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NCBI C++ ToolKit: include/algo/cobalt/cobalt.hpp Source File

eLastStatus = eOutOfMemory

SetInputMSAs(

objects::CSeq_align& msa1,

objects::CSeq_align& msa2,

vector< CRef<objects::CSeq_loc> >&

(

)

{

m_tQueries;}

{

m_Clusterer.GetClusters();}

FInterruptFn SetInterruptCallback(FInterruptFn fnptr,

* user_data =

);

vector<string>&

(

)

{

m_Messages;}

(

)

{

!m_Messages.empty();}

x_ValidateQueries(

)

;

x_ValidateInputMSAs(

)

;

x_ValidateUserHits(

);

vector<int>& indices);

x_CreatePatternQueries(vector<const CSequence*>& queries,

vector<int>& indices);

vector<int>& indices);

vector<int>& indices);

x_FindLocalInClusterHits(

vector<TPhyTreeNode*>& cluster_trees);

x_FindPatternHits(

vector<const CSequence*>& queries,

vector<int>& indices);

x_FindConsistentHitSubset(

);

x_ComputeTree();

x_BuildAlignment();

x_FindQueryClusters();

x_AlignInClusters();

x_MakeClusterResidueFrequencies();

x_MultiAlignClusters();

x_ComputeClusterTrees(vector<TPhyTreeNode*>& trees);

x_AttachClusterTrees(

vector<TPhyTreeNode*>& cluster_trees,

vector<TPhyTreeNode*>& cluster_leaves);

x_BuildFullTree(

vector<TPhyTreeNode*>& cluster_trees);

x_Run(

);

x_AlignMSAs(

);

vector<int>& indices,

objects::CBlast4_archive& archive);

: seq_index(s), range(

) {}

: seq_index(s), range(from, to) {}

kRpsScaleFactor = 100;

: hit(h), list_pos(list_pos),

path_next(0), best_score(0.0) {}

compare_sseg_db_idx;

.seq_index <

.seq_index;

fReduceBoth = fReduceLeft | fReduceRight

x_InitParams(

);

x_InitAligner(

);

{m_Interrupt =

;}

x_LoadBlockBoundaries(

blockfile,

vector<SSegmentLoc>& blocklist);

vector<int>& indices,

& rps_hits);

x_RealignBlocks(

& rps_hits,

vector<SSegmentLoc>& blocklist,

x_AssignRPSResFreqs(

& rps_hits,

x_AssignDefaultResFreqs();

vector<SSegmentLoc>& seg_list,

x_MakeFillerBlocks(

vector<int>& indices,

vector<SSegmentLoc>& filler_segs);

vector<int>& indices,

vector<SSegmentLoc>& filler_segs);

x_FindAlignmentSubsets();

SGraphNode * x_FindBestPath(vector<SGraphNode>& nodes);

x_BuildAlignmentIterative(vector<CTree::STreeEdge>& edges,

cluster_cutoff);

x_FindConservedColumns(vector<CSequence>& new_alignment,

vector<CSequence>& query_data,

iteration,

is_cluster);

x_RealignSequences(

*input_cluster,

vector<CSequence>& alignment,

vector<CTree::STreeLeaf>& node_list2,

vector<CSequence>& alignment,

x_AlignProfileProfileUsingHit(vector<CTree::STreeLeaf>& node_list1,

vector<CTree::STreeLeaf>& node_list2,

vector<CSequence>& alignment,

x_FindConstraints(vector<size_t>& constraint,

vector<CSequence>& alignment,

vector<CTree::STreeLeaf>& node_list1,

vector<CTree::STreeLeaf>& node_list2,

x_FindInClusterConstraints(vector<CSequence>& alignment,

vector<CTree::STreeLeaf>& node_list1,

vector<CTree::STreeLeaf>& node_list2,

vector<TRangePair>& match_ranges)

;

x_GetScoreOneCol(vector<CSequence>& align,

x_GetScore(vector<CSequence>& align);

vector<int>& indices)

;

x_InitColumn(vector<SColumn>::iterator& it,

);

x_InitInsertColumn(vector<SColumn>::iterator& it,

,

num,

cluster);

vector<CSequence>& query_data,

vector<TRange>& gaps);

unique_ptr< vector<int> > x_AlignClusterQueries(

* node);

x_ComputeProfileRangeAlignment(

vector<CTree::STreeLeaf>& node_list1,

vector<CTree::STreeLeaf>& node_list2,

vector<CSequence>& alignment,

vector<size_t>& constraints,

full_prof_len1,

full_prof_len2,

EEndGapCostStrategy strat,

kClusterNodeId = 16000;

class ::CMultiAlignerTest;

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Multiple aligner exceptions.

Interface for CHit class, used to encapsulate operations involving pairwise alignments.

Definitions used by all COBALT aligner components.

int TOffset

Basic data type for offsets into a sequence.

pair< string, biosample_util::EStatus > TStatus

Interface for CClusterer class used for clustering any type of data based on distance matrix.

vector< TSingleCluster > TClusters

An ordered collection of CHit objects.

A generalized representation of a pairwise alignment.

Test class for accessing CMultiAligner private attributes and methods.

bool operator()(const SSegmentLoc &a, const SSegmentLoc &b) const

Simultaneously align multiple protein sequences.

vector< CSequence > m_AllQueryData

EEndGapCostStrategy

Strategy for reducing end gap penalties for profile-profile alignment.

vector< vector< Uint4 > > m_ClusterGapPositions

CMultiAlignerOptions::EInClustAlnMethod m_ClustAlnMethod

SProgress m_ProgressMonitor

CRef< objects::CScope > m_Scope

CConstRef< CMultiAlignerOptions > GetOptions(void) const

Get mutli aligner parameters.

const vector< CSequence > & GetSeqResults(void) const

Retrieve the current aligned results in CSequence format.

const vector< CRef< objects::CSeq_loc > > & GetQueries(void) const

Get query sequences.

vector< int > m_Msa2Repr

Indices of sequence representatives in input alignment 2.

vector< CRef< objects::CSeq_loc > > m_tQueries

vector< CRef< objects::CSeq_loc > > m_AllQueries

CSparseKmerCounts TKmerCounts

const vector< string > & GetMessages(void) const

Get Error/Warning messages.

CHitList m_LocalInClusterHits

const TPhyTreeNode * GetTree(void) const

Get ree used guide in progressive alignment.

@ eOutOfMemory

Out of memory error.

@ eInternalError

Unexpected error occured.

@ eInterrupt

Alignment interruped through callback function.

@ eOptionsError

Error related to options occured.

@ eDatabaseError

Error related to RPS database occured.

@ eQueriesError

Error related to query sequences occured.

vector< CSequence > m_QueryData

const CClusterer::TClusters & GetQueryClusters(void) const

Get clusters of query sequences.

vector< bool > m_IsDomainSearched

Marks sequences with pre-computed domain hits.

TKmerMethods< TKmerCounts > TKMethods

vector< vector< TRange > > m_RPSLocs

vector< CSequence > m_InMSA1

Input alignment.

vector< CSequence > m_Results

CConstRef< CMultiAlignerOptions > m_Options

int GetScore(void) const

Get alignment score.

vector< string > m_Messages

CRef< objects::CScope > GetScope(void)

Get scope.

int m_Score

Alignment score.

void x_Init(void)

Initiate class attributes that are not alignment parameters.

pair< TRange, TRange > TRangePair

vector< int > m_Msa1Repr

Indices of sequence representatives in input alignment 1.

bool IsMessage(void) const

Check whether there are any error/warning messages.

vector< CSequence > m_InMSA2

Input alignment.

Represent databases of PSSM data and residue frequencies.

Kmer counts for alignment free sequence similarity computation implemented as a sparse vector.

definition of a Culling tree

A wrapper for controlling access to the phylogenetic tree generated by CDistMethods.

Interface for computing and manipulating k-mer counts vectors that allows for different implementatio...

Interface for CDistances class.

const Uint2 kMinorVersion

const Uint2 kMajorVersion

vector< ETranscriptSymbol > TTranscript

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

void Run(void)

Enter the main loop.

#define NCBI_COBALT_EXPORT

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

Interface for CHitList class.

int x_AlignProfileProfile(double **freq1_data, int freq1_size, double **freq2_data, int freq2_size, CPSSMAligner &aligner, bool local_alignment)

void x_SetScoreMatrix(const char *matrix_name, CPSSMAligner &aligner)

static const int kPatchVersion

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

Options for CMultiAligner.

Interface for CProfileData.

Interface for CSequence class.

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

Column in an alignment used for combining result from multiple alignment and pair-wise in-cluster ali...

int cluster

cluster index (inserted column only)

bool insert

Is the column an insertion from in-cluster alignment.

int number

number of letters in range (inserted column only)

vector< int > letters

Indices of letters in this column for regular column: index of a letter in input sequence (n-th lette...

double best_score

the score of that optimal path (assumes this node is the first entry in the path)

struct SGraphNode * path_next

the optimal path node belongs to

SGraphNode(CHit *h, int list_pos)

CHit * hit

the alignment represented by this node

Structure for reporting alignment progress.

SSegmentLoc(int s, TRange r)

SSegmentLoc(int s, TOffset from, TOffset to)

Interface for CTree class.

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