shi_loader.cpp

来自「ncbi源码」· C++ 代码 · 共 203 行

/*
 * ===========================================================================
 * PRODUCTION $Log: shi_loader.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 21:14:05  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: shi_loader.cpp,v 1000.1 2004/06/01 21:14:05 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:  Vladimir Tereshkov
 *
 * File Description:  
 *   Shi file reader. Code ported from shipr.c CGI.
 */

#include <ncbi_pch.hpp>
#include <corelib/ncbistd.hpp>
#include <corelib/ncbi_bswap.hpp>
#include <gui/widgets/taxplot3d/shi_loader.hpp>

USING_NCBI_SCOPE;

#define BIT32			0x80000000
#define BIT31			0x40000000
#define THREE			0x7
#define THIRTEEN		0x1FFF
#define EIGHTEEN		0x3FFFF
#define TWENTYSEVEN		0x7FFFFFF
#define THIRTYONE		0x7FFFFFFF

#define TAX0   0
#define TAX1   1
#define TAX2   2
#define CUT    3
#define XX    4
#define YY    5
#define LOG    6
#define QUERY	7
#define COGCLR	8
#define XMIN	9
#define XMAX	10
#define YMIN	11
#define YMAX	12
#define RADIUS_A	13
#define RADIUS_B	14
#define NAME0	15
#define NAME1	16
#define NAME2	17

#define NOTTAX1		0x80000000
#define NOTTAX2		0x40000000
#define TAXMASK		0x3FFFFFFF


void CShiFile::openFile(const string name)
{
    //m_FileStream.fastopen(name.c_str(), ios::binary);    
    m_FileStream.open(name.c_str(), ios::binary);    
    m_FileStream.seekg(0, ios::end);
    m_FileSize    = m_FileStream.tellg();
    m_FileStream.seekg(0, ios::beg);  

    CT_OFF_TYPE sz = m_FileSize - CT_POS_TYPE(0);

    m_Buff.reset(new unsigned char[sz]);
    m_FileStream.read((char*)m_Buff.get(), sz);


    no_more = 0; last_gi = 1;	
    m_FileCursor = 0;

    nshi =  getNextInt();
    value = getNextInt();
}


int CShiFile::getNextRecord(SShiRecord & rec)
{  	
    // no more records
    if (isEof())  return 0;

    // building rec. structure
    if (last_gi) {	
	    m_Record.m_Nqugi = THIRTYONE & value;		
        m_FileCursor +=1;
	    m_Record.m_Chromosome = getNextInt(); 
	    m_Record.m_Pdb        = getNextInt(); 
	    value                 = getNextInt(); 
    }
		
    m_Record.m_Symmet   = BIT31 & value;
    m_Record.m_Orgclass = THREE & (value>>27);
    m_Record.m_Dagi     = TWENTYSEVEN & value; 

    value = getNextInt();
    m_Record.m_Taxid = (BIT32&value)?((THIRTYONE & value)>>13):value;
    m_Record.m_Score = (BIT32&value)?(THIRTEEN & value):getNextInt(); 
	
	if(!isEof())	{	
		value = getNextInt();
		last_gi = (BIT32&value);		
	}
    else last_gi = 1;		      

    rec = m_Record;
    return 1;
}


int ShiLoader::loadFileNew(const char * file)
{
    auto_ptr<CShiFile>  shFile(new CShiFile);
    shFile->openFile(file);

    int cutoff  = 2000;

    SShiRecord rec;  
    map <int, int> taxMap;
        
    while  (shFile->getNextRecord(rec)){
        if ((rec.m_Score > cutoff) && (taxMap.insert(pair<int,int>(rec.m_Taxid, rec.m_Score)).second==false)){       
            if (taxMap[rec.m_Taxid] < rec.m_Score) taxMap[rec.m_Taxid] = rec.m_Score;      // already present      
        }  

        if (shFile->isLastGi()) {
            m_Cache.push_back(taxMap);
            taxMap.clear();    
            if (m_Handle && !shFile->isEof()){
                int value = 1 + (static_cast<Uint8>(shFile->getFileCursor())*400)/(shFile->getFileSize() - CT_POS_TYPE(0));
                if (!(value%10)) m_Handle->fireEvent(IShiLoaderEvents::eProgress, &value);
            }          
        }    
    }  
    if (m_Handle) m_Handle->fireEvent(IShiLoaderEvents::eLoaded, NULL);  
    return 0;
}

CTaxplot3dDataSource * ShiLoader::getData(int tax1, int tax2, int tax3)
{
    m_DS->clear();

    for (GIVECTOR::iterator it=m_Cache.begin(); it!=m_Cache.end(); it++){
        TSMAP::iterator itm;
        int score1 = ((itm=it->find(tax1))!=it->end()) ? itm->second : 0;
        int score2 = ((itm=it->find(tax2))!=it->end()) ? itm->second : 0;
        int score3 = ((itm=it->find(tax3))!=it->end()) ? itm->second : 0;

        if ((score1!=score2!=score3) && ((score1!=0 && score2!=0) || (score1!=0 && score3!=0) || (score2!=0 && score3!=0))){
          auto_ptr<CTaxplot3dDataSource::TVertex> newVertex(new CGraph3DVertex<float, float>(score1, score2, score3));      
          m_DS->addVertex(newVertex.get());						      
  
        }
    }
    return m_DS->normalizeAll();
}

/*
 * ===========================================================================
 * $Log: shi_loader.cpp,v $
 * Revision 1000.1  2004/06/01 21:14:05  gouriano
 * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.4
 *
 * Revision 1.4  2004/05/21 22:27:56  gorelenk
 * Added PCH ncbi_pch.hpp
 *
 * Revision 1.3  2004/02/20 20:03:28  ucko
 * Fix to compile with stricter implementations of CT_POS_TYPE
 *
 * Revision 1.2  2004/01/14 20:49:14  tereshko
 * Removed debugging code
 *
 * Revision 1.1  2004/01/05 16:21:24  tereshko
 * Initial revision
 *
 * ===========================================================================
 */