C++ (Cpp) CBlastVersionの例

コード例 #1

ファイル: psiblast_args.cpp プロジェクト: jackgopack4/pico-blast

CPsiBlastAppArgs::CPsiBlastAppArgs()
{
    bool const kQueryIsProtein = true;
    bool const kFilterByDefault = false;
    static const string kProgram("psiblast");
    CRef<IBlastCmdLineArgs> arg;
    arg.Reset(new CProgramDescriptionArgs(kProgram,
                                          "Position-Specific Initiated BLAST"));
    m_Args.push_back(arg);
    m_ClientId = kProgram + " " + CBlastVersion().Print();

    static const string kDefaultTask = "psiblast";
    SetTask(kDefaultTask);

    m_BlastDbArgs.Reset(new CBlastDatabaseArgs);
    arg.Reset(m_BlastDbArgs);
    m_Args.push_back(arg);

    m_StdCmdLineArgs.Reset(new CStdCmdLineArgs);
    arg.Reset(m_StdCmdLineArgs);
    m_Args.push_back(arg);

    arg.Reset(new CGenericSearchArgs(kQueryIsProtein));
    m_Args.push_back(arg);

    arg.Reset(new CFilteringArgs(kQueryIsProtein, kFilterByDefault));
    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);

    m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein));
    arg.Reset(m_QueryOptsArgs);
    m_Args.push_back(arg);

    m_FormattingArgs.Reset(new CFormattingArgs);
    arg.Reset(m_FormattingArgs);
    m_Args.push_back(arg);

    m_MTArgs.Reset(new CMTArgs);
    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);

    arg.Reset(new CGapTriggerArgs(kQueryIsProtein));
    m_Args.push_back(arg);

    m_PsiBlastArgs.Reset(new CPsiBlastArgs(CPsiBlastArgs::eProteinDb));
    arg.Reset(m_PsiBlastArgs);
    m_Args.push_back(arg);

    arg.Reset(new CPssmEngineArgs);
    m_Args.push_back(arg);

    arg.Reset(new CPhiBlastArgs);
    m_Args.push_back(arg);

    m_DebugArgs.Reset(new CDebugArgs);
    arg.Reset(m_DebugArgs);
    m_Args.push_back(arg);
}

コード例 #2

ファイル: igblastn_args.cpp プロジェクト: jackgopack4/pico-blast

CIgBlastnAppArgs::CIgBlastnAppArgs()
{
    CRef<IBlastCmdLineArgs> arg;
    static const string kProgram("igblastn");
    arg.Reset(new CProgramDescriptionArgs(kProgram,
                                          "Nucleotide-Nucleotide BLAST for immunoglobulin sequences"));
    const bool kQueryIsProtein = false;
    m_Args.push_back(arg);
    m_ClientId = kProgram + " " + CBlastVersion().Print();

    /*
    static const string kDefaultTask = "blastn";
    SetTask(kDefaultTask);
    set<string> tasks
        (CBlastOptionsFactory::GetTasks(CBlastOptionsFactory::eNuclNucl));
    arg.Reset(new CTaskCmdLineArgs(tasks, kDefaultTask));
    m_Args.push_back(arg); */

    m_IgBlastArgs.Reset(new CIgBlastArgs(false));
    arg.Reset(m_IgBlastArgs);
    m_Args.push_back(arg);    

    m_BlastDbArgs.Reset(new CBlastDatabaseArgs(false, false, true));
    m_BlastDbArgs->SetDatabaseMaskingSupport(true);
    arg.Reset(m_BlastDbArgs);
    m_Args.push_back(arg);

    m_StdCmdLineArgs.Reset(new CStdCmdLineArgs);
    arg.Reset(m_StdCmdLineArgs);
    m_Args.push_back(arg);

    arg.Reset(new CGenericSearchArgs(kQueryIsProtein, false, true, false, true));
    m_Args.push_back(arg);

    arg.Reset(new CNuclArgs);
    m_Args.push_back(arg);

    /*
    arg.Reset(new CDiscontiguousMegablastArgs);
    m_Args.push_back(arg);

    arg.Reset(new CFilteringArgs(kQueryIsProtein));
    m_Args.push_back(arg); */

    arg.Reset(new CGappedArgs);
    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 COffDiagonalRangeArg);
    m_Args.push_back(arg);

    /*
    arg.Reset(new CMbIndexArgs);
    m_Args.push_back(arg); */

    m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein));
    arg.Reset(m_QueryOptsArgs);
    m_Args.push_back(arg);

    m_FormattingArgs.Reset(new CFormattingArgs(true));
    arg.Reset(m_FormattingArgs);
    m_Args.push_back(arg);

    m_MTArgs.Reset(new CMTArgs);
    arg.Reset(m_MTArgs);
    m_Args.push_back(arg);

    m_RemoteArgs.Reset(new CRemoteArgs);
    arg.Reset(m_RemoteArgs);
    m_Args.push_back(arg);

    m_DebugArgs.Reset(new CDebugArgs);
    arg.Reset(m_DebugArgs);
    m_Args.push_back(arg);
}

コード例 #3

ファイル: blastn_args.cpp プロジェクト: DmitrySigaev/ncbi

CBlastnAppArgs::CBlastnAppArgs()
{
    CRef<IBlastCmdLineArgs> arg;
    static const char kProgram[] = "blastn";
    arg.Reset(new CProgramDescriptionArgs(kProgram,
                                          "Nucleotide-Nucleotide BLAST"));
    const bool kQueryIsProtein = false;
    m_Args.push_back(arg);
    m_ClientId = string(kProgram) + " " + CBlastVersion().Print();

    static const char kDefaultTask[] = "megablast";
    SetTask(kDefaultTask);
    set<string> tasks
        (CBlastOptionsFactory::GetTasks(CBlastOptionsFactory::eNuclNucl));
    tasks.erase("vecscreen"); // vecscreen has its own program
    arg.Reset(new CTaskCmdLineArgs(tasks, kDefaultTask));
    m_Args.push_back(arg);

    m_BlastDbArgs.Reset(new CBlastDatabaseArgs);
    m_BlastDbArgs->SetDatabaseMaskingSupport(true);
    arg.Reset(m_BlastDbArgs);
    m_Args.push_back(arg);

    m_StdCmdLineArgs.Reset(new CStdCmdLineArgs);
    arg.Reset(m_StdCmdLineArgs);
    m_Args.push_back(arg);

    arg.Reset(new CGenericSearchArgs(kQueryIsProtein, false, true));
    m_Args.push_back(arg);

    arg.Reset(new CNuclArgs);
    m_Args.push_back(arg);

    arg.Reset(new CDiscontiguousMegablastArgs);
    m_Args.push_back(arg);

    arg.Reset(new CFilteringArgs(kQueryIsProtein));
    m_Args.push_back(arg);

    arg.Reset(new CGappedArgs);
    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 COffDiagonalRangeArg);
    m_Args.push_back(arg);

    arg.Reset(new CMbIndexArgs);
    m_Args.push_back(arg);

    m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein));
    arg.Reset(m_QueryOptsArgs);
    m_Args.push_back(arg);

    m_FormattingArgs.Reset(new CFormattingArgs(false, CFormattingArgs::eIsSAM));
    arg.Reset(m_FormattingArgs);
    m_Args.push_back(arg);

    m_MTArgs.Reset(new CMTArgs);
    arg.Reset(m_MTArgs);
    m_Args.push_back(arg);

    m_RemoteArgs.Reset(new CRemoteArgs);
    arg.Reset(m_RemoteArgs);
    m_Args.push_back(arg);

    m_DebugArgs.Reset(new CDebugArgs);
    arg.Reset(m_DebugArgs);
    m_Args.push_back(arg);
}

コード例 #4

ファイル: blastn_args.cpp プロジェクト: OpenHero/gblastn

CBlastnAppArgs::CBlastnAppArgs()
{
    CRef<IBlastCmdLineArgs> arg;
    static const string kProgram("blastn");
    arg.Reset(new CProgramDescriptionArgs(kProgram,
                                          "Nucleotide-Nucleotide BLAST"));
    const bool kQueryIsProtein = false;
    m_Args.push_back(arg);
    m_ClientId = kProgram + " " + CBlastVersion().Print();

    static const string kDefaultTask = "megablast";
    SetTask(kDefaultTask);
    set<string> tasks
        (CBlastOptionsFactory::GetTasks(CBlastOptionsFactory::eNuclNucl));
    tasks.erase("vecscreen"); // SB-501: for now, remove vecscreen
    arg.Reset(new CTaskCmdLineArgs(tasks, kDefaultTask));
    m_Args.push_back(arg);

    m_BlastDbArgs.Reset(new CBlastDatabaseArgs);
    m_BlastDbArgs->SetDatabaseMaskingSupport(true);
    arg.Reset(m_BlastDbArgs);
    m_Args.push_back(arg);

    m_StdCmdLineArgs.Reset(new CStdCmdLineArgs);
    arg.Reset(m_StdCmdLineArgs);
    m_Args.push_back(arg);

    arg.Reset(new CGenericSearchArgs(kQueryIsProtein, false, true));
    m_Args.push_back(arg);

    arg.Reset(new CNuclArgs);
    m_Args.push_back(arg);

    arg.Reset(new CDiscontiguousMegablastArgs);
    m_Args.push_back(arg);

    arg.Reset(new CFilteringArgs(kQueryIsProtein));
    m_Args.push_back(arg);

    arg.Reset(new CGappedArgs);
    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 COffDiagonalRangeArg);
    m_Args.push_back(arg);

    arg.Reset(new CMbIndexArgs);
    m_Args.push_back(arg);

    m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein));
    arg.Reset(m_QueryOptsArgs);
    m_Args.push_back(arg);

    m_FormattingArgs.Reset(new CFormattingArgs);
    arg.Reset(m_FormattingArgs);
    m_Args.push_back(arg);

    m_MTArgs.Reset(new CMTArgs);
    arg.Reset(m_MTArgs);
    m_Args.push_back(arg);

    m_RemoteArgs.Reset(new CRemoteArgs);
    arg.Reset(m_RemoteArgs);
    m_Args.push_back(arg);

    m_DebugArgs.Reset(new CDebugArgs);
    arg.Reset(m_DebugArgs);
    m_Args.push_back(arg);

	//////////////////////////////////////////////////////////////////////////
	//added by kyzhao for GPU blastn
	/* *********** START ************* */

	m_GpuArgs.Reset(new CGpuArgs);
	arg.Reset(m_GpuArgs);
	m_Args.push_back(arg);

	/* ********** FINISH ************* */
}

コード例 #5

ファイル: blastp_args.cpp プロジェクト: jackgopack4/pico-blast

CBlastpAppArgs::CBlastpAppArgs()
{
    CRef<IBlastCmdLineArgs> arg;
    static const string kProgram("blastp");
    arg.Reset(new CProgramDescriptionArgs(kProgram, "Protein-Protein BLAST"));
    const bool kQueryIsProtein = true;
    bool const kFilterByDefault = false;
    m_Args.push_back(arg);
    m_ClientId = kProgram + " " + CBlastVersion().Print();

    static const string kDefaultTask = "blastp";
    SetTask(kDefaultTask);
    set<string> tasks
        (CBlastOptionsFactory::GetTasks(CBlastOptionsFactory::eProtProt));
    arg.Reset(new CTaskCmdLineArgs(tasks, kDefaultTask));
    m_Args.push_back(arg);

    m_BlastDbArgs.Reset(new CBlastDatabaseArgs);
    m_BlastDbArgs->SetDatabaseMaskingSupport(true);
    arg.Reset(m_BlastDbArgs);
    m_Args.push_back(arg);

    m_StdCmdLineArgs.Reset(new CStdCmdLineArgs);
    arg.Reset(m_StdCmdLineArgs);
    m_Args.push_back(arg);

    arg.Reset(new CGenericSearchArgs(kQueryIsProtein));
    m_Args.push_back(arg);

    arg.Reset(new CFilteringArgs(kQueryIsProtein, kFilterByDefault));
    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);

    m_QueryOptsArgs.Reset(new CQueryOptionsArgs(kQueryIsProtein));
    arg.Reset(m_QueryOptsArgs);
    m_Args.push_back(arg);

    m_FormattingArgs.Reset(new CFormattingArgs);
    arg.Reset(m_FormattingArgs);
    m_Args.push_back(arg);

    m_MTArgs.Reset(new CMTArgs);
    arg.Reset(m_MTArgs);
    m_Args.push_back(arg);

    arg.Reset(new CGappedArgs);
    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);
}