cuCdUpdater.hpp

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/* $Id: cuCdUpdater.hpp 102008 2024-03-18 16:00:56Z gaudaensj $
 * ===========================================================================
 *
 *                            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.
 *
 * ===========================================================================
 *
 * Author:  Charlie Liu
 *
 * File Description:
 *
 *       Update CDs
 *
 * ===========================================================================
 */
 
#ifndef CU_CDUPDATER_HPP
#define CU_CDUPDATER_HPP
 
#include <algo/blast/api/blast_prot_options.hpp>
#include <algo/blast/api/remote_blast.hpp>
#include <objects/blastdb/Blast_def_line_set.hpp>
#include <objects/general/User_field.hpp>
#include <algo/structure/cd_utils/cuCppNCBI.hpp>
#include <algo/structure/cd_utils/cuCdCore.hpp>
#include <algo/structure/cd_utils/cuCdUpdateParameters.hpp>
#include "objects/seqalign/Seq_align_set.hpp"
#include "objects/entrez2/entrez2_client.hpp"
#include <algo/structure/cd_utils/cuBlock.hpp>
#include <algo/structure/cd_utils/cuSequenceTable.hpp>
 
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
BEGIN_SCOPE(cd_utils)
 
class NCBI_CDUTILS_EXPORT CDRefresher
{
public:
    CDRefresher (CCdCore* cd);
 
    //return the gi that's replaced; return -1 if none is replaced
    TGi refresh(CRef< CSeq_align> seqAlign, CRef< CSeq_entry > seqEntry);
    bool hasOlderVersion(CRef< CBioseq > bioseq);
 
private:
    CCdCore* m_cd;
    typedef map<string, CRef< CBioseq > > AccessionBioseqMap;
    AccessionBioseqMap m_accSeqMap;
 
    void addSequences(CSeq_entry& seqEntry);
    void addSequence(CRef< CBioseq > bioseq);
};
 
struct NCBI_CDUTILS_EXPORT CDUpdateStats
{
    int numBlastHits;
    vector<TGi> envSeq;
    vector<TGi> fragmented;
    vector<TGi> overlap;
    vector<TGi> noSeq;
    vector<TGi> badAlign;
    vector<TGi> redundant;
    int numRedundant;
    typedef pair<TGi, TGi> OldNewGiPair;
    vector<OldNewGiPair> oldNewPairs;
    int numObsolete;
    int numFilteredByOverlap;
 
public:
    CDUpdateStats();
    string toString(bool detailed=true);
private:
    string toString(vector<TGi>& gis, string type);
    string toString(vector<TGi>& gis);
    string toString(vector<OldNewGiPair>& giPairs, string type);
};
 
class NCBI_CDUTILS_EXPORT UpdaterInterface
{
public:
    virtual ~UpdaterInterface() {};
    virtual int  submitBlast(bool wait=false, int row = 0) = 0;
    virtual bool getBlastHits() = 0;
    virtual bool processBlastHits() = 0; //true: new sequences recruited.
    virtual void getCds(vector<CCdCore*>&) = 0;
    virtual bool hasCd(CCdCore*) =0;
    
    // maniplate the updater store
    static void addUpdater(UpdaterInterface* updater);
    static bool IsEmpty();
    static int checkAllBlasts(vector< UpdaterInterface* >& blasted);
    static void removeUpdaters(const vector<CCdCore*>& cds);
    static void removeUpdaters(const vector<UpdaterInterface*>& updaters);
 
private:
    static list<UpdaterInterface*> m_updaterList;
};
 
class GroupUpdater;
 
class NCBI_CDUTILS_EXPORT CDUpdater : public UpdaterInterface
{
public:
    CDUpdater(CCdCore* cd, CdUpdateParameters& config);
    //CDUpdater(const string& rid);
    virtual ~CDUpdater();
    
    //UpdaterInterface
    int  submitBlast(bool wait = false, int row = 0);
    bool getBlastHits();
    bool processBlastHits();
    void getCds(vector<CCdCore*>&);
    bool hasCd(CCdCore*);
 
    // submit a remote blast query
    // if failed or any exception was encountered, returns false (call getLastError to see message)
    bool blast(bool wait = false, int row = 0);
 
    const string getRid() {return m_rid;}
    const string getLastError() {return m_lastError;}
    void setLastError(const string& lastError) { m_lastError = lastError;}
    bool getHits(CRef<CSeq_align_set> & hits);
    bool checkDone();    
    CCdCore* getCd() {return m_cd;}
    CRef<CSeq_align_set> getAlignments() {return m_hits;}
    const CRef<CSeq_align_set>& GetAlignments() const {return m_hits;}
    void SetAlignments(CRef<CSeq_align_set>& hits) { m_hits.Reset(hits); }
    
    //drive update
    bool checkBlastAndUpdate();
    void setHitsNeeded(int num) {m_hitsNeeded = num;}
    bool update(CCdCore* cd, CSeq_align_set& alignments);
 
    //for making a new CD
    void requireProcessPending(int threshold) {m_processPendingThreshold = threshold;};
    //return the number of pending rows filtered out
    static int processPendingToNormal(int overlap, CCdCore* cd);
    static int mergePending(CCdCore* cd, int threshold, bool remaster);
 
    bool isFragmentedSeq(CCdCore* cd, CRef< CSeq_align > seqAlign, 
                        CRef< CSeq_entry > seqEntry);
 
    CdUpdateParameters& getUpdateParameters() {return m_config;}
    CDUpdateStats& getStats() {return m_stats;}
    static int pickBioseq(CDRefresher* refresher, CRef< CSeq_align > seqAlignRef, 
                           vector< CRef< CBioseq > >&  bioseqVec);
    static int GetAllIdsFromSeqEntry(CRef< CSeq_entry > seqEntry, 
        vector< CRef< CSeq_id > >& slaveIds, bool pdbOnly=false);
    static bool GetOneBioseqFromSeqEntry(CRef< CSeq_entry > seqEntry, 
        CRef< CBioseq >& bioseq, const CSeq_id* seqId=0);
    static TGi getGi(CRef< CSeq_entry > seqEntry);
    static TGi getGi(CRef<CBioseq> bioseq);
    static bool SeqEntryHasSeqId(CRef< CSeq_entry > seqEntry, const CSeq_id& seqId);
    static bool BioseqHasSeqId(const CBioseq& bioseq, const CSeq_id& seqId);
 
    //get org-ref from seqEntry if bioseq does not have one
    //remove all unnecessary fields
    //replace ftable with mmdb-id
    static bool reformatBioseq(CRef< CBioseq > bioseq, CRef< CSeq_entry > seqEntry, CEntrez2Client& client);
 
    //copied from objtools/alnmgr/util/showalign.cpp
    static CRef<CBlast_def_line_set>  GetBlastDefline (const CBioseq& handle);
    static void RemoveBlastDefline (CBioseq& handle);
    static int SplitBioseqByBlastDefline (CRef< CBioseq > handle, vector< CRef<CBioseq> >& bioseqs);
    static void reformatBioseqByBlastDefline(CRef<CBioseq> bioseq, CRef< CBlast_def_line > blastDefline, int order);
private:
    bool passedFilters(CCdCore* cd, CRef< CSeq_align > seqAlign, 
                        CRef< CSeq_entry > seqEntry);
 
    //  Ignore overlaps and return 'false' when overlap <= CDUpdateStats::allowedOverlapWithCDRow, or ignore
    //  *all* overlaps when CDUpdateStats::allowedOverlapWithCDRow < 0.
    bool overlapWithCDRow(CCdCore* cd,CRef< CSeq_align > seqAlign);
    bool modifySeqAlignSeqEntry(CCdCore* cd, CRef< CSeq_align >& seqAlign, 
                        CRef< CSeq_entry > seqEntry);
    bool findRowsWithOldSeq(CCdCore* cd, CBioseq& bioseq);
    void retrieveAllSequences(CSeq_align_set& alignments, vector< CRef< CBioseq > >& bioseqs);
    bool findSeq(CRef<CSeq_id> seqID, vector< CRef< CBioseq > >& bioseqs, CRef<CSeq_entry>& seqEntry);
 
    double ComputePercentIdentity(const CRef< CSeq_align >& alignment, const string& queryString, const string& subjectString);
 
    void getSequencesFromGB(vector< CRef<CSeq_id> > seqids, vector< CRef< CBioseq > >& bioseqs);
    CdUpdateParameters m_config;
    CDUpdateStats m_stats;
    string m_rid;
    CCdCore* m_cd;
    string m_lastError;
    cd_utils::BlockModelPair* m_guideAlignment; //consensus::master
    string m_consensus;
    CEntrez2Client m_client;
    int m_processPendingThreshold; //<0, don't do it
    CRef< CSeq_id > m_masterPdb;
    CRef<CSeq_align_set> m_hits;
    int m_hitsNeeded;
    int m_blastQueryRow;
 
    static void OssToDefline(const CUser_field::TData::TOss & oss, CBlast_def_line_set& bdls);
};
 
class NCBI_CDUTILS_EXPORT GroupUpdater : public UpdaterInterface
{
public:
    GroupUpdater(vector<CCdCore*>& cds, CdUpdateParameters& config);
    virtual ~GroupUpdater(); //delete all in m_cdUpdaters
    
    //UpdaterInterface
    int  submitBlast(bool wait=false, int row=0);
    bool getBlastHits();
    bool processBlastHits();
    void getCds(vector<CCdCore*>&);
    bool hasCd(CCdCore*);
 
private:
    vector<CDUpdater*> m_cdUpdaters;
 
};
 
END_SCOPE(cd_utils)
END_NCBI_SCOPE
 
#endif