tree_loader.cpp

来自「ncbi源码」· C++ 代码 · 共 247 行

/*
 * ===========================================================================
 * PRODUCTION $Log: tree_loader.cpp,v $
 * PRODUCTION Revision 1000.2  2004/06/02 20:24:21  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: tree_loader.cpp,v 1000.2 2004/06/02 20:24:21 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:  Josh Cherry
 *
 * File Description:
 *    CDataPlugin_TreeLoader - load a phylogenetic tree from a file
 */

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

#include <gui/core/doc_exception.hpp>
#include <gui/core/doc_manager.hpp>
#include <gui/core/idocument.hpp>
#include <gui/core/plugin_utils.hpp>
#include <gui/core/version.hpp>
#include <gui/plugin/PluginCommandSet.hpp>
#include <gui/plugin/PluginInfo.hpp>
#include <gui/plugin/PluginValueConstraint.hpp>
#include <gui/utils/message_box.hpp>
#include <gui/objutils/utils.hpp>

#include <algo/phy_tree/phy_tree_serial.hpp>

#include <objects/biotree/BioTreeContainer.hpp>
#include <objects/biotree/FeatureDescr.hpp>
#include <objects/biotree/Node.hpp>
#include <objects/biotree/NodeSet.hpp>
#include <objects/biotree/NodeFeature.hpp>
#include <objects/biotree/NodeFeatureSet.hpp>
#include <objects/biotree/FeatureDictSet.hpp>


BEGIN_NCBI_SCOPE
USING_SCOPE(objects);

//
// factory implementations
//

void CDataPlugin_TreeLoader::GetInfo(CPluginInfo& info)
{
    info.Reset();

    // version info macro
    info.SetInfo(CPluginVersion::eMajor, CPluginVersion::eMinor, 0,
                 string(__DATE__) + " " + string(__TIME__),
                 "CDataPlugin_TreeLoader",
                 "Phylogenetic Tree File (Newick)",
                 "Read a phylogenetic tree in Newick format",
                 "");

    // command info
    CPluginCommandSet& cmds     = info.SetCommands();
    CPluginCommand& load_args   = cmds.AddDataCommand(eDataCommand_load);

    load_args.AddArgument("file", "File name", CPluginArg::eFile);
    load_args.AddArgument("make_btc",
                          "Create BioTreeContainer object "
                          "(experimental)",
                          CPluginArg::eBoolean);
}


//
// Default ctor
//
CDataPlugin_TreeLoader::CDataPlugin_TreeLoader()
{
}


//
// One and only dtor
//
CDataPlugin_TreeLoader::~CDataPlugin_TreeLoader()
{
}


/// Recursive function for adding TPhyTreeNodes to BioTreeContainer
static void s_AddNodeToBtc(CRef<CBioTreeContainer> btc, TPhyTreeNode* ptn,
                           int parent_uid, int& next_uid)
{
    const int label_fid = 0;
    const int dist_fid = 1;

    CRef<CNode> node;
    CRef<CNodeFeature> node_feature;
    int my_uid = next_uid++;

    // first do this node
    node = new CNode;
    node->SetId(my_uid);
    node->SetParent(parent_uid);
    if (ptn->GetValue().GetLabel() != "") {
        node_feature = new CNodeFeature;
        node_feature->SetFeatureid(label_fid);
        node_feature->SetValue(ptn->GetValue().GetLabel());
        node->SetFeatures().Set().push_back(node_feature);
    }
    if (ptn->GetValue().IsSetDist()) {
        node_feature = new CNodeFeature;
        node_feature->SetFeatureid(dist_fid);
        node_feature->SetValue
            (NStr::DoubleToString(ptn->GetValue().GetDist()));
        node->SetFeatures().Set().push_back(node_feature);
    }

    btc->SetNodes().Set().push_back(node);

    // now do its children
    for (TPhyTreeNode::TNodeList_CI it = ptn->SubNodeBegin();
         it != ptn->SubNodeEnd();  ++it) {
        s_AddNodeToBtc(btc, *it, my_uid, next_uid);
    }
}


/// Conversion from TPhyTreeNode to CBioTreeContainer
static CRef<CBioTreeContainer> s_MakeBtc(TPhyTreeNode *tree)
{
    const int label_fid = 0;
    const int dist_fid = 1;

    CRef<CBioTreeContainer> btc(new CBioTreeContainer);
    CRef<CFeatureDescr> fdescr;

    fdescr = new CFeatureDescr();
    fdescr->SetId(label_fid);
    fdescr->SetName("label");
    btc->SetFdict().Set().push_back(fdescr);
    
    fdescr = new CFeatureDescr();
    fdescr->SetId(dist_fid);
    fdescr->SetName("dist");
    btc->SetFdict().Set().push_back(fdescr);

    int next_uid = 0;
    s_AddNodeToBtc(btc, tree, -1, next_uid);
    // unset parent id of root node
    btc->SetNodes().Set().front()->ResetParent();
    return btc;
}


//
// Load()
// This is a pure virtual requirement and is the main plugin hook.
//
void CDataPlugin_TreeLoader::Load(CPluginMessage& msg)
{
    const CPluginCommand& args = msg.GetRequest().GetCommand();
    CPluginReply& reply = msg.SetReply();

    string fname = args["file"].AsString();

    try {
        // load the tree
        CNcbiIfstream istr(fname.c_str());
        TPhyTreeNode *tree = ReadNewickTree(istr);

        // make a document containing this
        CRef<CScope> scope(new CScope(CDocManager::GetObjectManager()));
        scope->AddDefaults();
        IDocument* new_doc;
        if (args["make_btc"].AsBoolean()) {
            CRef<CBioTreeContainer> btc = s_MakeBtc(tree);
            new_doc = CDocManager::CreateDocument(*scope, *btc);
        } else {
            CRef<CPhyTreeSerial> stree(new CPhyTreeSerial(*tree));
            new_doc = CDocManager::CreateDocument(*scope, *stree);
        }
        delete tree;
        reply.AddObject(*new_doc);
        reply.SetStatus(eMessageStatus_success);
    }
    catch (exception& e) {
        _TRACE("failed to read tree file: " << e.what());
    }
    catch (...) {
        _TRACE("failed to read tree file: unknown error");
    }
}


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: tree_loader.cpp,v $
 * Revision 1000.2  2004/06/02 20:24:21  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.5
 *
 * Revision 1.5  2004/06/02 19:47:04  jcherry
 * Added option for creating CBioTreeContainer rather than
 * CPhyTreeSerial
 *
 * Revision 1.4  2004/05/25 17:21:59  dicuccio
 * Modified class names.  Fonts to 12 point
 *
 * Revision 1.3  2004/05/21 22:27:48  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.2  2004/05/03 13:05:43  dicuccio
 * gui/utils --> gui/objutils where needed
 *
 * Revision 1.1  2004/02/17 05:39:02  jcherry
 * Initial version
 *
 * ===========================================================================
 */