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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/clusterer__app_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/cobalt/demo/clusterer_app.cpp Source File

(

);

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);

arg_desc->SetUsageContext(

().GetProgramBasename(),

);

arg_desc->AddKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

arg_desc->AddDefaultKey(

,

,

,

,

));

arg_desc->AddDefaultKey(

,

,

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arg_desc->AddDefaultKey(

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arg_desc->AddDefaultKey(

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arg_desc->AddDefaultKey(

,

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vector< CRef<CSeq_loc> > queries;

vector<TKmerCounts> kmer_counts;

kmer_len = (

)args[

].AsInteger();

TKMethods::ECompressedAlphabet alph = TKMethods::eRegular;

(args[

].AsString() ==

) {

alph = TKMethods::eRegular;

(args[

].AsString() ==

) {

alph = TKMethods::eSE_V10;

(args[

].AsString() ==

) {

alph = TKMethods::eSE_B15;

+ args[

].AsString();

TKMethods::ComputeCounts(queries, *scope, kmer_counts);

TKMethods::EDistMeasures dist_method = TKMethods::eFractionCommonKmersLocal;

(args[

].AsString() ==

) {

dist_method = TKMethods::eFractionCommonKmersLocal;

(args[

].AsString() ==

) {

dist_method = TKMethods::eFractionCommonKmersGlobal;

+ args[

].AsString();

max_diameter = args[

].AsDouble();

(args[

].AsString() ==

) {

links = TKMethods::ComputeDistLinks(kmer_counts, dist_method,

(

=0;

< (

)queries.size();

++) {

list< CRef<CSeq_id> > id;

<< id_str <<

<<

vector< CRef<CSeq_loc> > queries;

vector<TKmerCounts> kmer_counts;

kmer_len = (

)args[

].AsInteger();

TKMethods::ECompressedAlphabet alph = TKMethods::eRegular;

(args[

].AsString() ==

) {

alph = TKMethods::eRegular;

(args[

].AsString() ==

) {

alph = TKMethods::eSE_V10;

(args[

].AsString() ==

) {

alph = TKMethods::eSE_B15;

+ args[

].AsString();

TKMethods::ComputeCounts(queries, *scope, kmer_counts);

TKMethods::EDistMeasures dist_method = TKMethods::eFractionCommonKmersLocal;

(args[

].AsString() ==

) {

dist_method = TKMethods::eFractionCommonKmersLocal;

(args[

].AsString() ==

) {

dist_method = TKMethods::eFractionCommonKmersGlobal;

+ args[

].AsString();

max_diameter = args[

].AsDouble();

(args[

].AsString() ==

) {

links = TKMethods::ComputeDistLinks(kmer_counts, dist_method,

(

=0;

< (

)queries.size();

++) {

list< CRef<CSeq_id> > id;

<< id_str <<

<<

(args[

].AsString() ==

) {

(

argc,

* argv[])

Declares class to display one-line descriptions at the top of the BLAST report.

K-mer counts implemented as bit vectors.

virtual int Run(void)

Run the application.

virtual void Init(void)

Initialize the application.

virtual void Exit(void)

Cleanup on application exit.

CRef< CObjectManager > m_ObjMgr

int x_RunBinary(const CArgs &args)

int x_RunSparse(const CArgs &args)

Interface for CClusterer class used for clustering any type of data based on distance matrix.

int GetClusterId(int elem) const

Find id of cluster to which given element belongs.

EClustMethod

Method for clustering from links.

@ eDist

Clusters can be joined if there is a link between at least one pair of elements.

@ eClique

Clusters can be joined if there is a link between all pairs of their elements.

void SetMakeTrees(bool trees)

Set make cluster tree/dendrogram option.

void SetLinks(CRef< CLinks > links)

Set distance links.

void Run(void)

Cluster elements.

void SetClustMethod(EClustMethod method)

Set clustering method for links.

static void GetSeqIdList(const objects::CBioseq_Handle &bh, list< CRef< objects::CSeq_id > > &ids)

Converts a Bioseq handle's sequence id type into a list of objects::CSeq_id references,...

static string GetSeqIdListString(const list< CRef< objects::CSeq_id > > &id, bool show_gi)

Creates a '|' delimited string, corresponding to a list of Seq-ids.

Kmer counts for alignment free sequence similarity computation implemented as a sparse vector.

Interface for computing and manipulating k-mer counts vectors that allows for different implementatio...

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

void GetSeqLocFromStream(CNcbiIstream &instream, vector< CRef< objects::CSeq_loc > > &seqs, CRef< objects::CScope > &scope, objects::CFastaReader::TFlags flags)

Reads fasta sequences from stream, adds them to scope, and returns them as the list of Seq_locs.

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.

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.

@ 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.

@ fForceType

Force specified type regardless of accession.

@ fAssumeProt

Assume prots unless accns indicate otherwise.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

@ eGetBioseq_All

Search bioseq, load if not loaded yet.

virtual void SetParams()

Called at the beginning of Run, before creating thread pool.

unsigned int

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

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines command line argument related classes.

Defines unified interface to application:

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