[Sashimi-commit] trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML SequestParams.cxx, 1.9, 1.10

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

Update of /cvsroot/sashimi/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML
In directory sc8-pr-cvs8.sourceforge.net:/tmp/cvs-serv30553

Modified Files:
	SequestParams.cxx 
Log Message:
now storing database as part of the class, also bug fix of Min NTT parameter getting recorded.

Index: SequestParams.cxx
===================================================================
RCS file: /cvsroot/sashimi/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/SequestParams.cxx,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** SequestParams.cxx	14 Jul 2006 15:08:46 -0000	1.9
--- SequestParams.cxx	27 Jul 2006 19:09:20 -0000	1.10
***************
*** 49,53 ****
    const int line_width = 10000;
    char nextline[line_width];
! 
    char mod_tag[] = "diff_search_options =";
    char first[100];
--- 49,53 ----
    const int line_width = 10000;
    char nextline[line_width];
!   
    char mod_tag[] = "diff_search_options =";
    char first[100];
***************
*** 58,61 ****
--- 58,63 ----
    char static_mod_tag[] = "add_";
  
+   char db_tag[] = "database_name =";
+ 
    char sequence_constr_tag[] = "partial_sequence =";
    //char sequence_constraint[25];
***************
*** 265,269 ****
      }
      else if(matchStart(nextline, "ion_cutoff_percentage =")) {
!       sscanf(nextline + strlen("ion_cutoff_percentage ="), "%lf", &ion_cutoff_percentage_);
      }
      else if(matchStart(nextline, "match_peak_count =")) {
--- 267,271 ----
      }
      else if(matchStart(nextline, "ion_cutoff_percentage =")) {
!       sscanf(nextline + strlen("ion_cutoff_percentage ="), "%f", &ion_cutoff_percentage_);
      }
      else if(matchStart(nextline, "match_peak_count =")) {
***************
*** 274,278 ****
      }
      else if(matchStart(nextline, "match_peak_tolerance =")) {
!       sscanf(nextline + strlen("match_peak_tolerance ="), "%lf", &match_peak_tolerance_);
      }
      else if(matchStart(nextline, "protein_mass_filter =")) {
--- 276,280 ----
      }
      else if(matchStart(nextline, "match_peak_tolerance =")) {
!       sscanf(nextline + strlen("match_peak_tolerance ="), "%f", &match_peak_tolerance_);
      }
      else if(matchStart(nextline, "protein_mass_filter =")) {
***************
*** 290,294 ****
      }
      else if(matchStart(nextline, "NumEnzymeTermini =")) {
!       sscanf(nextline + strlen("num_output_lines ="), "%d", &min_num_tol_term_);
      }
  
--- 292,299 ----
      }
      else if(matchStart(nextline, "NumEnzymeTermini =")) {
!       sscanf(nextline + strlen("NumEnzymeTermini ="), "%d", &min_num_tol_term_);
!     }
!     else if(matchStart(nextline, db_tag)) {
!       sscanf(nextline + strlen(db_tag), "%s", &database_);
      }
  
***************
*** 309,312 ****
--- 314,322 ----
  }
  
+ Array<Tag*>* SequestParams::getSearchParamTags(char* basename, char* engine) {
+   return SearchParams::getSearchParamTags( basename, engine, this->database_);
+ }
+ 
+ 
  
  char* SequestParams::getEnzyme(int index) {