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

;

(

);

(

);

LoadInputAlns(

&

,

& asn_type);

m_AlnContainer.insert(*aln);

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddOptionalKey(

,

,

,

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

arg_desc->AddFlag(

,

);

prog_description =

;

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

prog_description,

);

SetupArgDescriptions(arg_desc.release());

binary = !asn_type.empty();

cout << ind <<

<< endl;

cout << ind <<

<< pw.

()->AsString() <<

;

cout << ind <<

<< pw.

()->AsString() <<

<< rit->GetSecondFrom() << (rg.

() ?

:

) <<

<< rit->GetLength() << endl;

cout << ind <<

<< pw.

()->AsString() <<

<< endl;

cout << ind <<

<<

gap->GetFirstFrom() << (gap->IsFirstDirect() ?

:

) <<

<< gap->GetSecondFrom() <<

(gap->IsDirect() ?

:

) <<

<< gap->GetLength() << endl;

cout << ind <<

<< endl;

cout << ind <<

<<

it.GetFirstRange().

() <<

<< it.GetFirstRange().GetToOpen() <<

(it.IsFirstDirect() ?

:

) <<

<< it.GetSecondRange().GetFrom() <<

<< it.GetSecondRange().GetToOpen() <<

(it.IsDirect() ?

:

) <<

<< it.GetFirstRange().GetLength() <<

<<

cout << ind <<

<< endl;

cout <<

<< endl;

cout <<

<< sparse_aln.

() << endl;

cout <<

<< sparse_aln.

() << endl;

cout <<

<<

<<

cout <<

<< native_rg.

() <<

<< frames.first <<

<< native_rg.

() <<

<< frames.second <<

<< rg.

() <<

<< rg.

() <<

;

cout <<

<< rg.

() <<

<< rg.

();

aln_len = sequence.size();

cout <<

<< sequence << endl;

seq_len = sequence.size();

cout <<

<< sequence << endl;

cout <<

<< aln_len <<

<< seq_len << endl;

aln_total, seq_total;

aln_data, seq_data, aln_gap, seq_gap;

( aln_rg.

() ) {

aln_gap =

(seq_data.size(),

);

( seq_rg.

() ) {

seq_gap =

(aln_data.size(),

);

(!aln_data.empty()) {

aln_total.append(aln_data);

aln_total.append(aln_gap);

seq_total.append(seq_gap);

seq_total.append(seq_data);

(aln_data.size() + aln_gap.size() != seq_data.size() + seq_gap.size()) {

cout <<

<< aln_data.size() + aln_gap.size() <<

<< seq_gap.size() + seq_data.size() << endl;

cout <<

<< aln_data + aln_gap << endl;

cout <<

<< seq_gap + seq_data << endl;

(!aln_total.empty() || !seq_total.empty()) {

cout <<

<< endl;

cout <<

<< aln_total << endl;

cout <<

<< seq_total << endl;

cout <<

<< endl;

<< it->GetAlnRange().GetFrom() <<

<< it->GetAlnRange().GetTo() <<

<< it->GetAlnRange().GetLength() <<

<< (it.IsAnchorDirect() ?

:

)

<< it->GetRange().GetFrom() <<

<< it->GetRange().GetTo() <<

<< it->GetRange().GetLength() <<

<< (it->IsReversed() ?

:

)

cout <<

;

aln.

(), it->GetAlnRange().GetFrom(),

aln.

(), it->GetAlnRange().GetTo(),

cout <<

<< anchor_from <<

<< anchor_to <<

;

cout <<

<< endl;

(

== anchor_row) {

cout <<

;

cout <<

<<

<<

;

cout << aln.

(

).AsFastaString() << endl;

cout <<

<< endl;

cout <<

<< endl;

cout <<

<< endl;

cout <<

<< endl;

(

.empty() ) {

= args[

].AsString();

asn_type = args[

].AsString();

anchor_row_idx = args[

].AsInteger();

id_extract(**aln_it,

);

ids.insert(ids.end(),

.begin(),

.end());

cerr <<

<< e.what() << endl;

cout <<

<< endl;

cout <<

<< (*id)->AsString() <<

<< (*id)->GetBaseWidth() << endl;

( args[

] ) {

(

= 0;

< (

)aln_id_map.

();

++) {

cout <<

<<

<< endl;

&

(*aln_id_map[

][0]))));

&

(*aln_id_map[

][1]))));

cout <<

<< endl;

, aln_user_options, anchor_row_idx);

cout <<

<< anchored_aln->

() << endl;

cout <<

<< endl;

( !args[

] ) {

( args[

] ) {

( args[

] ) {

(anchor_row_idx < 0) anchor_row_idx = 0;

cout <<

<< endl;

cout <<

<< endl << endl;

(anchored_aln_vec, built_aln, merge_options, pseudo_id);

cout <<

<< endl;

(

= 0;

< sparse_aln.

(); ++

) {

cout <<

<<

<< endl;

cout << ((*it)->IsAligned() ?

:

) <<

it_aln_rg.

() <<

<<

it_aln_rg.

() <<

<<

cout <<

<< native_rg.

() <<

<< fr.first <<

<< native_rg.

() <<

<< fr.second <<

;

cout <<((*it)->IsReversed() ?

:

) << endl;

(

argc,

* argv[])

static CRef< CScope > m_Scope

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

Build anchored alignment from a set of alignmnets.

void ConvertSeqAlignToPairwiseAln(CPairwiseAln &pairwise_aln, const objects::CSeq_align &sa, objects::CSeq_align::TDim row_1, objects::CSeq_align::TDim row_2, CAlnUserOptions::EDirection direction=CAlnUserOptions::eBothDirections, const TAlnSeqIdVec *ids=0)

Build pairwise alignment from the selected rows of a seq-align.

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.

vector< TAlnSeqIdIRef > TAlnSeqIdVec

CSeq_align::TDim TDim

Types we use here:

vector< TSeqIdPtr > TSeqIdVector

void DumpSparseAln(const CSparseAln &sparse_aln)

void TestSparseIt(const CSparseAln &aln, int row, const CSparse_CI::TSignedRange &rg, CSparse_CI::EFlags flags)

void DumpPairwiseAln(const CPairwiseAln &pw, const string ind)

vector< const CSeq_align * > TAlnVector

void DumpAnchoredAln(const CAnchoredAln &aaln, const string &ind)

void TestIterators(const CSparseAln &aln, const CSparse_CI::TSignedRange &rg)

const CSeq_id * TSeqIdPtr

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

void TestSparseIterator(const CSparseAln &aln)

TAlnSeqIdIRef ArgToSeq_id(const CArgValue &arg)

const_iterator begin() const

TSignedSeqPos GetSecondPosByFirstPos(position_type pos, ESearchDirection dir=eNone) const

position_type GetFirstFrom() const

CRange< position_type > GetFirstRange() const

@ fIgnoreInsertions

allows segments not separated by gaps

@ fDefaultPolicy

do not store insertions

const TInsertions & GetInsertions() const

Each insertion shows where the 'first' sequence has a gap while the 'second' sequence has the inserti...

vector< TAlignRange > TInsertions

class CAlignRangeCollection<TAlignRange> represent a sorted collection of TAlignRange.

CAlignRange Represents an element of pairwise alignment of two sequences.

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.

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

size_type size(void) const

Size (number of alignments)

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,...

const TIdVec & GetAnchorIdVec(void) const

Get vector of potential anchor ids.

virtual void Init(void)

Initialize the application.

CRef< CObjectManager > m_ObjMgr

CAlnContainer m_AlnContainer

virtual int Run(void)

Run the application.

void LoadInputAlns(const string &file_name, const string &asn_type)

CScope & GetScope(void) const

bool InsertAln(const CSeq_align *aln)

Options for different alignment manager operations.

void SetAnchorId(const TAlnSeqIdIRef &anchor_id)

Set anchor id.

@ eBothDirections

No filtering: use both direct and reverse sequences.

void SetMergeFlags(TMergeFlags flags, bool set)

Set/clear merge flags.

@ fUseAnchorAsAlnSeq

Use the anchor sequence as the alignment sequence.

@ fTruncateOverlaps

Truncate overlapping ranges.

@ fIgnoreInsertions

Do not collect and store insertions (gaps on the anchor).

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?

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

A pairwise aln is a collection of ranges for a pair of rows.

const TAlnSeqIdIRef & GetFirstId(void) const

Get first sequence id.

const TAlnSeqIdIRef & GetSecondId(void) const

Get second sequence id.

CPairwiseAln iterator. Iterates over aligned ranges and gaps.

@ eGap

Gap or unaligned range.

Scope-aware seq-id converter.

void Validate(bool full_test=false) const

TSignedSeqPos GetSeqAlnStart(TNumrow row) const

TRng GetAlnRange(void) const

Get whole alignment range.

TNumrow GetNumRows(void) const

Synonym of the above.

int GetBaseWidth(TNumrow row) const

Get base width for the sequence (1 for nucleotides, 3 for proteins).

TSignedSeqPos GetSeqAlnStop(TNumrow row) const

TRange GetSeqRange(TNumrow row) const

Get sequence range in sequence coords.

pair< int, int > TFrames

Get start and stop frames for the selected row/range.

CAnchoredAln::TDim TDim

Synonym of TNumrow.

_TRange AlnRangeToNativeSeqRange(TNumrow row, _TRange aln_range) const

Convert alignment range (genomic coordinates) on the selected row to real sequence range.

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.

TFrames AlnRangeToNativeFrames(TNumrow row, _TRange aln_range) const

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)

TNumrow GetAnchor(void) const

Get anchor row index.

TSignedRange GetSeqAlnRange(TNumrow row) const

Get sequence range in alignment coords (strand ignored).

string & GetSeqString(TNumrow row, string &buffer, TSeqPos seq_from, TSeqPos seq_to, bool force_translation=false) const

Fetch sequence data for the given row and range.

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

Get seq-id for the row.

Implementation of IAlnSegmentIterator for CSparseAln.

@ eForward

Towards higher seq coord (to the right if plus strand, left if minus)

Alignment segment iterator interface.

@ eSkipInserts

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

@ eInsertsOnly

Iterate only ranges not participating in the alignment (unaligned segments)

@ eAllSegments

Iterate all segments.

@ eSkipGaps

Skip gap segments (show only aligned ranges)

Alignment segment interface.

virtual const TSignedRange & GetRange(void) const =0

Get the selected row range.

@ fAligned

Aligned segment.

@ fIndel

Either anchor or the selected row is not present in the segment.

@ fUnaligned

The range on the selected sequence does not participate in the alignment (the alignment range of the ...

@ 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.

static const char * str(char *buf, int n)

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.

int TSignedSeqPos

Type for signed sequence position.

virtual const string & AsString(void) const =0

Get the argument's string value.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eInteger

Convertible into an integer number (int or Int8)

#define MSerial_AsnText

I/O stream manipulators –.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

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.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

TThisType & SetToOpen(position_type toOpen)

position_type GetToOpen(void) const

position_type GetFrom(void) const

bool IsFirstDirect() const

position_type GetFirstFrom(void) const

static TThisType GetWhole(void)

void Run(void)

Enter the main loop.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

E_Choice Which(void) const

Which variant is currently selected.

@ e_not_set

No variant selected.

unsigned int

A callback function used to compare two keys in a database.

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_)

vector< CRef< CAnchoredAln > > TAnchoredAlnVec

Collection of anchored alignments.

#define row(bind, expected)

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