shi_loader.cpp
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- /*
- * ===========================================================================
- * 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
- *
- * ===========================================================================
- */
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