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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alnmix_8cpp_source.html below:

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

62

x_CalculateScore(calc_score)

135 string

errstr =

string

(

"CAlnMix::Add(): "

)

136

"Cannot force translation for Dense_seg " 138

"Neither CDense_seg::m_Widths are supplied, " 139

"nor OM is used to identify molecule type."

;

157 "Score calculation requested without providing " 158 "a scope in the CAlnMix constructor."

);

175 "CAlnMix::x_ExtendDSWithWidths(): " 176 "Widths already exist for the input alignment"

);

179 bool

contains_AA =

false

, contains_NA =

false

;

189 if

(contains_AA && contains_NA) {

191 "CAlnMix::x_ExtendDSWithWidths(): " 192 "Incorrect input Dense-seg: Contains both AAs and NAs but " 193 "widths do not exist!"

);

206 if

(lens[numseg] % 3) {

208 string

(

"CAlnMix::x_ExtendDSWithWidths(): "

) +

210 " is not divisible by 3."

;

213

new_lens[numseg] = lens[numseg] / 3;

220

new_widths.resize(ds.

GetDim

(), contains_NA ? 3 : 1);

236 string

(

"CAlnMix::ChooseSeqId(CSeq_id& id1, const CSeq_id& id2):"

)

239

" do not resolve to the same bioseq handle," 240 " but are used on the same 'row' in different segments." 241 " This is legally allowed in a Std-seg, but conversion to" 242 " Dense-seg cannot be performed."

;

253

" instead of GI "

<< id1.

GetGi

());

258

SerialAssign<CSeq_id>(id1, id2);

261 else if

(id2.

IsGi

()) {

265

" instead of GI "

<< id2.

GetGi

());

static CRef< CScope > m_Scope

void Add(const CDense_seg &ds, TAddFlags flags=0)

"Add" a Dense-seg to the existing matches.

void SortByScore()

Modifying algorithms.

void Merge(TMergeFlags flags=0)

const CSeq_align & GetSeqAlign(void) const

const CDense_seg & GetDenseg(void) const

const CBioseq_Handle * m_BioseqHandle

void Add(const CDense_seg &ds, TAddFlags flags=0)

void x_IdentifyAlnMixSeq(CRef< CAlnMixSeq > &aln_seq, const CSeq_id &seq_id)

void Add(const CDense_seg &ds, TAddFlags flags=0)

CRef< CAlnMixSequences > m_AlnMixSequences

CRef< CAlnMixMerger > m_AlnMixMerger

TCalcScoreMethod x_CalculateScore

CAlnMixMatches::TCalcScoreMethod TCalcScoreMethod

CRef< CAlnMixMatches > m_AlnMixMatches

virtual void ChooseSeqId(CSeq_id &id1, const CSeq_id &id2)

void Merge(TMergeFlags flags=0)

TConstDSsMap m_InputDSsMap

const CSeq_align & GetSeqAlign(void) const

const CDense_seg & GetDenseg(void) const

CRef< CDense_seg > x_ExtendDSWithWidths(const CDense_seg &ds)

TConstAlnsMap m_InputAlnsMap

int CalculateScore(TNumrow row1, TNumrow row2) const

TWidths & SetWidths(void)

bool IsSetWidths(void) const

void Validate(bool full_test=false) const

void Assign(const CSerialObject &obj, ESerialRecursionMode how=eRecursive)

overloaded Assign()

CRef< CSeq_align > CreateDensegFromStdseg(SSeqIdChooser *SeqIdChooser=0) const

---------------------------------------------------------------------------- PRE : the Seq-align has ...

void x_SetTaskName(const string &name)

Methods for reporting task progress.

ITaskProgressCallback * x_GetTaskProgressCallback() const

Callback accessor.

void SetTaskProgressCallback(ITaskProgressCallback *callback)

Hook a callback to a task.

const_iterator end() const

const_iterator find(const key_type &key) const

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string AsFastaString(void) const

static int BestRank(const CRef< CSeq_id > &id)

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

bool IsNull(void) const THROWS_NONE

Check if pointer is null â same effect as Empty().

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

const TDenseg & GetDenseg(void) const

Get the variant data.

TLens & SetLens(void)

Assign a value to Lens data member.

const TLens & GetLens(void) const

Get the Lens member data.

TDim GetDim(void) const

Get the Dim member data.

bool IsStd(void) const

Check if variant Std is selected.

bool IsDisc(void) const

Check if variant Disc is selected.

const TIds & GetIds(void) const

Get the Ids member data.

TNumseg GetNumseg(void) const

Get the Numseg member data.

list< CRef< CSeq_align > > Tdata

const TDisc & GetDisc(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

virtual void Reset(void)

Reset the whole object.

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

bool IsSetVersion(void) const

Check if a value has been assigned to Version data member.

const TAccession & GetAccession(void) const

Get the Accession member data.

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