[Sashimi-commit] trans_proteomic_pipeline/src/Visualization/Comet/sequest-tgz-out sequest-tgz-out1.c, 1.9, 1.10

[Jimmy E. <en...@us...>]

Update of /cvsroot/sashimi/trans_proteomic_pipeline/src/Visualization/Comet/sequest-tgz-out
In directory sc8-pr-cvs8.sourceforge.net:/tmp/cvs-serv22330

Modified Files:
	sequest-tgz-out1.c 
Log Message:
fix parsing static modifications for partial enzyme search


Index: sequest-tgz-out1.c
===================================================================
RCS file: /cvsroot/sashimi/trans_proteomic_pipeline/src/Visualization/Comet/sequest-tgz-out/sequest-tgz-out1.c,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** sequest-tgz-out1.c	9 Aug 2006 18:06:21 -0000	1.9
--- sequest-tgz-out1.c	25 Sep 2006 22:51:25 -0000	1.10
***************
*** 255,258 ****
--- 255,266 ----
           sscanf(pStr+1, "%lf", &dMass3);
  
+       /*
+        * delete terminating semi-cleavage output as this adversely affects the
+        * next strrchr() command logic if left in place; relevant only to isb but
+        * shouldn't affect other versions
+        */
+       if (pStr=strstr(szBuf, "(2:1)"))
+          *pStr='\0';
+ 
        /* look for static modifications */
        if (pStr=strrchr(szBuf, ')'))
***************
*** 260,296 ****
           int i,
               iLen;
- 	 
-          strcpy(szBuf, pStr+2);
- 	 iLen=strlen(szBuf);
- 	 
           char tmp[32];
! 	 int tmp_i = 0;
  
! 	 for (i=1; i<iLen; i++)
! 	   {
! 	     if (szBuf[i]=='=')
! 	       {
! 		 double dMass=0.0;
       
! 		 sscanf(szBuf+i+1, "%lf", &dMass);
! 		 if (pStr=strstr(tmp, "N-term")) {
! 		   sprintf(szMod+strlen(szMod), "&amp;Nterm=%0.4f", dMass);
! 		 }
! 		 else if (pStr=strstr(tmp, "C-term")) {
! 		   sprintf(szMod+strlen(szMod), "&amp;Cterm=%0.4f", dMass);
! 		 }
! 		 else {
! 		   sprintf(szMod+strlen(szMod), "&amp;Mass%c=%0.4f", szBuf[i-1], dMass);
! 		 }
! 		 tmp_i=0;
! 		 tmp[tmp_i] = '\0';
! 	       }
! 	     else 
! 	       {
! 		 tmp[tmp_i] = szBuf[i];
! 		 tmp_i++;
! 		 tmp[tmp_i] = '\0';
! 	     }
! 	   }
        }
     }
--- 268,303 ----
           int i,
               iLen;
           char tmp[32];
!          int tmp_i = 0;
!  
!          strcpy(szBuf, pStr+2);
!          iLen=strlen(szBuf);
  
!          for (i=1; i<iLen; i++)
!          {
!             if (szBuf[i]=='=')
!             {
!                double dMass=0.0;
       
!                sscanf(szBuf+i+1, "%lf", &dMass);
!                if (pStr=strstr(tmp, "N-term")) {
!                   sprintf(szMod+strlen(szMod), "&amp;Nterm=%0.4f", dMass);
!                }
!                else if (pStr=strstr(tmp, "C-term")) {
!                   sprintf(szMod+strlen(szMod), "&amp;Cterm=%0.4f", dMass);
!                }
!                else {
!                   sprintf(szMod+strlen(szMod), "&amp;Mass%c=%0.4f", szBuf[i-1], dMass);
!                }
!                tmp_i=0;
!                tmp[tmp_i] = '\0';
!             }
!             else 
!             {
!                tmp[tmp_i] = szBuf[i];
!                tmp_i++;
!                tmp[tmp_i] = '\0';
!             }
!          }
        }
     }