dyaln Class Reference

#include <mlocalS_str.h>

List of all members.

Public Member Functions

 dyaln ()
 ~dyaln ()
void freeTrace ()
int align (const char s1n[], const char s1str[], const char s2n[], const char s2str[])
void setup ()
void outputTab (ostream &os)
void outputTabPos (ostream &os)
void outputAln (FILE *ou=stdout)
void setMatrix (char m[])
void setGapCost (int alpha, int beta)
void setcsub (int cs)
void setNaligns (int n)
bool isSimple (float &ms) const

Private Member Functions

void allocateMem ()
void initParameter ()

Private Attributes

struct SEQALN_SEQUENCE * seq1
struct SEQALN_SEQUENCE * seq2
struct SEQALN_CONSTANTS * scoring
struct SEQALN_RESULTS * results
struct SEQALN_IO * io
char distrib_file1 [51]
char distrib_file2 [51]
pair< float, char > sortedFreq1 [20]
pair< float, char > sortedFreq2 [20]

Constructor & Destructor Documentation

dyaln::dyaln (  ) 

References allocateMem(), initParameter(), and setup().

dyaln::~dyaln (  ) 

References io, memfree(), results, scoring, seq1, and seq2.

Member Function Documentation

void dyaln::allocateMem (  )  [private]

References io, newmem(), results, scoring, seq1, and seq2.

Referenced by dyaln().

void dyaln::initParameter (  )  [private]

References SEQALN_CONSTANTS::btype, SEQALN_CONSTANTS::csub, SEQALN_CONSTANTS::Debug, distrib_file1, distrib_file2, SEQALN_CONSTANTS::envelope, SEQALN_CONSTANTS::flip, FULL, io, loadDeltaFunction(), LOCAL, MATRIX, SEQALN_CONSTANTS::memuse, SEQALN_CONSTANTS::mtype, SEQALN_CONSTANTS::ptype, SEQALN_CONSTANTS::rptalign, SEQALN_CONSTANTS::rptboth, SEQALN_CONSTANTS::rptmat, SEQALN_CONSTANTS::rptscore, SEQALN_CONSTANTS::rpttrace, scoring, SEQALN_CONSTANTS::showmmatch, SIMILARITY, SQUARE, SEQALN_IO::STDERR, SEQALN_IO::STDIN, SEQALN_IO::STDOUT, SEQALN_CONSTANTS::stype, and SEQALN_CONSTANTS::traceupper.

Referenced by dyaln().

void dyaln::freeTrace (  )  [inline]

References freeTraceList(), and results.

Referenced by main().

int dyaln::align ( const char  s1n[],
const char  s1str[],
const char  s2n[],
const char  s2str[] 
)

References SEQALN_CONSTANTS::btype, io, load_seq_fromstr(), localS(), results, results_init(), scoring, SELF, seq1, and seq2.

Referenced by main().

void dyaln::setup (  ) 

References SEQALN_CONSTANTS::btype, SEQALN_RESULTS::collen, distrib_file1, distrib_file2, io, load_distrib(), load_mat(), SEQALN_CONSTANTS::match, MATRIX, SEQALN_RESULTS::max_align_len, SEQALN_CONSTANTS::mismatch, SEQALN_CONSTANTS::mtype, PROFILE, SEQALN_RESULTS::pvalue, PVALUE, results, SEQALN_RESULTS::rowlen, SEQALN_RESULTS::S_size, scoring, SEQALN_PVALUE::seq1dist, SEQALN_PVALUE::seq1len, SEQALN_PVALUE::seq2dist, SEQALN_PVALUE::seq2len, setGapCost(), SIMILARITY, SEQALN_CONSTANTS::stats, SEQALN_CONSTANTS::stype, TANDEM, and SEQALN_CONSTANTS::window.

Referenced by dyaln().

void dyaln::outputTab ( ostream &  os  ) 

For relational database. Output fields: seq1Name, seq1Len, seq1cov, seq2Name, seq2Len, seq2cov overall_match_len, nogap_len, identity, nogapIdentity, similarity score, is_simple

References SEQALN_RESULTS::align1, SEQALN_RESULTS::align2, SEQALN_RESULTS::align_len, SEQALN_RESULTS::end1, SEQALN_RESULTS::end2, SEQALN_SEQUENCE::fstart, SEQALN_LSTRUCT::i, SEQALN_RESULTS::iden_count, isSimple(), SEQALN_LSTRUCT::j, SEQALN_SEQUENCE::len, LINEAR, SEQALN_RESULTS::match_freq1, SEQALN_RESULTS::match_freq2, SEQALN_CONSTANTS::memuse, SEQALN_SEQUENCE::name, SEQALN_RESULTS::nogap_len, results, scoring, seq1, seq2, SEQALN_RESULTS::siml_count, sortedFreq1, sortedFreq2, SEQALN_RESULTS::start1, SEQALN_RESULTS::start2, SEQALN_RESULTS::trace, and while().

Referenced by main().

void dyaln::outputTabPos ( ostream &  os  ) 

For relational database. Out put positional information instead of the coverage info; coverage can be derived easily from alignment position and the length of the sequences, Output fields: seq1Name, seq1Len, seq2Name, seq2Len, seq1begin, seq1end, seq2begin, seq2end, overall_match_len, nogap_match_len, identical_count, similar_count, score, is_simple, maxsimple

References SEQALN_RESULTS::align1, SEQALN_RESULTS::align2, SEQALN_RESULTS::align_len, SEQALN_RESULTS::bestS, SEQALN_RESULTS::end1, SEQALN_RESULTS::end2, SEQALN_SEQUENCE::fstart, SEQALN_LSTRUCT::i, SEQALN_RESULTS::iden_count, isSimple(), SEQALN_LSTRUCT::j, SEQALN_SEQUENCE::len, LINEAR, SEQALN_RESULTS::match_freq1, SEQALN_RESULTS::match_freq2, SEQALN_CONSTANTS::memuse, SEQALN_SEQUENCE::name, SEQALN_RESULTS::nogap_len, results, scoring, seq1, seq2, SEQALN_RESULTS::siml_count, sortedFreq1, sortedFreq2, SEQALN_RESULTS::start1, SEQALN_RESULTS::start2, and SEQALN_RESULTS::trace.

Referenced by main().

void dyaln::outputAln ( FILE *  ou = stdout  ) 

References SEQALN_RESULTS::bestS, SEQALN_CONSTANTS::cutoff, gen_align(), io, LINEAR, lsdeclump(), SEQALN_CONSTANTS::memuse, SEQALN_RESULTS::naligns, print_trace(), results, rpt_align(), rpt_scores(), SEQALN_CONSTANTS::rptalign, SEQALN_CONSTANTS::rptboth, SEQALN_CONSTANTS::rptmat, SEQALN_CONSTANTS::rptscore, SEQALN_CONSTANTS::rpttrace, scoring, seq1, seq2, SEQALN_IO::STDOUT, trace(), and SEQALN_CONSTANTS::traceupper.

Referenced by main().

void dyaln::setMatrix ( char  m[]  )  [inline]

References io, load_mat(), and scoring.

Referenced by main().

void dyaln::setGapCost ( int  alpha,
int  beta 
)

References SEQALN_CONSTANTS::alpha, SEQALN_CONSTANTS::beta, SEQALN_CONSTANTS::btype, SEQALN_CONSTANTS::mtype, scoring, SIMILARITY, and TANDEM.

Referenced by main(), and setup().

void dyaln::setcsub ( int  cs  )  [inline]

References SEQALN_CONSTANTS::csub, and scoring.

void dyaln::setNaligns ( int  n  )  [inline]

References SEQALN_CONSTANTS::naligns, and scoring.

Referenced by main().

bool dyaln::isSimple ( float &  ms  )  const

References SEQALN_RESULTS::end1, SEQALN_RESULTS::end2, getcount(), results, sortedFreq1, sortedFreq2, SEQALN_RESULTS::start1, and SEQALN_RESULTS::start2.

Referenced by outputTab(), and outputTabPos().

Member Data Documentation

struct SEQALN_SEQUENCE* dyaln::seq1 [read, private]

Referenced by align(), allocateMem(), outputAln(), outputTab(), outputTabPos(), and ~dyaln().

struct SEQALN_SEQUENCE * dyaln::seq2 [read, private]

Referenced by align(), allocateMem(), outputAln(), outputTab(), outputTabPos(), and ~dyaln().

struct SEQALN_CONSTANTS* dyaln::scoring [read, private]

Referenced by align(), allocateMem(), initParameter(), outputAln(), outputTab(), outputTabPos(), setcsub(), setGapCost(), setMatrix(), setNaligns(), setup(), and ~dyaln().

struct SEQALN_RESULTS* dyaln::results [read, private]

Referenced by align(), allocateMem(), freeTrace(), isSimple(), outputAln(), outputTab(), outputTabPos(), setup(), and ~dyaln().

struct SEQALN_IO* dyaln::io [read, private]

Referenced by align(), allocateMem(), initParameter(), outputAln(), setMatrix(), setup(), and ~dyaln().

char dyaln::distrib_file1[51] [private]

Referenced by initParameter(), and setup().

char dyaln::distrib_file2[51] [private]

Referenced by initParameter(), and setup().

pair<float, char> dyaln::sortedFreq1[20] [private]

Referenced by isSimple(), outputTab(), and outputTabPos().

pair<float, char> dyaln::sortedFreq2[20] [private]

Referenced by isSimple(), outputTab(), and outputTabPos().

The documentation for this class was generated from the following files:
Generated on Wed Aug 10 11:57:09 2011 for Softwares from Orpara by  doxygen 1.5.6