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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/cuHitsDistributor_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/structure/cd_utils/cuHitsDistributor.cpp Source File

44  const CSeq_id

& seqId = seqAlign->GetSeq_id(1);

48

from = seqAlign->GetSeqStart(1);

49

to = seqAlign->GetSeqStop(1);

63  if

(!seqAlignSet.

Empty

())

66  if

(seqAlignSet->

IsSet

())

68

list< CRef< CSeq_align > >& seqAlignList = seqAlignSet->

Set

();

69

list< CRef< CSeq_align > >::iterator lit = seqAlignList.begin();

71  for

(; lit != seqAlignList.end(); lit++)

77  ERR_POST

(

"A SeqAlign without a GI is detected."

);

81  ERR_POST

(

"No hit for this Blast."

);

84  ERR_POST

(

"No hit for this Blast."

);

92

vector< CRef< CSeq_align >* >& hits = fit->second;

96  double

min_evalue, evalue;

98  if

(!(*seqAlignRef)->GetNamedScore(

"e_value"

, min_evalue))

100  ERR_POST

(

"Can't get evalue from SeqAlign. Something is wrong"

);

103  for

(

int i

= 1;

i

< (

int

) hits.size();

i

++)

105

seqAlignRef = hits[

i

];

106  if

(!(*seqAlignRef)->GetNamedScore(

"e_value"

, evalue))

108  ERR_POST

(

"Can't get evalue from SeqAlign. Something is wrong"

);

111  if

(evalue < min_evalue)

117  for

(

int i

= 0;

i

< (

int

) hits.size();

i

++)

119

seqAlignRef = hits[

i

];

125

seqAlignRef->

Reset

();

136

list< CRef< CSeq_align > >& seqAlignList =

m_batches

[

b

]->Set();

137

list< CRef< CSeq_align > >::iterator lit = seqAlignList.begin();

139  while

(lit != seqAlignList.end())

143

lit = seqAlignList.erase(lit);

158

err =

"Cannot open file for writing"

;

164

vector< CRef< CSeq_align >* >& hits = fit->second;

166

outStream<<

"GI-Footprint"

<<gfp.

gi

<<

':'

<<gfp.

from

<<

'-'

<<gfp.

to

<<endl;

167  for

(

unsigned int i

= 0;

i

< hits.size();

i

++)

170  LOG_POST

(

"Failed to write to "

<<filename<<

" because of "

<<err);

void dump(string filename)

void addBatch(CRef< CSeq_align_set > seqAlignSet)

FootprintToHitMap m_hitTable

vector< CRef< CSeq_align_set > > m_batches

container_type::iterator iterator

const_iterator begin() const

const_iterator end() const

static bool WriteASNToStream(ncbi::CNcbiOstream &os, const ASNClass &ASNobject, bool isBinary, std::string *err, ncbi::EFixNonPrint fixNonPrint=ncbi::eFNP_Default)

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

main entry point for tests

#define ERR_POST(message)

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

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#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.

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

Tdata & Set(void)

Assign a value to data member.

virtual void Reset(void)

Reset the whole object.

bool IsSet(void) const

Check if a value has been assigned to data member.

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

unsigned int

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

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