          m_BlastDbArgs->ExtractAlgorithmOptions(args, opts);
    }
    if (CMbIndexArgs::HasBeenSet(args)) {
        NON_CONST_ITERATE(TBlastCmdLineArgs, arg, m_Args) {
            if (dynamic_cast<CMbIndexArgs*>(arg->GetPointer()) != NULL) {
                (*arg)->ExtractAlgorithmOptions(args, opts);
            }
        }
    }
    m_IsUngapped = !opts.GetGappedMode();
    x_IssueWarningsForIgnoredOptions(args);
    try { m_OptsHandle->Validate(); }
    catch (const CBlastException& e) {
        NCBI_THROW(CInputException, eInvalidInput, e.GetMsg());
    }
    return m_OptsHandle;
}
 
END_SCOPE(blast)
END_NCBI_SCOPE