select_feature.cpp

来自「ncbi源码」· C++ 代码 · 共 218 行

/*
 * ===========================================================================
 * PRODUCTION $Log: select_feature.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 20:55:46  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: select_feature.cpp,v 1000.1 2004/06/01 20:55:46 gouriano Exp $
 * ===========================================================================
 *
 *                            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.
 *
 * ===========================================================================
 *
 * Authors:  Mike DiCuccio
 *
 * File Description:
 *    CAlgoPlugin_SelectFeature -- implements the algorithm to calculate GC composition
 */

#include <ncbi_pch.hpp>
#include "select_feature.hpp"

#include <gui/core/plugin_utils.hpp>
#include <gui/core/version.hpp>
#include <gui/dialogs/col/multi_col_dlg.hpp>
#include <gui/plugin/AlgoCommand.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginRequest.hpp>
#include <gui/plugin/PluginValueConstraint.hpp>
#include <gui/objutils/utils.hpp>
#include <objects/seqfeat/SeqFeatData.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objmgr/feat_ci.hpp>
#include <util/static_map.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);


//
// static lookup table for converting string-based feature type to actual
// feature type
//
// these must be in "ASCIIbetical" order; beware of the fact that
// closing quotes sort after spaces.
//
typedef pair<const char*, CSeqFeatData::E_Choice> TFeatType;
static const TFeatType s_FeatureTypes[] = {
    TFeatType("Biological source",           CSeqFeatData::e_Biosrc),
    TFeatType("Bond",                        CSeqFeatData::e_Bond),
    TFeatType("Coding region",               CSeqFeatData::e_Cdregion),
    TFeatType("Comment",                     CSeqFeatData::e_Comment),
    TFeatType("Gene",                        CSeqFeatData::e_Gene),
    TFeatType("Heterogen",                   CSeqFeatData::e_Het),
    TFeatType("Imported feature",            CSeqFeatData::e_Imp),
    TFeatType("Non-standard residue",        CSeqFeatData::e_Non_std_residue),
    TFeatType("Numbering system",            CSeqFeatData::e_Num),
    TFeatType("Organism",                    CSeqFeatData::e_Org),
    TFeatType("Protein",                     CSeqFeatData::e_Prot),
    TFeatType("Protein secondary structure", CSeqFeatData::e_Psec_str),
    TFeatType("Publication",                 CSeqFeatData::e_Pub),
    TFeatType("RNA",                         CSeqFeatData::e_Rna),
    TFeatType("Region",                      CSeqFeatData::e_Region),
    TFeatType("Restriction site",            CSeqFeatData::e_Rsite),
    TFeatType("Sequence",                    CSeqFeatData::e_Seq),
    TFeatType("Site",                        CSeqFeatData::e_Site),
    TFeatType("Transcription Initiation",    CSeqFeatData::e_Txinit),
    TFeatType("User-defined",                CSeqFeatData::e_User)
};

typedef CStaticArrayMap<const char*, CSeqFeatData::E_Choice, PCase> TFeatTypeMap;
static const TFeatTypeMap s_FeatureMap(s_FeatureTypes, sizeof(s_FeatureTypes));


CAlgoPlugin_SelectFeature::~CAlgoPlugin_SelectFeature()
{
}


// standard info boilerplate
void CAlgoPlugin_SelectFeature::GetInfo(CPluginInfo& info)
{
    info.Reset();

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CAlgoPlugin_SelectFeature", "Search/Features",
                 "Search for features matching particular critera",
                 "");

    // command info
    CPluginCommandSet& cmds = info.SetCommands();
    CPluginCommand&    args = cmds.AddAlgoCommand(eAlgoCommand_run);
    args.AddArgument("locs", "Locations to evaluate",
                     CSeq_loc::GetTypeInfo(),
                     CPluginArg::TData::e_Array);

    // create a constraint type for features
    CRef<CPluginValueConstraint> type_cons
        (CPluginValueConstraint::CreateSet());
    ITERATE (TFeatTypeMap, iter, s_FeatureMap) {
        *type_cons, iter->first;
    }

    // constrain to features of type
    args.AddOptionalArgument("type", "Feature type",
                             CPluginArg::eString);
    args.SetConstraint("type", *type_cons);

    // constrain to features of subtype

    // constrain to features whose label matches a given pattern
    args.AddOptionalArgument("label_pattern",
                             "Feature label like",
                             CPluginArg::eString);

    // constrain to features within near_range bases of a feature of a given
    // type
    args.AddOptionalArgument("near_type", "Near features of type",
                             CPluginArg::eString);
    args.SetConstraint("near_type", *type_cons);
    args.AddOptionalArgument("near_range", "Near range",
                             CPluginArg::eInteger);
}


void CAlgoPlugin_SelectFeature::RunCommand(CPluginMessage& msg)
{
    const CPluginCommand& args = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();
    reply.SetStatus(eMessageStatus_failed);

    plugin_args::TLocList locs;
    GetArgValue(args["locs"], locs);

    SAnnotSelector sel = CSeqUtils::GetAnnotSelector();

    if (args.HasArgument("type")  &&  CPluginUtils::IsValid(args["type"])) {
        CSeqFeatData::E_Choice type =
            s_FeatureMap.find(args["type"].AsString().c_str())->second;
        sel.SetFeatType(type);
    }

    string pattern;
    if (args.HasArgument("label_pattern")  &&
        CPluginUtils::IsValid(args["label_pattern"])) {
        pattern = args["label_pattern"].AsString();
    }

    ITERATE (plugin_args::TLocList, iter, locs) {
        const CSeq_loc& loc  = *iter->second;
        const IDocument& doc = *iter->first;

        CFeat_CI feat_iter(doc.GetScope(), loc, sel);
        for ( ;  feat_iter;  ++feat_iter) {
            reply.AddObject(doc, feat_iter->GetOriginalFeature());
        }
    }

    reply.SetStatus(eMessageStatus_success);
}


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: select_feature.cpp,v $
 * Revision 1000.1  2004/06/01 20:55:46  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.6
 *
 * Revision 1.6  2004/05/21 22:27:47  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.5  2004/05/03 13:05:42  dicuccio
 * gui/utils --> gui/objutils where needed
 *
 * Revision 1.4  2004/02/04 18:05:34  grichenk
 * Added annotation filtering by set of types/subtypes.
 * Renamed *Choice to *Type in SAnnotSelector.
 *
 * Revision 1.3  2004/01/29 17:27:18  ucko
 * Ensure that TFeatTypeMap specifies comparing C strings by value rather
 * than memory location.
 *
 * Revision 1.2  2004/01/28 03:59:43  ucko
 * Fix order of s_FeatureTypes.
 *
 * Revision 1.1  2004/01/27 18:38:31  dicuccio
 * Initial revision
 *
 * ===========================================================================
 */