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NCBI C++ ToolKit: src/objtools/readers/bed_autosql_standard.cpp Source File

49

mColChrom(-1), mColSeqStart(-1), mColSeqStop(-1), mColStrand(-1),

50

mColName(-1), mColScore(-1), mNumFields(0)

57  const string

& colName,

58  const string

& colFormat)

62  if

(colName ==

"chrom"

&& colFormat ==

"string"

) {

66  if

(colName ==

"chromStart"

&& colFormat ==

"uint"

) {

70  if

(colName ==

"chromEnd"

&& colFormat ==

"uint"

) {

74  if

(colName ==

"strand"

&& colFormat ==

"char[1]"

) {

78  if

(colName ==

"name"

&& colFormat ==

"string"

) {

82  if

(colName ==

"score"

&& colFormat ==

"uint"

) {

101  auto

&

location

= feat.SetLocation().SetInt();

110  "BED: Invalid data for column \"chromStart\". Feature omitted"

);

111

messageHandler.Report(

error

);

122  "BED: Invalid data for column \"chromEnd\". Feature omitted"

);

123

messageHandler.Report(

error

);

127  if

(mColStrand == -1) {

134  "BED: Invalid data for column \"strand\". Defaulting to \"+\""

);

137  auto

strandStr = columnData[mColStrand];

138  if

(strandStr.size() != 1) {

139

messageHandler.Report(warning);

142  auto

strandChar = strandStr[0];

143  if

(

string

(

"+-."

).find(strandChar) == string::npos) {

144

messageHandler.Report(warning);

146  else if

(strandChar ==

'-'

) {

161  if

(mColChrom == -1) {

164

feat.SetTitle(columnData[mColChrom]);

201

pDisplayData->SetType().SetStr(

"DisplaySettings"

);

202

pDisplayData->AddField(

"score"

,

205

feat.

SetExts

().push_back(pDisplayData);

217  if

(mColChrom == -1 || mColSeqStart == -1 || mColSeqStop == -1) {

221  "AutoSql: Table does not contain enough information to set a feature location."

);

222

messageHandler.Report(

fatal

);

static CRef< CSeq_id > AsSeqId(const string &rawId, long flags=0, bool localInts=true)

Convert a raw ID string to a Seq-id, based in given customization flags.

namespace ncbi::objects::

The NCBI C++ standard methods for dealing with std::string.

static void fatal(const char *msg,...)

static const char location[]

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

CRef< C > Ref(C *object)

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

#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.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static unsigned int StringToUInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to unsigned int.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fAllowTrailingSymbols

Ignore trailing non-numerics characters.

TExts & SetExts(void)

Assign a value to Exts data member.

void SetData(TData &value)

Assign a value to Data data member.

bool SetLocation(const CBedColumnData &, int bedFlags, CSeq_feat &, CReaderMessageHandler &) const

bool Validate(CReaderMessageHandler &) const

bool SetRegion(const CBedColumnData &columnData, CSeq_feat &feat, CReaderMessageHandler &messageHandler) const

bool SetDisplayData(const CBedColumnData &columnData, int bedFlags, CSeq_feat &feat, CReaderMessageHandler &messageHandler) const

bool ProcessTableRow(size_t, const string &, const string &)

bool SetTitle(const CBedColumnData &, CSeq_feat &, CReaderMessageHandler &) const

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