[Sashimi-commit] trans_proteomic_pipeline/src/Validation/MixtureModel MixtureModel.cxx, 1.33, 1.34

[David S. <ds...@us...>]

Update of /cvsroot/sashimi/trans_proteomic_pipeline/src/Validation/MixtureModel
In directory sc8-pr-cvs8.sourceforge.net:/tmp/cvs-serv7678

Modified Files:
	MixtureModel.cxx 
Log Message:
Now using adjusted probability to compute the total probability in a given charge state.

Index: MixtureModel.cxx
===================================================================
RCS file: /cvsroot/sashimi/trans_proteomic_pipeline/src/Validation/MixtureModel/MixtureModel.cxx,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** MixtureModel.cxx	28 Jun 2007 17:15:19 -0000	1.33
--- MixtureModel.cxx	28 Jun 2007 18:53:35 -0000	1.34
***************
*** 780,786 ****
--- 780,812 ----
    }
    double tot = 0.0;
+ 
    for(int k = 0; k < (*probs_)[charge]->size(); k++) {
      tot += (*(*probs_)[charge])[k];
    }
+   
+   return tot;
+ }
+ 
+ double MixtureModel::getTotalAdjProb(int charge) {
+   if(negOnly_[charge]) {
+     return 0.0;
+   }
+ 
+   double tot = 0.0;
+   if(charge > 0 && charge < 3 && use_adj_probs_) {
+     if (pairedspecs_ == NULL) {
+       computeAdjDoubleTriplySpectraProbs();
+     }
+     for(int k = 0; k < num_pairs_; k+=2) {
+       if(! negOnly_[atoi(pairedspecs_[k].name_ + strlen(pairedspecs_[k].name_)-1)-1]) {
+ 	tot += pairedspecs_[k+charge-1].prob_;
+       }
+     }
+   }
+   else {
+     for(int k = 0; k < (*probs_)[charge]->size(); k++) {
+       tot += (*(*probs_)[charge])[k];
+     }
+   }
    return tot;
  }
***************
*** 1528,1532 ****
    Tag* nexttag = NULL;
    char text[500];
! 
    nexttag = new Tag("analysis_summary", True, False);
    nexttag->setAttributeValue("analysis", prog_name);
--- 1554,1558 ----
    Tag* nexttag = NULL;
    char text[500];
!   
    nexttag = new Tag("analysis_summary", True, False);
    nexttag->setAttributeValue("analysis", prog_name);
***************
*** 1544,1548 ****
      nexttag->setAttributeValue("options", options);
  
!   sprintf(text, "%0.1f", getTotalProb(0)+getTotalProb(1)+getTotalProb(2)+getTotalProb(3)+getTotalProb(4));
    nexttag->setAttributeValue("est_tot_num_correct", text);
    output->insertAtEnd(nexttag);
--- 1570,1574 ----
      nexttag->setAttributeValue("options", options);
  
!   sprintf(text, "%0.1f", getTotalAdjProb(0)+getTotalAdjProb(1)+getTotalAdjProb(2)+getTotalAdjProb(3)+getTotalAdjProb(4));
    nexttag->setAttributeValue("est_tot_num_correct", text);
    output->insertAtEnd(nexttag);
***************
*** 1592,1596 ****
      sprintf(text, "%0.3f", priors_[charge]);
      nexttag->setAttributeValue("prior_probability", text);
!     sprintf(text, "%0.1f", getTotalProb(charge));
      nexttag->setAttributeValue("est_tot_correct", text);
      sprintf(text, "%d", (*spectra_)[charge]->size());
--- 1618,1622 ----
      sprintf(text, "%0.3f", priors_[charge]);
      nexttag->setAttributeValue("prior_probability", text);
!     sprintf(text, "%0.1f", getTotalAdjProb(charge));
      nexttag->setAttributeValue("est_tot_correct", text);
      sprintf(text, "%d", (*spectra_)[charge]->size());
***************
*** 2235,2239 ****
      }
  
!     fprintf(fout, "\tprior: %0.3f, est. total no. correct: %0.1f\n", priors_[charge], getTotalProb(charge));
      for(int k = 0; k < (*mixtureDistrs_)[charge]->size(); k++) {
        (*(*mixtureDistrs_)[charge])[k]->writeDistr(fout);
--- 2261,2265 ----
      }
  
!     fprintf(fout, "\tprior: %0.3f, est. total no. correct: %0.1f\n", priors_[charge], getTotalAdjProb(charge));
      for(int k = 0; k < (*mixtureDistrs_)[charge]->size(); k++) {
        (*(*mixtureDistrs_)[charge])[k]->writeDistr(fout);
***************
*** 2268,2272 ****
  	next[strlen((*(*spectra_)[charge])[k]) + 1] = charge + 49;
  	next[strlen((*(*spectra_)[charge])[k]) + 2] = 0;
! 	Spectrum* spec = new Spectrum(next, (*(*probs_)[charge])[k], ((NTTMixtureDistr*)(getMixtureDistr(ntt_name_, charge)))->getNTTValue(k), (*(*inds_)[charge])[k], k);
  	delete [] next;
  	pairedspecs_[total++] = *spec;
--- 2294,2299 ----
  	next[strlen((*(*spectra_)[charge])[k]) + 1] = charge + 49;
  	next[strlen((*(*spectra_)[charge])[k]) + 2] = 0;
! 	Spectrum* spec = new Spectrum(next, (*(*probs_)[charge])[k], 
! 				      ((NTTMixtureDistr*)(getMixtureDistr(ntt_name_, charge)))->getNTTValue(k), (*(*inds_)[charge])[k], k);
  	delete [] next;
  	pairedspecs_[total++] = *spec;
***************
*** 2300,2306 ****
    char text[500];
  
-   if(use_adj_probs_ && pairedspecs_ == NULL) {
-     computeAdjDoubleTriplySpectraProbs();
-   }
    int total = 0;
    for(int charge = 0; charge < 5; charge++) {
--- 2327,2330 ----