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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/alnvwrapp_8cpp_source.html below:

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

82 virtual void Init

(

void

);

83 virtual int Run

(

void

);

86 void View8

(

int

aln_pos);

87 void View9

(

int

row0,

int

row1);

111

arg_desc->SetUsageContext

113 "Alignment manager demo program"

);

116

arg_desc->AddDefaultKey

117

(

"in"

"InputFile"

118 "Name of file to read the Dense-seg from (standard input by default)"

121

arg_desc->AddDefaultKey

122

(

"b"

"bin_obj_type"

123 "This forced the input file to be read in binary ASN.1 mode\n" 124 "and specifies the type of the top-level ASN.1 object.\n"

127

arg_desc->AddOptionalKey

128

(

"se_in"

"SeqEntryInputFile"

129 "An optional Seq-entry file to load a local top level seq entry from."

132

arg_desc->AddOptionalKey

133

(

"log"

"LogFile"

134 "Name of log file to write to"

137

arg_desc->AddOptionalKey

138

(

"a"

"AnchorRow"

139 "Anchor row (zero based)"

146 "2. Popset style using GetAlnSeqString\n" 147 " (memory efficient for large alns, but slower)\n" 148 "3. Popset style using GetSeqString\n" 149 " (memory inefficient)\n" 150 "4. Popset style using GetWholeAlnSeqString\n" 151 " (fastest, but memory inefficient)\n" 152 "5. Print segments\n" 154 "7. Alternative ways to get sequence\n" 155 "8. Demonstrate obtaining column vector in two alternative ways.\n" 156 " (Use numeric param n to choose alignment position)\n" 157 "9. Print relative residue index mapping for two rows.\n" 158 " (Use row0 and row1 params to choose the rows)\n" 159 "10. Iterate forward and backwards through alignment positions\n" 160 " and show corresponding native sequence positions for each row.\n" 161 "11. Clustal style\n"

164

arg_desc->AddDefaultKey

165

(

"w"

"ScreenWidth"

166 "Screen width for some of the viewers"

169

arg_desc->AddDefaultKey

171 "Generic Numeric Parameter, used by some viewers"

174

arg_desc->AddDefaultKey

176 "Generic Row Parameter, used by some viewers"

179

arg_desc->AddDefaultKey

181 "Generic Row Parameter, used by some viewers"

184

arg_desc->AddDefaultKey

185

(

"cf"

"GetChunkFlags"

186 "Flags for GetChunks (CAlnMap::TGetChunkFlags)"

206 string

sname = args[

"in"

].AsString();

209 string

asn_type = args[

"b"

].AsString();

210 bool

binary = !asn_type.empty();

211

unique_ptr<CObjectIStream>

in 221 if

( args[

"se_in"

] ) {

226

unique_ptr<CObjectIStream> se_in

229

se_asn_type = se_in->ReadFileHeader();

234

unique_ptr<CObjectIStream> se_in

237 if

(se_asn_type ==

"Seq-entry"

) {

242

cerr <<

"se_in only accepts a Seq-entry asn text file."

;

261 NcbiCout

"row "

row

", seg "

<< seg <<

" "

;

292

rng.

Set

(aln_pos, aln_pos);

313

vector<TSignedSeqPos>

result

;

321 for

(

size_t i

= 0;

size

;

++) {

331

vector<TSignedSeqPos> last_seq_pos(dim, -1);

333 for

(

int

reverse = 0; reverse < 2; ++reverse) {

345

}

else if

(last_seq_pos[

row

] >= 0) {

349 if

(it.

GetSeqPos

(

row

) >= 0 && last_seq_pos[row2] >= 0) {

352 if

(it.

GetSeqPos

(row2) >= 0 && last_seq_pos[

row

] >= 0) {

359

}

while

(reverse ? --it : ++it);

369 if

( args[

"log"

] ) {

380 int

screen_width = args[

"w"

].AsInteger();

381 int number

= args[

"n"

].AsInteger();

382 int

row0 = args[

"row0"

].AsInteger();

383 int

row1 = args[

"row1"

].AsInteger();

390 switch

(args[

"v"

].AsInteger()) {

410

printer.

Chunks

(args[

"cf"

].AsInteger());

440 int main

(

int

argc,

const char

* argv[])

User-defined methods of the data storage class.

void LogTime(const string &s)

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

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.

void Chunks(CAlnMap::TGetChunkFlags flags=CAlnMap::fAlnSegsOnly)

void CsvTable(char delim=',')

Printing methods.

TSignedSeqPos GetStop(TNumrow row, TNumseg seg, int offset=0) const

void GetResidueIndexMap(TNumrow row0, TNumrow row1, TRange aln_rng, vector< TSignedSeqPos > &result, TRange &rng0, TRange &rng1) const

TSignedSeqPos GetStart(TNumrow row, TNumseg seg, int offset=0) const

TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

TDim GetNumRows(void) const

TSeqPos GetAlnStop(TNumseg seg) const

void SetAnchor(TNumrow anchor)

TSeqPos GetLen(TNumseg seg, int offset=0) const

CDense_seg::TNumseg TNumseg

TSeqPos GetAlnStart(TNumseg seg) const

TNumseg GetNumSegs(void) const

TSignedSeqPos GetSeqPosFromSeqPos(TNumrow for_row, TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

TSignedSeqPos GetSeqPos(CAlnMap::TNumrow row) const

TSeqPos GetAlnPos(void) const

void PopsetStyle(int scrn_width=70, EAlgorithm algorithm=eUseAlnSeqString)

Printing methods.

@ eUseWholeAlnSeqString

memory efficient, recommended for large alns

@ eUseAlnSeqString

memory ineficient

void ClustalStyle(int scrn_width=50, EAlgorithm algorithm=eUseAlnSeqString)

string & GetSeqString(string &buffer, TNumrow row, TSeqPos seq_from, TSeqPos seq_to) const

void SetEndChar(TResidue gap_char)

void SetGapChar(TResidue gap_char)

string & GetColumnVector(string &buffer, TSeqPos aln_pos, TResidueCount *residue_count=0, bool gaps_in_count=false) const

string & GetAlnSeqString(string &buffer, TNumrow row, const CAlnMap::TSignedRange &aln_rng) const

TResidue GetResidue(TNumrow row, TSeqPos aln_pos) const

int CalculatePercentIdentity(TSeqPos aln_pos) const

string & GetSegSeqString(string &buffer, TNumrow row, TNumseg seg, TNumseg offset=0) const

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

CRef< CObjectManager > m_ObjMgr

bool AddAlnToMix(const CSeq_align *aln)

void View9(int row0, int row1)

void Validate(bool full_test=false) const

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

ESearchDirection

Position search options.

@ eRight

Towards higher aln coord (always to the right)

@ eLeft

Towards lower aln coord (always to the left)

static const char * column

unsigned int TSeqPos

Type for sequence locations and lengths.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

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.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

int TSignedSeqPos

Type for signed sequence position.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ fPreOpen

Open file right away; for eInputFile, eOutputFile, eIOFile.

@ eInputFile

Name of file (must exist and be readable)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

void SetDiagStream(CNcbiOstream *os, bool quick_flush=true, FDiagCleanup cleanup=0, void *cleanup_data=0, const string &stream_name="")

Set diagnostic stream.

@ eDS_Default

Try standard log file (app.name + ".log") in /log/, use stderr on failure.

@ 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.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

TThisType & Set(position_type from, position_type to)

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

const TDenseg & GetDenseg(void) const

Get the variant data.

const TSegs & GetSegs(void) const

Get the Segs member data.

bool IsDenseg(void) const

Check if variant Denseg is selected.

unsigned int

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

const struct ncbi::grid::netcache::search::fields::SIZE size

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

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

std::istream & in(std::istream &in_, double &x_)

#define row(bind, expected)

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