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NCBI C++ ToolKit: src/algo/blast/unit_tests/api/seqalign_cmp.cpp Source File

template <class Container>

Container::const_iterator itr = c.begin();

(; itr != c.end(); ++itr) {

s_PrintNeutralSeqAlign(ofstream&

,

& alignment)

<<

<< alignment.

<< endl

<<

<< alignment.

<< endl

<<

<< alignment.

<< endl

<<

<< alignment.

<< endl

<<

<< alignment.match << endl

<<

<< alignment.

<< endl

<<

<< alignment.

<< endl

<< endl <<

<< alignment.

.size()

<< endl <<

<< alignment.

.size()

ofstream

(fname.c_str());

runtime_error(

+ fname);

<<

<< ++index << endl;

s_PrintNeutralSeqAlign(

, *alignment);

: m_Ref(ref), m_Test(

), m_Opts(opts)

(*errors) +=

;

TSeqAlignSet::size_type kMaxSize =

(

.size(),

.size());

(TSeqAlignSet::size_type

= 0;

< kMaxSize;

++) {

max_diff_value = 0,

invalid_value, max_diff_value),

(std::

(reference_value - test_value))

reference_value,

max_diff_value = 0.0,

:

<double>(field_name, reference_value, test_value,

invalid_value, max_diff_value),

(std::

(reference_value - test_value) / reference_value)

* errors =

)

(*errors) +=

+

(aln_num) +

;

(*errors) += value_holder.

() +

;

(*errors) +=

+

(aln_num) +

;

(*errors) += value_holder.

() +

;

(*errors) +=

+

(aln_num) +

;

(*errors) +=

+ value_holder.

() +

;

(*errors) +=

;

pair<int, int>

vector<TSeqPos>& lengths)

query_length = 0;

subject_length = 0;

(vector<TSeqPos>::size_type

= 0;

< lengths.size();

++) {

query_length += lengths[

];

subject_length += lengths[

];

make_pair(query_length, subject_length);

allow_fuzziness)

field(

);

field(

);

field(

);

field(

);

field(

);

->GetNumSegments());

field(

);

field(

);

pair<int, int> ref_lengths =

pair<int, int> test_lengths =

field(

);

field(

);

field(

);

field(

);

virtual bool ReportDiffs() const

CDoubleValueHolder(string &field_name, double reference_value, double test_value, double max_diff_value=0.0, double invalid_value=kInvalidDoubleValue)

CIntValueHolder(string &field_name, int reference_value, int test_value, int max_diff_value=0, int invalid_value=kInvalidIntValue)

virtual bool ReportDiffs() const

Configuration options for CSeqAlignCmp class.

int GetMaxOffsetDiff() const

double GetMinEvalue() const

int GetMaxLengthDiff() const

double GetMaxEvalueDiff() const

double GetMaxEvalue() const

const TSeqAlignSet & m_Test

The sequence alignment to be used as test (compared with reference)

const TSeqAlignSet & m_Ref

The sequence alignment to be used as reference (assumed correct)

bool x_MeetsEvalueRequirements(double reference, double test)

If reference and test alignments do not fall into the evalue range specified, don't perform the compa...

int x_CompareOneAlign(const SeqAlign *ref, const SeqAlign *test, int index, string *errors=NULL, bool allow_fuzziness=true)

Compare alignment ref with alignment test (which correspond to entry index in the TMatchedAlignments.

CSeqAlignCmp(const TSeqAlignSet &ref, const TSeqAlignSet &test, const CSeqAlignCmpOpts &options)

Parametrized constructor.

const CSeqAlignCmpOpts & m_Opts

Our configuration options.

bool Run(string *errors=NULL)

Main function for this object, compare the input Seq-aligns.

Interface class to hold values and to determine whether some difference in these values should be rep...

CValueHolder(string &field_name, T reference_value, T test_value, T invalid_value, T max_diff_value)

T GetInvalidValue() const

virtual bool ReportDiffs() const =0

T GetMaximumAcceptableDiff() const

string & GetFieldName() const

std::ofstream out("events_result.xml")

main entry point for tests

#define test(a, b, c, d, e)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_SCOPE(ns)

Define a new scope.

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

Convert size_t to string.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

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

Convert int to string.

@ fDoubleScientific

DoubleToString*(): Use scientific format for double conversions.

unsigned int

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

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

const GenericPointer< typename T::ValueType > T2 value

const int kInvalidIntValue

std::vector< SeqAlign > TSeqAlignSet

Vector of neutral sequence alignments.

const double kInvalidDoubleValue

static pair< int, int > s_GetAlignmentLengths(const vector< int > &starts, const vector< TSeqPos > &lengths)

Returns a pair containing the length of the aligned region in the query and the length of the aligned...

bool s_CompareValues(const CValueHolder< T > &value_holder, int aln_num=0, string *errors=NULL)

Compare values in the CValueHolder object.

string s_ToString(T value)

Template wrapper around NStr::XToString functions, where X is a data type.

static void s_PrintTSeqAlignSet(const string &fname, const TSeqAlignSet &neutral_seqaligns)

void s_PrintContainer(ofstream &out, const Container &c)

BEGIN: Debugging functions.

API to compare CSeq-aligns produced by BLAST.

Neutral sequence alignment (for representing an HSP in BLAST)

int GetNumSegments() const

Return the number of segments in the HSP.

std::vector< TSeqPos > lengths

Lengths of aligned segments.

double bit_score

HSP bit score.

int num_ident

Number of identical residues.

double evalue

HSP evalue.

std::vector< int > starts

Query/Subject starting offsets.

int query_strand

Strand of the query sequence.

int subject_strand

Strand of the subject sequence.

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