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  C++/include/algo/cobalt/cobalt.hpp


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#ifndef ALGO_COBALT___COBALT__HPP #define ALGO_COBALT___COBALT__HPP /* $Id: cobalt.hpp 65958 2015-01-15 15:12:11Z boratyng $ * =========================================================================== * * 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 offical 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. * * ===========================================================================*/ /***************************************************************************** File name: cobalt.hpp Author: Jason Papadopoulos Contents: Interface for CMultiAligner ******************************************************************************/ #include <util/math/matrix.hpp> #include <corelib/ncbifile.hpp> #include <algo/align/nw/nw_pssm_aligner.hpp> #include <objects/seqalign/Seq_align.hpp> #include <objects/seqloc/Seq_loc.hpp> #include <objects/biotree/BioTreeContainer.hpp> #include <objects/blast/Blast4_archive.hpp> #include <algo/cobalt/base.hpp> #include <algo/cobalt/resfreq.hpp> #include <algo/cobalt/seq.hpp> #include <algo/cobalt/hit.hpp> #include <algo/cobalt/hitlist.hpp> #include <algo/cobalt/dist.hpp> #include <algo/cobalt/tree.hpp> #include <algo/cobalt/exception.hpp> #include <algo/cobalt/kmercounts.hpp> #include <algo/cobalt/clusterer.hpp> #include <algo/cobalt/options.hpp> /// @file cobalt.hpp /// Interface for CMultiAligner class CMultiAlignerTest; BEGIN_NCBI_SCOPE BEGIN_SCOPE(cobalt) /// Simultaneously align multiple protein sequences class NCBI_COBALT_EXPORT CMultiAligner : public CObject { public: /// Version information static const int kMajorVersion = 2; static const int kMinorVersion = 0; static const int kPatchVersion = 2; /// Return status enum EStatus { eSuccess = 0, ///< Alignment successfully completed eOptionsError, ///< Error related to options occured eQueriesError, ///< Error related to query sequences occured eDatabaseError, ///< Error related to RPS database occured eInternalError, ///< Unexpected error occured eInterrupt, ///< Alignment interruped through callback function eOutOfMemory, ///< Out of memory error eLastStatus = eOutOfMemory }; typedef int TStatus; enum EAlignmentStage { eBegin, eQueryClustering, eDomainHitsSearch, eLocalHitsSearch, ePatternHitsSearch, eTreeComputation, eProgressiveAlignment, eIterativeAlignment }; /// Structure for reporting alignment progress struct SProgress { EAlignmentStage stage; void* user_data; SProgress(void) : stage(eBegin), user_data(NULL) {} }; /// Prototype for function pointer to dertermine whether alignment should /// proceed of be interrupted. If this function returns true, all /// processing stops typedef bool(*FInterruptFn)(SProgress* progress); typedef CSparseKmerCounts TKmerCounts; typedef TKmerMethods<TKmerCounts> TKMethods; typedef pair<TRange, TRange> TRangePair; public: //------------------ Constructors ---------------------------- /// Create mutli aligner with default options /// CMultiAligner(void); /// Create multi aligner with selected RPS data base and default options /// @param rps_db RPS data base path [in] /// CMultiAligner(const string& rps_db); /// Create mutli aligner with given options /// @param options Parameters [in] /// CMultiAligner(const CConstRef<CMultiAlignerOptions>& options); //------------------ Sequences to align -------------------------- /// Set query sequences. /// This automatically clears out the intermediate state /// of the last alignment. /// @param queries List of query sequences or seq-ids [in] /// @param scope Scope object [in] /// void SetQueries(const vector< CRef<objects::CSeq_loc> >& queries, CRef<objects::CScope> scope); /// Set query sequences. /// This automatically clears out the intermediate state /// of the last alignment. /// @param queries List of query sequences [in] /// void SetQueries(const vector< CRef<objects::CBioseq> >& queries); /// Set query sequences. /// This automatically clears out the intermediate state /// of the last alignment. /// @param queries List of query sequences [in] /// void SetQueries(const blast::TSeqLocVector& queries); /// Set input alignments /// @param msa1 The first input alignment [in] /// @param msa2 The second input alignment [in] /// @param representatives1 List of sequence indices in msa1 /// to be used for computing constraints [in] /// @param representatives2 List of sequence indices in msa2 /// to be used for computing constraints [in] /// @param scope Scope [in] /// void SetInputMSAs(const objects::CSeq_align& msa1, const objects::CSeq_align& msa2, const set<int>& representatives1, const set<int>& representatives2, CRef<objects::CScope> scope); /// Get query sequences /// @return List of seq-ids and locations [in] /// const vector< CRef<objects::CSeq_loc> >& GetQueries(void) const {return m_tQueries;} /// Get scope /// @return Scope /// CRef<objects::CScope> GetScope(void) {return m_Scope;} //------------------ Options -------------------------- /// Get mutli aligner parameters /// @return Options /// CConstRef<CMultiAlignerOptions> GetOptions(void) const {return m_Options;} // ---------------- Running the aligner ----------------------- /// Align the current set of input sequences (reset any existing /// alignment information). /// /// This function handles the generation of all internal state in the /// correct order. It is sufficient for 'black box' applications that /// only want a final answer without tweaking internal state. /// x_Run() is called for computing alignment. /// @return Computation status: success (0), warnings (1), error (>1) /// TStatus Run(void); /// Clear out the state left by the previous alignment operation /// void Reset(void); // ---------------- Results ----------------------- /// Retrieve the current aligned results in Seq-align format. /// The Seq-align is of global type, with a single denseg /// @return The results /// CRef<objects::CSeq_align> GetResults(void) const; /// Retrieve a selection of the current aligned results, /// in Seq-align format. The Seq-align is of global type, /// with a single denseg. Columns that have gaps in all the /// selected sequences are removed /// @param indices List of ordinal IDs of sequences that the /// Seq-align will contain. Indices may appear /// in any order and may be repeated /// @return The results /// CRef<objects::CSeq_align> GetResults(vector<int>& indices) const; /// Retrieve the current aligned results in CSequence format. Included /// for backward compatibility with previous API. /// @return The results, on CSequence for each input sequence /// const vector<CSequence>& GetSeqResults(void) const {return m_Results;} /// Get ree used guide in progressive alignment /// @return Tree /// const TPhyTreeNode* GetTree(void) const {return m_Tree.GetTree();} /// Get serializable tree used as guide in progressive alignment /// @return Tree /// CRef<objects::CBioTreeContainer> GetTreeContainer(void) const; /// Get clusters of query sequences /// @return Query clusters /// const CClusterer::TClusters& GetQueryClusters(void) const {return m_Clusterer.GetClusters();} /// Get alignment score /// @return Alignment score /// int GetScore(void) const {return m_Score;} // ---------------- Interrupt --------------------------- /// Set a function callback to be invoked by multi aligner to allow /// interrupting alignment in progress /// @param fnptr Pointer to callback function [in] /// @param user_data user data to be attached to progress structure [in] /// @return Previously set callback function /// FInterruptFn SetInterruptCallback(FInterruptFn fnptr, void* user_data = NULL); // -------------- Errors/Warnings ----------------------- /// Get Error/Warning messages /// /// Errors are reported by exceptions, hence the messages will be mostly /// warnings. /// @return Messages /// const vector<string>& GetMessages(void) const {return m_Messages;} /// Check whether there are any error/warning messages /// @return True if there are messages, false otherwise /// bool IsMessage(void) const {return !m_Messages.empty();} //////////////////////////////////////////////////////////// public: /// Default gap open penalty static const CNWAligner::TScore kDefaultGapOpen = -11; /// Default gap extension penalty static const CNWAligner::TScore kDefaultGapExtend = -1; protected: /// Validate query sequences. Check for gaps in sequences. Throws if /// queries do not pass validation. /// @return True if validation passed /// bool x_ValidateQueries(void) const; /// Validate input alignments. Throws if alignments do not pass validation. /// @param True if validation passed // bool x_ValidateInputMSAs(void) const; /// Validate user constraints with queries. Throws if constraints do not /// pass validation. /// @return True if validation passed /// bool x_ValidateUserHits(void); /// Create query set for RPS Blast and Blastp searches along with indices /// in multiple alignment queries array. /// /// Searches for conserved regions can be performed for a subset of /// multiple alignment queries (typically to reduce computation time). /// @param queries Queries for RPS Blast and Blastp searches [out] /// @param indices Indexes of each query in m_tQueries [out] /// void x_CreateBlastQueries(blast::TSeqLocVector& queries, vector<int>& indices); /// Create query set for PROSITE pattern search along with indices /// in multiple alignment queries array. /// /// Searches for conserved regions can be performed for a subset of /// multiple alignment queries (typically to reduce computation time). /// @param queries Queries for PROSITE patterns searches [out] /// @param indices Indexes of each query in m_tQueries [out] /// void x_CreatePatternQueries(vector<const CSequence*>& queries, vector<int>& indices); /// Run RPS blast on seletced input sequences and postprocess the /// results. Intended for applications that want fine-grained control of /// the alignment process. /// @param queries Queries for RPS Blast search [in] /// @param indices Index of each RPS Blast query in the array of input /// sequences [in] /// void x_FindDomainHits(blast::TSeqLocVector& queries, const vector<int>& indices); /// Run blast on selected input sequences and postprocess the results. /// Intended for applications that want fine-grained control of the /// alignment process /// @param queries Queries for Blast alignment [in] /// @param indices Index of each Blast query in the array of input /// sequences [in] /// void x_FindLocalHits(const blast::TSeqLocVector& queries, const vector<int>& indices); /// Run blast on sequences from each cluster subtree. Each tree is /// traversed. Blast is run for pairs of most similar sequences such that /// each belongs to different subtree. Indented for use with query /// clustering for faster in-cluster pair-wise alignments. /// @param cluster_trees List of query cluster trees [in] /// void x_FindLocalInClusterHits(const vector<TPhyTreeNode*>& cluster_trees); /// Find PROSITE pattern hits on selected input sequences. /// Intended for applications that want fine-grained control of the /// alignment process /// @param queries Queries for PROSITE patter search [in] /// @param indices Index of each PROSITE pattern search query in the /// array of input sequences [in] /// void x_FindPatternHits(const vector<const CSequence*>& queries, const vector<int>& indices); /// Find consistent subset of pair-wise hits that can be used as /// alignment constraints /// void x_FindConsistentHitSubset(void); /// Given the current list of domain and local hits, generate a /// phylogenetic tree that clusters the current input sequences. /// Intended for applications that want fine-grained control of the /// alignment process /// void x_ComputeTree(); /// Given the current domain, local, pattern and user hits, along with /// the current tree, compute a multiple alignment of the input sequences. /// Intended for applications that want fine-grained control of the /// alignment process /// void x_BuildAlignment(); /// Find clusters of similar queries, select cluster representative /// sequences, and prepare input to multiple alignement composed of /// only representatives /// @return True if at least one cluster was found, false otherwise /// bool x_FindQueryClusters(); /// Pair-wise align each cluster sequence to cluster representative /// void x_AlignInClusters(); /// Compute profile residue frequencies for clusters. Frequencies are not /// normalized. /// void x_MakeClusterResidueFrequencies(); /// Combine pair-wise in-cluster alignements with multiple alignments of /// cluster prototypes /// void x_MultiAlignClusters(); /// Compute independent phylogenetic trees each cluster. /// @param Array of tree roots. Each array element corresponds to /// the cluster. One element clusters yield NULL tree. [out] /// void x_ComputeClusterTrees(vector<TPhyTreeNode*>& trees); /// Replace leaves in the alignment guide tree of clusters with cluster /// trees. /// @param cluster_trees List of phylogenetic trees computed for each /// cluster of input sequences [in] /// @param cluster_leaves List of pointers to leaves of the alignment guide /// tree computed for clusters [in] /// void x_AttachClusterTrees(const vector<TPhyTreeNode*>& cluster_trees, const vector<TPhyTreeNode*>& cluster_leaves); /// Combine alignment guide tree computed for clusters with guide trees /// computed for each cluster. /// /// Leaves of the guide tree computed for cluster prototypes are replaced /// with clusters trees. Cluster trees are rescaled so that distance from /// root to cluster prototype in cluster tree is the same as length of /// the leaf edge in the alignment guide tree (for cluster prototypes). /// @param cluster_trees List of cluster trees [in] /// void x_BuildFullTree(const vector<TPhyTreeNode*>& cluster_trees); /// Align the current set of input sequences (reset any existing /// alignment information). /// /// This function handles the generation of all internal state in the /// correct order. It is sufficient for 'black box' applications that /// only want a final answer without tweaking internal state. /// virtual void x_Run(void); /// Align multiple sequence alignments /// void x_AlignMSAs(void); /// Set pre-computed domain hits using BLAST archive format /// @param queries Sequences for which alignment hits will be searched for /// in the pre-computed set [in] /// @param indices Index of each query in the array of sequences to /// align [in] /// @param archive BLAST archive format [in] /// /// Queries from the archive are matched to COBALT queries by Seq_ids. /// The two sets of queries do not need to be the same. Domain hits for /// the archive queries that do match to any of the COBALT queries are /// ignored. COBALT will do RPS-BLAST search for all of its sequences that /// were not matched to the archive queries. It is the responsibility of /// user to ensure that the pre-computed hits and COBALT refer to the same /// domain database. void x_SetDomainHits(const blast::TSeqLocVector& queruies, const vector<int>& indices, const objects::CBlast4_archive& archive); protected: typedef struct SSegmentLoc { int seq_index; TRange range; SSegmentLoc() {} SSegmentLoc(int s, TRange r) : seq_index(s), range(r) {} SSegmentLoc(int s, TOffset from, TOffset to) : seq_index(s), range(from, to) {} TOffset GetFrom() const { return range.GetFrom(); } TOffset GetTo() const { return range.GetTo(); } } SSegmentLoc; private: static const int kRpsScaleFactor = 100; typedef struct SGraphNode { CHit *hit; ///< the alignment represented by this node int list_pos; struct SGraphNode *path_next;///< the optimal path node belongs to double best_score; ///< the score of that optimal path /// (assumes this node is the first entry /// in the path) SGraphNode() {} SGraphNode(CHit *h, int list_pos) : hit(h), list_pos(list_pos), path_next(0), best_score(0.0) {} } SGraphNode; class compare_sseg_db_idx; friend class compare_sseg_db_idx; class compare_sseg_db_idx { public: bool operator()(const SSegmentLoc& a, const SSegmentLoc& b) const { return a.seq_index < b.seq_index; } }; /// Column in an alignment used for combining result from multiple /// alignment and pair-wise in-cluster alignments typedef struct SColumn { /// Is the column an insertion from in-cluster alignment bool insert; /// Indices of letters in this column /// for regular column: index of a letter in input sequence /// (n-th letter) /// for inserted column: index of a letter in in-cluster alignment vector<int> letters; /// number of letters in range (inserted column only) int number; /// cluster index (inserted column only) int cluster; SColumn(void) : insert(false), number(1), cluster(-1) {} } SColumn; /// Strategy for reducing end gap penalties for profile-profile alignment enum EEndGapCostStrategy { /// Reduce penalty only for left end gaps fReduceLeft = 1, /// Reduce penalty only for right end gaps fReduceRight = 2, /// Reduce penalty for both end gaps fReduceBoth = fReduceLeft | fReduceRight }; private: /// Initiate parameters using m_Options void x_InitParams(void); /// Initiate PSSM aligner parameters void x_InitAligner(void); /// Set the score matrix the aligner will use. NOTE that at present /// any hits between sequences will always be scored using BLOSUM62; /// the matrix chosen here is only used when forming the complete /// alignment /// @param matrix_name The score matrix to use; limited to /// the same list of matrices as blast [in] void x_SetScoreMatrix(const char *matrix_name); /// Initiate class attributes that are not alignment parameters void x_Init(void) {m_Interrupt = NULL;} void x_LoadBlockBoundaries(string blockfile, vector<SSegmentLoc>& blocklist); void x_FindRPSHits(blast::TSeqLocVector& queries, const vector<int>& indices, CHitList& rps_hits); void x_RealignBlocks(CHitList& rps_hits, vector<SSegmentLoc>& blocklist, CProfileData& profile_data); void x_AssignRPSResFreqs(CHitList& rps_hits, CProfileData& profile_data); void x_AssignDefaultResFreqs(); void x_AddNewSegment(vector< CRef<objects::CSeq_loc> >& loc_list, const CRef<objects::CSeq_loc>& query, TOffset from, TOffset to, vector<SSegmentLoc>& seg_list, int query_index); void x_MakeFillerBlocks(const vector<int>& indices, vector< CRef<objects::CSeq_loc> >& filler_locs, vector<SSegmentLoc>& filler_segs); void x_AlignFillerBlocks(const blast::TSeqLocVector& queries, const vector<int>& indices, vector< CRef<objects::CSeq_loc> >& filler_locs, vector<SSegmentLoc>& filler_segs); void x_FindAlignmentSubsets(); SGraphNode * x_FindBestPath(vector<SGraphNode>& nodes); void x_BuildAlignmentIterative(vector<CTree::STreeEdge>& edges, double cluster_cutoff); void x_FindConservedColumns(vector<CSequence>& new_alignment, CHitList& conserved); void x_AlignProgressive(const TPhyTreeNode *tree, vector<CSequence>& query_data, CNcbiMatrix<CHitList>& pair_info, int iteration, bool is_cluster); double x_RealignSequences(const TPhyTreeNode *input_cluster, vector<CSequence>& alignment, CNcbiMatrix<CHitList>& pair_info, double score, int iteration); void x_AlignProfileProfile(vector<CTree::STreeLeaf>& node_list1, vector<CTree::STreeLeaf>& node_list2, vector<CSequence>& alignment, CNcbiMatrix<CHitList>& pair_info, int iteration); /// Align two profiles with all sequences that belong to the same cluster /// /// A pair-wise constraint alignment between the most similar sequences is /// used for aligning the profiles. Sequence positions that match in the /// pair-wise alignment will also match in the profile alignment. Ranges /// between the matching positions are aligned with CPSSMAligner. void x_AlignProfileProfileUsingHit(vector<CTree::STreeLeaf>& node_list1, vector<CTree::STreeLeaf>& node_list2, vector<CSequence>& alignment, CNcbiMatrix<CHitList>& pair_info, int iteration); void x_FindConstraints(vector<size_t>& constraint, vector<CSequence>& alignment, vector<CTree::STreeLeaf>& node_list1, vector<CTree::STreeLeaf>& node_list2, CNcbiMatrix<CHitList>& pair_info, int iteration); void x_FindInClusterConstraints(vector<CSequence>& alignment, vector<CTree::STreeLeaf>& node_list1, vector<CTree::STreeLeaf>& node_list2, CNcbiMatrix<CHitList>& pair_info, vector<TRangePair>& match_ranges) const; double x_GetScoreOneCol(vector<CSequence>& align, int col); double x_GetScore(vector<CSequence>& align); CRef<objects::CSeq_align> x_GetSeqalign(const vector<CSequence>& align, vector<int>& indices) const; static void x_InitColumn(vector<SColumn>::iterator& it, size_t len); static void x_InitInsertColumn(vector<SColumn>::iterator& it, size_t len, int num, int cluster); void x_AddRpsFreqsToCluster(const CClusterer::CSingleCluster& cluster, vector<CSequence>& query_data, const vector<TRange>& gaps); auto_ptr< vector<int> > x_AlignClusterQueries(const TPhyTreeNode* node); void x_ComputeProfileRangeAlignment( vector<CTree::STreeLeaf>& node_list1, vector<CTree::STreeLeaf>& node_list2, vector<CSequence>& alignment, vector<size_t>& constraints, const TRange& range1, const TRange& range2, int full_prof_len1, int full_prof_len2, EEndGapCostStrategy strat, CNWAligner::TTranscript& t); protected: // Input sequences CConstRef<CMultiAlignerOptions> m_Options; vector< CRef<objects::CSeq_loc> > m_tQueries; CRef<objects::CScope> m_Scope; vector<CSequence> m_QueryData; /// Input alignment vector<CSequence> m_InMSA1; /// Input alignment vector<CSequence> m_InMSA2; /// Indices of sequence representatives in input alignment 1 vector<int> m_Msa1Repr; /// Indices of sequence representatives in input alignment 2 vector<int> m_Msa2Repr; vector<CSequence> m_Results; /// Alignment score int m_Score; // Server classes CPSSMAligner m_Aligner; CTree m_Tree; CClusterer m_Clusterer; // Intermediate results CHitList m_DomainHits; CHitList m_LocalHits; CHitList m_CombinedHits; CHitList m_PatternHits; CHitList m_LocalInClusterHits; CHitList m_UserHits; /// Marks sequences with pre-computed domain hits vector<bool> m_IsDomainSearched; vector< vector<Uint4> > m_ClusterGapPositions; vector< CRef<objects::CSeq_loc> > m_AllQueries; vector<CSequence> m_AllQueryData; // Ranges of conserved domains in query sequences identified by RPS Blast vector< vector<TRange> > m_RPSLocs; // Running and monitoring FInterruptFn m_Interrupt; SProgress m_ProgressMonitor; vector<string> m_Messages; // Query clustering // Modified by x_FindQueryClusters() if no clusters found CMultiAlignerOptions::EInClustAlnMethod m_ClustAlnMethod; // Minimum tree node id for root of cluster subtree static const int kClusterNodeId = 16000; friend class ::CMultiAlignerTest; }; END_SCOPE(cobalt) END_NCBI_SCOPE #endif /* ALGO_COBALT___COBALT__HPP */

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