[Sashimi-commit] trans_proteomic_pipeline/src/Visualization/Comet/plot-msms plot-msms1.c, 1.33, 1.34

[Josh T <spa...@us...>]

Update of /cvsroot/sashimi/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms
In directory sc8-pr-cvs8.sourceforge.net:/tmp/cvs-serv17315

Modified Files:
	plot-msms1.c 
Log Message:
fixing scan-number extraction from dta filenames to allow for maldi-type names which include spot numbers.

Index: plot-msms1.c
===================================================================
RCS file: /cvsroot/sashimi/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms1.c,v
retrieving revision 1.33
retrieving revision 1.34
diff -C2 -d -r1.33 -r1.34
*** plot-msms1.c	19 Mar 2007 20:23:32 -0000	1.33
--- plot-msms1.c	26 Mar 2007 19:52:35 -0000	1.34
***************
*** 218,221 ****
--- 218,223 ----
  void HIGHLIGHT(double dMass,
           int iWhichIonSeries);
+ int GET_SCANNUM_FROM_DTA_NAME(const char* dtaName);
+ 
  #include "util.h"
  
***************
*** 2319,2337 ****
     {
        /* mzXML file: read file index and parse scan # from encoded .dta file*/
! 
!       char szTmp[500];
!       char *pStr;
! 
!       if ( (pStr = strchr(pEnvironment.szInputFile, '.'))==NULL)
!       {
!          printf(" Error - cannot get scan number from input file %s\n", pEnvironment.szInputFile);
!          exit(1);
!       }
! 
!       strcpy(szTmp, pStr+1);
!       pStr = strchr(szTmp, '.');
!       *pStr = '\0';
! 
!       sscanf(szTmp, "%d", &iScanNum);
  
        /* read mzXML file offset scan index */
--- 2321,2325 ----
     {
        /* mzXML file: read file index and parse scan # from encoded .dta file*/
!       iScanNum = GET_SCANNUM_FROM_DTA_NAME(pEnvironment.szInputFile);
  
        /* read mzXML file offset scan index */
***************
*** 2861,2878 ****
        /* mzXML file: read file index and parse scan # from encoded .dta file*/
  
!       char szTmp[500];
!       char *pStr;
! 
!       if ( (pStr = strchr(pEnvironment.szInputFile, '.'))==NULL)
!       {
!          printf(" Error - cannot get scan number from input file %s\n", pEnvironment.szInputFile);
!          exit(1);
!       }
! 
!       strcpy(szTmp, pStr+1);
!       pStr = strchr(szTmp, '.');
!       *pStr = '\0';
! 
!       sscanf(szTmp, "%d", &iScanNum);
  
        /* read mzXML file offset scan index */
--- 2849,2853 ----
        /* mzXML file: read file index and parse scan # from encoded .dta file*/
  
!       iScanNum = GET_SCANNUM_FROM_DTA_NAME(pEnvironment.szInputFile);
  
        /* read mzXML file offset scan index */
***************
*** 3146,3147 ****
--- 3121,3164 ----
        return (0);
  } /*SORT_LABELIONS_INTEN*/
+ 
+ 
+ /*
+  * extract the scan number from the dta file name, which is expected be of the format
+  * xxxxxxxxxxxxxx.scanstart.scanend.charge
+  */
+ int GET_SCANNUM_FROM_DTA_NAME(const char* dtaName) {
+   int scanNum = -1;
+   char szTmp[500];
+   char *pStr;
+ 
+   /* 
+      assume dta filename format is xxxxxxxx.scanstart.scanend.charge.dta
+       
+      start from right to left, in order to avoid issues with messy naming schemes,
+      like maldi, which may have a format like xxxxxxx.SPOT_DESIGNATOR.xxxx.xxxx.xxx.dta
+   */
+ 
+   strcpy(szTmp, dtaName);
+ 
+   int fieldCount=4;
+   while (fieldCount != 0) {
+     pStr = strrchr(szTmp, '.');
+     if (pStr == NULL) {
+       printf(" Error - cannot get scan number from input file %s; unexpected dta name format\n", dtaName);
+       exit(1);
+     }
+     /* 
+        first time here: pStr is one before 'dta'
+        second time: pStr is one before charge
+        third time: pStr is one before scanend
+        forth: one before scanstart (what we want)
+     */
+     *pStr = '\0';
+     --fieldCount;
+   }
+   /* szTemp is now xxxxxxx.scanstartNULLxxxxxx */
+   pStr++;
+   sscanf(pStr, "%d", &scanNum);
+ 
+   return scanNum;
+ }