blastx_args.cpp

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/*  $Id: blastx_args.cpp 100875 2023-09-22 12:46:36Z madden $
 * ===========================================================================
 *
 *                            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 official 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.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  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.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Author: Christiam Camacho
 *
 */
 
/** @file blastx_args.cpp
 * Implementation of the BLASTX command line arguments
 */
 
#include <ncbi_pch.hpp>
#include <algo/blast/blastinput/blastx_args.hpp>
#include <algo/blast/api/blastx_options.hpp>
#include <algo/blast/blastinput/blast_input_aux.hpp>
#include <algo/blast/api/version.hpp>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(blast)
USING_SCOPE(objects);
 
CBlastxAppArgs::CBlastxAppArgs()
{
    CRef<IBlastCmdLineArgs> arg;
    static const string kProgram("blastx");
    arg.Reset(new CProgramDescriptionArgs(kProgram,
                                  "Translated Query-Protein Subject BLAST"));
    const bool kQueryIsProtein = false;
    m_Args.push_back(arg);
    m_ClientId = kProgram + " " + CBlastVersion().Print();
 
    static const char kDefaultTask[] = "blastx";
    SetTask(kDefaultTask);
    set<string> tasks;
    tasks.insert(kDefaultTask);
    tasks.insert("blastx-fast");
    arg.Reset(new CTaskCmdLineArgs(tasks, kDefaultTask));
    m_Args.push_back(arg);
 
    m_BlastDbArgs.Reset(new CBlastDatabaseArgs);
    m_BlastDbArgs->SetDatabaseMaskingSupport(true);
    m_BlastDbArgs->SetIPGFilteringSupport(true);
    arg.Reset(m_BlastDbArgs);
    m_Args.push_back(arg);
 
    m_StdCmdLineArgs.Reset(new CStdCmdLineArgs);
    arg.Reset(m_StdCmdLineArgs);
    m_Args.push_back(arg);
 
    // N.B.: query is not protein because the options are applied on the 
    // translated query
    arg.Reset(new CGenericSearchArgs( !kQueryIsProtein ));
    m_Args.push_back(arg);
 
    //Disable until OOF is supported in align manager
    //SB-1043
    //arg.Reset(new CFrameShiftArgs);
    //m_Args.push_back(arg);
 
    arg.Reset(new CLargestIntronSizeArgs);
    m_Args.push_back(arg);
 
    // N.B.: query is not protein because the filtering is applied on the 
    // translated query
    arg.Reset(new CFilteringArgs( !kQueryIsProtein ));
    m_Args.push_back(arg);
 
    arg.Reset(new CMatrixNameArg);
    m_Args.push_back(arg);
 
    arg.Reset(new CWordThresholdArg);
    m_Args.push_back(arg);
 
    m_HspFilteringArgs.Reset(new CHspFilteringArgs);
    arg.Reset(m_HspFilteringArgs);
    m_Args.push_back(arg);
 
    arg.Reset(new CWindowSizeArg);
    m_Args.push_back(arg);
 
    arg.Reset(new CGappedArgs);
    m_Args.push_back(arg);
 
    m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein));
    arg.Reset(m_QueryOptsArgs);
    m_Args.push_back(arg);
 
    arg.Reset(new CGeneticCodeArgs(CGeneticCodeArgs::eQuery));
    m_Args.push_back(arg);
 
    m_FormattingArgs.Reset(new CFormattingArgs);
    arg.Reset(m_FormattingArgs);
    m_Args.push_back(arg);
 
    m_MTArgs.Reset(new CMTArgs(CThreadable::kMinNumThreads, CMTArgs::eSplitByDB));
    arg.Reset(m_MTArgs);
    m_Args.push_back(arg);
 
    m_RemoteArgs.Reset(new CRemoteArgs);
    arg.Reset(m_RemoteArgs);
    m_Args.push_back(arg);
 
    arg.Reset(new CCompositionBasedStatsArgs);
    m_Args.push_back(arg);
 
    m_DebugArgs.Reset(new CDebugArgs);
    arg.Reset(m_DebugArgs);
    m_Args.push_back(arg);
}
 
CRef<CBlastOptionsHandle> 
CBlastxAppArgs::x_CreateOptionsHandle(CBlastOptions::EAPILocality locality,
                                      const CArgs& args)
{
    _ASSERT(args.Exist(kTask));
    _ASSERT(args[kTask].HasValue());
    return x_CreateOptionsHandleWithTask(locality, args[kTask].AsString());
}
 
int
CBlastxAppArgs::GetQueryBatchSize() const
{
    bool is_remote = (m_RemoteArgs.NotEmpty() && m_RemoteArgs->ExecuteRemotely());
    bool is_default = true;
    return blast::GetQueryBatchSize(eBlastx, m_IsUngapped, is_remote, is_default, 
          GetTask());
}
 
/// Get the input stream
CNcbiIstream&
CBlastxNodeArgs::GetInputStream()
{
    if ( !m_InputStream ) {
        abort();
    }
    return *m_InputStream;
}
/// Get the output stream
CNcbiOstream&
CBlastxNodeArgs::GetOutputStream()
{
    return m_OutputStream;
}
 
CBlastxNodeArgs::CBlastxNodeArgs(const string & input)
{
    m_InputStream = new CNcbiIstrstream(input);
}
 
CBlastxNodeArgs::~CBlastxNodeArgs()
{
    if (m_InputStream) {
        delete m_InputStream;
        m_InputStream = NULL;
    }
}
 
int
CBlastxNodeArgs::GetQueryBatchSize() const
{
    bool is_remote = (m_RemoteArgs.NotEmpty() && m_RemoteArgs->ExecuteRemotely());
    bool split_by_query = true;
    bool use_default = true;
    return blast::GetQueryBatchSize(eBlastx, m_IsUngapped, is_remote, use_default, GetTask(), split_by_query);
}
 
CRef<CBlastOptionsHandle>
CBlastxNodeArgs::x_CreateOptionsHandle(CBlastOptions::EAPILocality locality, const CArgs& args)
{
    return CBlastxAppArgs::x_CreateOptionsHandle(locality, args);
}
 
END_SCOPE(blast)
END_NCBI_SCOPE