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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/hyperclust_8cpp_source.html below:

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

55  virtual void Init

(

void

);

56  virtual int Run

(

void

);

57  virtual void Exit

(

void

);

69

arg_desc->SetUsageContext(

GetArguments

().GetProgramBasename(),

70  "Distances and clustering of multiple alignment" 73

arg_desc->AddKey(

"i"

,

"infile"

,

"file containing names of alignment files"

,

75

arg_desc->AddOptionalKey(

"d"

,

"defline_file"

,

76  "file containing deflines corrsponding to alignment files"

,

78

arg_desc->AddDefaultKey(

"first"

,

"first"

,

79  "produce alignments from alignment number 'first' " 80  "to all succeeding alignments in the list"

,

82

arg_desc->AddDefaultKey(

"last"

,

"index"

,

83  "Compare alignments from first to last against the rest " 84  "in the list. Indices start from 1 " 85  "(default indicates an all vs. all comparison)."

,

87

arg_desc->AddDefaultKey(

"g0"

,

"penalty"

,

88  "gap open penalty for initial/terminal gaps"

,

90

arg_desc->AddDefaultKey(

"e0"

,

"penalty"

,

91  "gap extend penalty for initial/terminal gaps"

,

93

arg_desc->AddDefaultKey(

"g1"

,

"penalty"

,

94  "gap open penalty for middle gaps"

,

96

arg_desc->AddDefaultKey(

"e1"

,

"penalty"

,

97  "gap extend penalty for middle gaps"

,

99

arg_desc->AddDefaultKey(

"matrix"

,

"matrix"

,

100  "score matrix to use"

,

102

arg_desc->AddDefaultKey(

"v"

,

"verbose"

,

103  "turn on verbose output"

,

105

arg_desc->AddDefaultKey(

"local"

,

"local"

,

106  "reduce end gap penalties in profile-profile alignment"

,

108

arg_desc->AddFlag(

"pairs"

,

"Report pairwise distances up to a cutoff " 109  "value instead of the distance matrix"

);

110

arg_desc->AddDefaultKey(

"cutoff"

,

"distance"

,

111  "Maximum pairwise distance to report"

,

113

arg_desc->AddDefaultKey(

"out"

,

"outfile"

,

"Output file name"

,

135  while

(!line_reader.

AtEOF

()) {

145  "Could not retrieve seq entry"

);

151

seqloc->

SetWhole

().Assign(*itr->GetId().front());

152

blast::SSeqLoc sl(seqloc, scope);

153

retval.push_back(sl);

162  if

(

strcmp

(matrix_name,

"BLOSUM62"

) == 0)

164  else if

(

strcmp

(matrix_name,

"BLOSUM45"

) == 0)

166  else if

(

strcmp

(matrix_name,

"BLOSUM80"

) == 0)

168  else if

(

strcmp

(matrix_name,

"PAM30"

) == 0)

170  else if

(

strcmp

(matrix_name,

"PAM70"

) == 0)

172  else if

(

strcmp

(matrix_name,

"PAM250"

) == 0)

180

vector<CSequence>& query_data)

182  int

align_length = query_data[0].GetLength();

183  int

num_seqs = (

int

)query_data.size();

184  for

(

int i

= 0;

i

< align_length;

i

++) {

185  for

(

int

j = 0; j < num_seqs; j++)

186

freq_data[

i

][query_data[j].GetLetter(

i

)]++;

194  for

(

int i

= 0;

i

< freq_size;

i

++) {

200

sum += freq_data[

i

][j];

205

freq_data[

i

][j] *= sum;

212  double

**freq1,

int

len1,

213  double

**freq2,

int

len2,

224  const size_t

dim = transcript.size();

227  for

(

size_t i

= 0;

i

< dim; ++

i

) {

229  int

wg1 = end_gap_open, ws1 = end_gap_extend;

230  int

wg2 = end_gap_open, ws2 = end_gap_extend;

232  if

(offset1 >= 0 && offset1 < len1 - 1) {

233

wg1 = aligner.

GetWg

();

234

ws1 = aligner.

GetWs

();

237  if

(offset2 >= 0 && offset2 < len2 - 1) {

238

wg2 = aligner.

GetWg

();

239

ws2 = aligner.

GetWs

();

249

++offset1; ++offset2;

250  double

accum = 0.0, sum = 0.0;

255  if

(freq1[offset1][m] < freq2[offset2][m]) {

256

accum += freq1[offset1][m] * (double)sm[m][m];

258

diff_freq2[m] = freq2[offset2][m] - freq1[offset1][m];

261

accum += freq2[offset2][m] * (double)sm[m][m];

262

diff_freq1[m] = freq1[offset1][m] -

268  if

(freq1[offset1][0] <= freq2[offset2][0]) {

270

sum += diff_freq1[m];

273

sum += diff_freq2[m];

277  if

(freq1[offset1][0] <= freq2[offset2][0]) {

279

diff_freq1[m] /= sum;

282

diff_freq2[m] /= sum;

287

accum += diff_freq1[m] *

294

freq1[offset1][0] * aligner.

GetWs

() * (1-freq2[offset2][0]) +

295

freq2[offset2][0] * aligner.

GetWs

() * (1-freq1[offset1][0]);

301  if

(state1 != 1) dscore += wg1 * (1.0 - freq2[offset2][0]);

302

state1 = 1; state2 = 0;

309  if

(state2 != 1) dscore += wg2 * (1.0 - freq1[offset1][0]);

310

state1 = 0; state2 = 1;

321  return

(

int

)(dscore + 0.5);

328  int

freq_size = alignment[0].GetLength();

333

freq_data =

new double

* [freq_size];

336  for

(

int i

= 1;

i

< freq_size;

i

++)

339

memset(freq_data[0], 0,

kAlphabetSize

* freq_size *

sizeof

(

double

));

356  double

**freq2_data,

int

freq2_size,

358  bool

local_alignment)

364

aligner.

SetSequences

((

const double

**)freq1_data, freq1_size,

365

(

const double

**)freq2_data, freq2_size,

369

freq1_data, freq1_size,

370

freq2_data, freq2_size,

371

local_alignment ? 0 : end_gap_open,

372

local_alignment ? 0 : end_gap_extend);

381  for

(

int i

= 0;

i

< freq_size;

i

++) {

383

score += freq_data[

i

][j] * matrix.

s

[j][j];

398

vector<SAlignEntry>& aligns)

402  for

(

i

= 0;

i

< level;

i

++)

406  if

(

tree

->GetValue().GetId() >= 0)

407

printf(

"cluster %d (%s) "

,

tree

->GetValue().GetId(),

408

aligns[

tree

->GetValue().GetId()].name);

409  if

(

tree

->GetValue().IsSetDist())

410

printf(

"distance %lf"

,

tree

->GetValue().GetDist());

413  if

(

tree

->IsLeaf())

419  while

(child !=

tree

->SubNodeEnd()) {

420  for

(

i

= 0;

i

< level;

i

++)

423

printf(

"%d:\n"

, j);

438

vector<CTree::STreeLeaf> left_leaves;

439

vector<CTree::STreeLeaf> right_leaves;

443

(*child)->GetValue().GetDist());

446

(*child)->GetValue().GetDist());

448  for

(

size_t i

= 0;

i

< left_leaves.size();

i

++) {

449  for

(

size_t

j = 0; j < right_leaves.size(); j++) {

450  int

idx1 = left_leaves[

i

].query_idx;

451  double

dist1 = left_leaves[

i

].distance;

452  int

idx2 = right_leaves[j].query_idx;

453  double

dist2 = right_leaves[j].distance;

459

matrix(idx1, idx2) = matrix(idx2, idx1) = dist1 + dist2;

463

right_leaves.clear();

479  bool verbose

= args[

"v"

].AsBoolean();

500

vector<SAlignEntry> align_list;

514  for

(

size_t i

= 0;

i

< align_read.size();

i

++) {

515

e.

align

.push_back(

CSequence

(*align_read[

i

].seqloc, *align_read[

i

].scope));

522  char

*name_ptr =

buf

+ strlen(

buf

) - 1;

523  while

(name_ptr >

buf

&&

524

name_ptr[-1] !=

'/'

&&

525

name_ptr[-1] !=

'\\'

) {

528

strcpy(e.

name

, name_ptr);

531  int

first_index = args[

"first"

].AsInteger();

532  int

last_index = args[

"last"

].AsInteger();

533  if

(last_index == 0) {

534

last_index = (

int

)align_list.size() - 1;

541  if

(first_index != 0) {

542  NcbiCerr

<<

"error: all-against-all alignment required"

<< endl;

549  for

(

int i

= first_index;

i

<= last_index;

i

++) {

550  for

(

size_t

j =

i

+ 1; j < align_list.size(); j++) {

552  if

(last_index < (

int

)align_list.size() - 1 && (

int

)j <= last_index) {

556  int

len1 = align_list[

i

].align[0].GetLength();

557  int

len2 = align_list[j].align[0].GetLength();

560  if

(args[

"local"

].AsBoolean() ==

true

) {

561  if

(len1 > 1.5 * len2 || len2 > 1.5 * len1) {

564  else if

(len1 > 1.2 * len2 || len2 > 1.2 * len1) {

571

align_list[

i

].length,

572

align_list[j].profile,

573

align_list[j].length,

575

args[

"local"

].AsBoolean());

578

printf(

"%s %s %.2f\n"

, align_list[

i

].name,

579

align_list[j].name, (

double

)score / 100);

585

distances(

i

, j) = distances(j,

i

) = 1.0 - (double)score *

586

(1.0 / align_list[

i

].self_score +

587

1.0 / align_list[j].self_score) / 2;

594  int

num_clusters = (

int

)align_list.size();

599  while

(!dfile.fail() && !dfile.eof()) {

608

dfile.getline(defline,

sizeof

(defline),

'\n'

);

612  for

(

int i

= 0;

i

< num_clusters;

i

++) {

613  if

(strstr(align_list[

i

].name, name)) {

614

snprintf(align_list[

i

].name,

sizeof

(align_list[

i

].name),

615  "%s %s"

, name, defline);

616  char

*

tmp

= align_list[

i

].name;

627  if

(args[

"pairs"

]) {

628  for

(

int i

=0;

i

<= last_index;

i

++) {

629  for

(

int

j=(

i

+1);j < num_clusters; j++) {

631  if

(last_index < (

int

)align_list.size() - 1 && j <= last_index) {

635  if

(distances(

i

, j) < args[

"cutoff"

].AsDouble()) {

636

args[

"out"

].AsOutputFile() << align_list[

i

].name <<

"\t" 637

<< align_list[j].name <<

"\t" 644

printf(

"%d\n"

, num_clusters);

645  for

(

int i

= 0;

i

< num_clusters;

i

++) {

646

printf(

"%s\n"

, align_list[

i

].name);

647  for

(

int

j = 0; j < num_clusters; j++) {

648

printf(

"%5.4f "

, distances(

i

, j));

665

printf(

"\n\nNew Distance matrix:\n "

);

666  for

(

int i

= (

int

)align_list.size() - 1;

i

> 0;

i

--)

667

printf(

"%5d "

,

i

);

670  for

(

int i

= 0;

i

< (

int

)align_list.size() - 1;

i

++) {

671

printf(

"%2d: "

,

i

);

672  for

(

int

j = (

int

)align_list.size() - 1; j >

i

; j--) {

673

printf(

"%5.3f "

, new_distances(

i

, j));

679

printf(

"\n\nPercent relative error:\n "

);

680  for

(

int i

= (

int

)align_list.size() - 1;

i

> 0;

i

--)

681

printf(

"%5d "

,

i

);

684  for

(

int i

= 0;

i

< (

int

)align_list.size() - 1;

i

++) {

685

printf(

"%2d: "

,

i

);

686  for

(

int

j = (

int

)align_list.size() - 1; j >

i

; j--) {

687

printf(

"%5.2f "

, 100*

fabs

(new_distances(

i

, j) -

688

distances(

i

, j)) / distances(

i

, j));

704 int main

(

int

argc,

const char

* argv[])

static const int kAlphabetSize

The aligner internally works only with the ncbistdaa alphabet.

Data loader implementation that uses the blast databases.

Base class for reading FASTA sequences.

virtual void Exit(void)

Cleanup on application exit.

virtual void Init(void)

Initialize the application.

virtual int Run(void)

Run the application.

virtual void Exit(void)

Cleanup on application exit.

virtual void Init(void)

Initialize the application.

CRef< CObjectManager > m_ObjMgr

virtual int Run(void)

Run the application.

Simple implementation of ILineReader for i(o)streams.

definition of a Culling tree

A wrapper for controlling access to the phylogenetic tree generated by CDistMethods.

static void ListTreeLeaves(const TPhyTreeNode *node, vector< STreeLeaf > &node_list, double curr_dist=0)

Traverse a tree below a given starting point, listing all leaves encountered along the way.

Template class for iteration on objects of class C (non-medifiable version)

Interface for CMultiAligner.

Operators to edit gaps in sequences.

void SetStartWg(TScore value)

TTranscript GetTranscript(bool reversed=true) const

void SetEndWs(TScore value)

virtual CNWAligner::TScore Run(void)

TScore GetStartWs() const

void SetScoreMatrix(const SNCBIPackedScoreMatrix *scoremat)

SNCBIFullScoreMatrix & GetMatrix()

void SetEndWg(TScore value)

vector< ETranscriptSymbol > TTranscript

void SetSequences(const char *seq1, size_t len1, const char *seq2, size_t len2, bool verify=true)

TScore GetStartWg() const

void SetEndSpaceFree(bool Left1, bool Right1, bool Left2, bool Right2)

void SetStartWs(TScore value)

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.

@ eInputFile

Name of file (must exist and be readable)

@ eBoolean

{'true', 't', 'false', 'f'}, case-insensitive

@ 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)

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

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.

@ eDiag_Warning

Warning message.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual CRef< CSeq_entry > ReadOneSeq(ILineErrorListener *pMessageListener=nullptr)

Read a single effective sequence, which may turn out to be a segmented set.

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

@ fNoParseID

Generate an ID (whole defline -> title)

@ fForceType

Force specified type regardless of accession.

@ fParseRawID

Try to identify raw accessions.

@ fAssumeProt

Assume prots unless accns indicate otherwise.

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

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.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

TNodeList_CI SubNodeBegin(void) const

Return first const iterator on subnode list.

TNodeList::const_iterator TNodeList_CI

bool IsLeaf() const

Report whether this is a leaf node.

TNodeList_CI SubNodeEnd(void) const

Return last const iterator on subnode list.

unsigned int

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

static void x_NormalizeResidueFrequencies(double **freq_data, int freq_size)

static void x_FillResidueFrequencies(double **freq_data, vector< CSequence > &query_data)

static double x_GetSelfScore(double **freq_data, int freq_size, SNCBIFullScoreMatrix &matrix)

static void x_PrintTree(const TPhyTreeNode *tree, int level, vector< SAlignEntry > &aligns)

static int x_ScoreFromTranscriptCore(CPSSMAligner &aligner, double **freq1, int len1, double **freq2, int len2, int end_gap_open, int end_gap_extend)

int x_AlignProfileProfile(double **freq1_data, int freq1_size, double **freq2_data, int freq2_size, CPSSMAligner &aligner, bool local_alignment)

static blast::TSeqLocVector x_GetSeqLocFromStream(CNcbiIstream &instream, CObjectManager &objmgr)

void x_SetScoreMatrix(const char *matrix_name, CPSSMAligner &aligner)

static double ** x_GetProfile(vector< CSequence > &alignment)

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

static void x_FillNewDistanceMatrix(const TPhyTreeNode *node, CDistMethods::TMatrix &matrix)

static const int kScaleFactor

CSequnceHelper< CObject > CSequence

int strcmp(const char *str1, const char *str2)

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

const SNCBIPackedScoreMatrix NCBISM_Pam30

const SNCBIPackedScoreMatrix NCBISM_Blosum62

const SNCBIPackedScoreMatrix NCBISM_Pam250

#define NCBI_FSM_DIM

Recommended approach: unpack and index directly.

const SNCBIPackedScoreMatrix NCBISM_Blosum80

const SNCBIPackedScoreMatrix NCBISM_Pam70

const SNCBIPackedScoreMatrix NCBISM_Blosum45

The standard matrices.

int TNCBIScore

data types

vector< SSeqLoc > TSeqLocVector

Vector of sequence locations.

vector< CSequence > align

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