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NCBI C++ ToolKit: src/app/blastfmt/guide_tree_app.cpp Source File

60 virtual void Init

(

void

);

61 virtual int Run

(

void

);

62 virtual void Exit

(

void

);

79

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

80 "Application for computing and printing, " 81 "phylogenetic trees"

);

84

arg_desc->AddKey(

"i"

"filename"

"File with Seq-annot or tree in ASN format"

87

arg_desc->AddKey(

"o"

"filename"

"File name"

92

arg_desc->SetCurrentGroup(

"Input options"

);

93

arg_desc->AddDefaultKey(

"type"

"Type of input data"

97 "seqalignset"

"tree"

));

101

arg_desc->SetCurrentGroup(

"Tree computation options"

);

103

arg_desc->AddDefaultKey(

"divergence"

"value"

"Maximum divergence" 104 " between sequences"

107

arg_desc->AddDefaultKey(

"distance"

"method"

"Evolutionary correction for" 108 " sequence divergence - distance"

112 "jukes_cantor"

"poisson"

"kimura"

113 "grishin"

"grishin2"

));

115

arg_desc->AddDefaultKey(

"treemethod"

"method"

"Algorithm for phylogenetic" 116 " tree computation"

125

arg_desc->SetCurrentGroup(

"Tree manipulation options"

);

127

arg_desc->AddOptionalKey(

"simpl"

"method"

"Tree simplification method"

131 "blastname"

"full"

));

133

arg_desc->AddOptionalKey(

"expcol"

"num"

"Expand or collapse node"

136

arg_desc->AddOptionalKey(

"reroot"

"num"

"Re-root tree"

139

arg_desc->AddOptionalKey(

"subtree"

"num"

"Show sub-tree"

144

arg_desc->SetCurrentGroup(

"Output options"

);

146

arg_desc->AddDefaultKey(

"outfmt"

"format"

"Format for saving tree"

150 "newick"

"nexus"

));

152

arg_desc->AddDefaultKey(

"labels"

"Sequence labels in the tree"

156 "seqtitle"

"blastname"

"seqid"

157 "seqid_and_blastname"

));

159

arg_desc->AddOptionalKey(

"seqalign"

"filename"

"Write seq_align " 160 "correspoinding to the tree to a file"

188

unique_ptr<CPhyTreeFormatter> gtree;

191 if

(args[

"type"

].AsString() ==

"seqalignset"

) {

194 else if

(args[

"type"

].AsString() ==

"seqalign"

) {

217

calc->SetMaxDivergence(args[

"divergence"

].AsDouble());

220 if

(args[

"labels"

].AsString() ==

"taxname"

) {

222

}

else if

(args[

"labels"

].AsString() ==

"seqtitle"

) {

224

}

else if

(args[

"labels"

].AsString() ==

"blastname"

) {

226

}

else if

(args[

"labels"

].AsString() ==

"seqid"

) {

228

}

else if

(args[

"labels"

].AsString() ==

"seqid_and_blastname"

) {

236 if

(args[

"distance"

].AsString() ==

"jukes_cantor"

) {

238

}

else if

(args[

"distance"

].AsString() ==

"poisson"

) {

240

}

else if

(args[

"distance"

].AsString() ==

"kimura"

) {

242

}

else if

(args[

"distance"

].AsString() ==

"grishin"

) {

244

}

else if

(args[

"distance"

].AsString() ==

"grishin2"

) {

250

calc->SetDistMethod(dist);

253 if

(args[

"treemethod"

].AsString() ==

"fastme"

) {

255

}

else if

(args[

"treemethod"

].AsString() ==

"nj"

) {

258 NcbiCerr

"Error: Unrecognized tree computation method." 262

calc->SetTreeMethod(method);

264 if

(calc->CalcBioTree()) {

268 ITERATE

(vector<string>, it, calc->GetMessages()) {

276 if

(calc->IsMessage()) {

277 ITERATE

(vector<string>, it, calc->GetMessages()) {

284 if

(args[

"seqalign"

]) {

297 if

(args[

"simpl"

]) {

298 if

(args[

"simpl"

].AsString() ==

"blastname"

) {

300

}

else if

(args[

"simpl"

].AsString() ==

"full"

) {

306 if

(args[

"reroot"

]) {

307

gtree->RerootTree(args[

"reroot"

].AsInteger());

311 if

(args[

"expcol"

]) {

312

gtree->ExpandCollapseSubtree(args[

"expcol"

].AsInteger());

316 if

(args[

"subtree"

]) {

317

gtree->ShowSubtree(args[

"subtree"

].AsInteger());

323 if

(args[

"outfmt"

].AsString() ==

"asn"

) {

325

}

else if

(args[

"outfmt"

].AsString() ==

"newick"

) {

327

}

else if

(args[

"outfmt"

].AsString() ==

"nexus"

) {

334

gtree->WriteTreeAs(args[

"o"

].AsOutputFile(), tree_format);

356 int main

(

int

argc,

const char

* argv[])

User-defined methods of the data storage class.

Things for representing and manipulating bio trees.

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

virtual void Exit(void)

Cleanup on application exit.

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

Computaion of distance-based phylognetic tree.

ETreeMethod

Algorithms for phylogenetic tree reconstruction.

@ eFastME

Fast Minumum Evolution.

EDistMethod

Methods for computing evolutionary distance.

Class for adding tree features, maniplating and printing tree in standard text formats.

ELabelType

Information shown as labels in the guide tree.

@ eFullyExpanded

Tree fully expanded.

@ eByBlastName

Subtrees that contain sequences with the the same Blast Name are collapsed.

ETreeFormat

Output formats.

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

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.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CNcbiArguments & GetArguments(void) const

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

@ fHideXmlHelp

Hide XML help description.

@ fHideLogfile

Hide log file description.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

@ fHideVersion

Hide version description.

@ eInputFile

Name of file (must exist and be readable)

@ eDouble

Convertible into a floating point number (double)

@ 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.

#define MSerial_AsnText

I/O stream manipulators â.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

void Reset(void)

Reset reference object.

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

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

The NCBI C++/STL use hints.

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NCBI C++ ToolKit: src/app/blastfmt/guide_tree_app.cpp Source File

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/guidetreeapp_8cpp_source.html below: