"Fossies" - the Fresh Open Source Software Archive  

Source code changes of the file "src/igenictrain.cc" between
augustus-3.3.2.tar.gz and augustus-3.3.3.tar.gz

About: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.

igenictrain.cc  (augustus-3.3.2):igenictrain.cc  (augustus-3.3.3)
/********************************************************************** /*
* file: igenictrain.cc * igenictrain.cc
* licence:
* *
* descr.: training for intergenic region * License: Artistic License, see file LICENSE.TXT or
* authors: Mario Stanke, mario@gobics.de * https://opensource.org/licenses/artistic-license-1.0
* *
* date | author | changes * Description: training for intergenic region
* --------|---------------|------------------------------------------ */
* 27.03.06| Mario Stanke | took introns in cds out of the training
**********************************************************************/
#include "igenicmodel.hh" #include "igenicmodel.hh"
// project includes // project includes
#include "gene.hh" #include "gene.hh"
#include "properties.hh" #include "properties.hh"
#include "merkmal.hh" #include "merkmal.hh"
#include "intronmodel.hh" // so splice sites models can be reused here #include "intronmodel.hh" // so splice sites models can be reused here
// standard C/C++ includes // standard C/C++ includes
skipping to change at line 174 skipping to change at line 171
/* /*
* ===[ IGenicModel::processSequence ]==================================== * ===[ IGenicModel::processSequence ]====================================
*/ */
void IGenicModel::processSequence( const char* start, const char* end ){ void IGenicModel::processSequence( const char* start, const char* end ){
Seq2Int s2i( k+1 ); Seq2Int s2i( k+1 );
for( ; start <= end; start++){ for( ; start <= end; start++){
try { try {
emicount[ s2i( start-k ) ] += gweight ; emicount[ s2i( start-k ) ] += gweight ;
emicount[ s2i.rc( start-k ) ] += gweight ; emicount[ s2i.rc( start-k ) ] += gweight ;
gesbasen += 2*gweight; gesbasen += 2*gweight;
} catch (InvalidNucleotideError e) {} } catch (InvalidNucleotideError &e) {}
} }
} }
/* /*
* storeGCPars * storeGCPars
* store GC dependent model probabilities in the respective array variables * store GC dependent model probabilities in the respective array variables
*/ */
void IGenicModel::storeGCPars(int idx){ void IGenicModel::storeGCPars(int idx){
GCemiprobs[idx] = emiprobs; GCemiprobs[idx] = emiprobs;
std::stringstream out; std::stringstream out;
skipping to change at line 251 skipping to change at line 248
ostrm << "# patterns" << endl; ostrm << "# patterns" << endl;
for( int j = 0; j < emicount.size(); j++ ) for( int j = 0; j < emicount.size(); j++ )
ostrm << s2i.INV(j) << "\t" << emicount[j] << endl; ostrm << s2i.INV(j) << "\t" << emicount[j] << endl;
// *************/ // *************/
ostrm.close(); ostrm.close();
} }
} }
catch( ProjectError ) { catch( ProjectError& ) {
if (verbosity) if (verbosity)
cout << "Intergenic Region model parameters not saved." << endl; cout << "Intergenic Region model parameters not saved." << endl;
} }
} }
 End of changes. 5 change blocks. 
11 lines changed or deleted 8 lines changed or added

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