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NCBI C++ ToolKit: src/objtools/alnmgr/demo/aln_build_app.cpp Source File

;

(

);

(

);

LoadInputAlns(

);

m_AlnContainer.insert(*aln);

ReportTime(

&

);

PrintAnchoredAln(

& anchored_aln);

arg_desc->AddDefaultKey

(

,

,

,

arg_desc->AddDefaultKey

(

,

,

,

arg_desc->AddDefaultKey

(

,

,

,

arg_desc->AddDefaultKey

(

,

,

,

arg_desc->AddDefaultKey

,

arg_desc->AddDefaultKey

(

,

,

arg_desc->AddDefaultKey

(

,

,

,

arg_desc->AddOptionalKey

(

,

,

,

arg_desc->AddDefaultKey

(

,

,

,

arg_desc->AddDefaultKey

(

,

,

,

prog_description =

;

arg_desc->SetUsageContext(GetArguments().GetProgramBasename(),

prog_description,

);

SetupArgDescriptions(arg_desc.release());

asn_type = args[

].AsString();

binary = !asn_type.empty();

unique_ptr<CObjectIStream>

<<

<<

<< endl;

m_StopWatch.Restart();

ReportTime(

);

(

()[

].AsBoolean()) {

cout <<

<<

<<

<< sparse_aln.

(

).AsFastaString() << endl;

cout << sequence << endl;

unique_ptr<IAlnSegmentIterator> sparse_ci

cout << **sparse_ci << endl;

cout <<

<<

<<

<< aln_seg.

().

() <<

cout <<

<<

<<

<< aln_seg.

().

() <<

ReportTime(

);

ReportTime(

);

aln_id_map(id_extract, m_AlnContainer.size());

cerr <<

<< e.what() << endl;;

ReportTime(

);

ReportTime(

);

m_StopWatch.Restart();

ReportTime(

);

cerr << aln_stats.

()[0]->AsString()

<<

<< endl;

cerr << (*id_it)->AsString() << endl;

m_StopWatch.Restart();

cout <<

<< endl;

anchor_row =

()[

].AsInteger();

TAlnStats::TIdxVec::const_iterator find_it = find(idx_vec.begin(), idx_vec.end(), anchor_row);

(find_it == idx_vec.end()) {

cerr <<

;

(idx_vec.begin(), idx_vec.end(), ostream_iterator<int>(cerr,

));

cout <<

<< aln_user_options.

();

cout <<

;

cout << endl << endl;

(

()[

].AsBoolean()) {

()[

] ?

()[

].AsInteger() : -1);

cout <<

<< endl;

cout << *single_anchored_aln;

PrintAnchoredAln(*single_anchored_aln);

ReportTime(

);

cout << **aln_vec_it;

m_StopWatch.Restart();

ReportTime(

);

cout << out_anchored_aln;

cout << out_anchored_aln;

m_StopWatch.Restart();

PrintAnchoredAln(out_anchored_aln);

ReportTime(

);

unique_ptr<CObjectOStream> asn_out

()[

].AsString()));

vector<CRef<CSeq_align> > out_seqaligns;

(

argc,

* argv[])

static CRef< CScope > m_Scope

int main(int argc, const char *argv[])

void BuildAln(TAnchoredAlnVec &in_alns, CAnchoredAln &out_aln, const CAlnUserOptions &options, TAlnSeqIdIRef pseudo_seqid=TAlnSeqIdIRef())

Build anchored alignment from a set of alignmnets.

void CreateAnchoredAlnVec(_TAlnStats &aln_stats, TAnchoredAlnVec &out_vec, const CAlnUserOptions &options)

Create anchored alignment from each seq-align in the stats.

CRef< CAnchoredAln > CreateAnchoredAlnFromAln(const _TAlnStats &aln_stats, size_t aln_idx, const CAlnUserOptions &options, objects::CSeq_align::TDim explicit_anchor_row=-1)

Create an anchored alignment from Seq-align using hints.

void CreateSeqAlignFromEachPairwiseAln(const CAnchoredAln::TPairwiseAlnVector pairwises, CAnchoredAln::TDim anchor, vector< CRef< CSeq_align > > &out_seqaligns, CSeq_align::TSegs::E_Choice choice, CScope *scope=NULL)

Create seq-align from each of the pairwise alignments vs the selected anchor row.

CRef< CSeq_align > CreateSeqAlignFromAnchoredAln(const CAnchoredAln &anchored_aln, CSeq_align::TSegs::E_Choice choice, CScope *scope=NULL)

Convert CAnchoredAln to seq-align of the selected type.

CRef< CDense_seg > CreateDensegFromPairwiseAln(const CPairwiseAln &pairwise_aln, CScope *scope=NULL)

Helper class for reading seq-align objects from a CObjectIStream.

void Read(CObjectIStream *obj_in_stream, TCallback callback, const string &top_level_asn_object=kEmptyStr)

Read all seq-align objects from the stream.

CRef< CObjectManager > m_ObjMgr

void PrintAnchoredAln(const CAnchoredAln &anchored_aln)

CScope & GetScope(void) const

bool InsertAln(const CSeq_align *aln)

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

void ReportTime(const string &msg)

CAlnContainer m_AlnContainer

Container mapping seq-aligns to vectors of participating seq-ids.

void push_back(const CSeq_align &aln)

Adding an alignment.

Default IAlnSeqId implementation based on CSeq_id_Handle.

Helper class which collects seq-align statistics: seq-ids participating in alignments and rows,...

_TAlnIdVec::TIdVec TIdVec

Vector of ids used in all alignments.

const TIdxVec & GetAnchorIdxVec(void) const

Get vector of id indexes (from IdVec) for potential anchors.

const TIdVec & GetIdVec(void) const

Get vector of all ids from all alignments.

bool CanBeAnchored(void) const

Check if there are any ids which can be used as anchors for the whole set of alignments.

vector< size_t > TIdxVec

Vector of indexes in TIdVec.

const TIdVec & GetAlignedIds(const TAlnSeqIdIRef &id) const

Get a set of ids that are aligned to a particular id.

Options for different alignment manager operations.

void SetAnchorId(const TAlnSeqIdIRef &anchor_id)

Set anchor id.

const TAlnSeqIdIRef & GetAnchorId(void) const

Get anchor id.

EMergeAlgo

Alignment merging algorithm.

EDirection

Row direction flags.

EMergeFlags

Additional merge flags.

Query-anchored alignment can be 2 or multi-dimentional.

const TPairwiseAlnVector & GetPairwiseAlns(void) const

The vector of pairwise alns.

vector< CRef< CPairwiseAln > > TPairwiseAlnVector

TDim GetAnchorRow(void) const

Which is the anchor row?

bool SplitStrands(void)

Split rows with mixed dir into separate rows returns true if the operation was performed.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

void Validate(bool full_test=false) const

TRng GetAlnRange(void) const

Get whole alignment range.

CAnchoredAln::TDim TDim

Synonym of TNumrow.

virtual IAlnSegmentIterator * CreateSegmentIterator(TNumrow row, const TSignedRange &range, IAlnSegmentIterator::EFlags flags) const

Create segment iterator.

string & GetAlnSeqString(TNumrow row, string &buffer, const TSignedRange &rq_aln_rng, bool force_translation=false) const

Fetch alignment sequence data.

TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

TDim GetDim(void) const

Alignment dimension (number of sequence rows in the alignment)

TSignedRange GetSeqAlnRange(TNumrow row) const

Get sequence range in alignment coords (strand ignored).

const objects::CSeq_id & GetSeqId(TNumrow row) const

Get seq-id for the row.

@ eRight

Towards higher aln coord (always to the right)

@ eLeft

Towards lower aln coord (always to the left)

@ eSkipInserts

Iterate segments where at least some rows are aligned (including gap segments)

Alignment segment interface.

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

@ fGap

Both anchor row and the selected row are not included in the segment (some other row is present and t...

virtual TSegTypeFlags GetType(void) const =0

Get current segment type.

virtual const TSignedRange & GetAlnRange(void) const =0

Get alignment range for the segment.

Include a standard set of the NCBI C++ Toolkit most basic headers.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eInputFile

Name of file (must exist and be readable)

@ eBoolean

{'true', 't', 'false', 'f'}, case-insensitive

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

@ fText

Open file in text mode.

@ fBinary

Open file in binary mode.

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

void Run(void)

Enter the main loop.

void CONNECT_Init(const IRWRegistry *reg=0, CRWLock *lock=0, TConnectInitFlags flag=eConnectInit_OwnNothing, FSSLSetup ssl=0)

Init [X]CONNECT library with the specified "reg" and "lock" (ownership for either or both can be deta...

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

Magic spell ;-) needed for some weird compilers... very empiric.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

#define GetArgs

Avoid preprocessor name clash with the NCBI C Toolkit.

Defines command line argument related classes.

Defines unified interface to application:

std::istream & in(std::istream &in_, double &x_)

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

vector< CRef< CAnchoredAln > > TAnchoredAlnVec

Collection of anchored alignments.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

#define row(bind, expected)

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