[Sashimi-commit] trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML CombineOut.cxx, 1.2, 1.3

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

Update of /cvsroot/sashimi/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML
In directory sc8-pr-cvs8.sourceforge.net:/tmp/cvs-serv32661/Parsers/Algorithm2XML/Sequest2XML

Modified Files:
	CombineOut.cxx 
Log Message:
New code for processing TGZ files (not yet functional).

Index: CombineOut.cxx
===================================================================
RCS file: /cvsroot/sashimi/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/CombineOut.cxx,v
retrieving revision 1.2
retrieving revision 1.3
diff -C2 -d -r1.2 -r1.3
*** CombineOut.cxx	29 Nov 2006 20:58:29 -0000	1.2
--- CombineOut.cxx	8 Dec 2006 20:26:47 -0000	1.3
***************
*** 20,29 ****
      outpath_[strlen(outpath_)-1] = '\0';
    }
    sprintf(pepXmlPath_, "%s.xml", outpath_);
    sprintf(paramsPath_, "%s/sequest.params", outpath_);
!   strcpy(inpath1_, path1);
!   strcpy(inpath2_, path1);
!   readOutDir(path1, outFiles1_, seqParams1_);
!   readOutDir(path2, outFiles2_, seqParams2_);
  }
  
--- 20,55 ----
      outpath_[strlen(outpath_)-1] = '\0';
    }
+ 
+   strcpy(inpath1_, path1);
+   strcpy(inpath2_, path2);
+   
+   tgzfile1_ = False;
+   tgzfile2_ = False;
+ 
+   if (strstr(inpath1_, ".tgz") != NULL) {
+      tgzfile1_ = True;
+   }
+   if (strstr(inpath2_, ".tgz") != NULL) {
+      tgzfile2_ = True;
+   }
+   
+   if (tgzfile1_) {
+     readTgzFile(path1, outFiles1_, seqParams1_);
+   }
+   else {
+     readOutDir(path1, outFiles1_, seqParams1_);
+   }  
+ 
+   if (tgzfile2_) {
+     readTgzFile(path2, outFiles2_, seqParams2_);
+   }
+   else {
+     readOutDir(path2, outFiles2_, seqParams2_);
+   }
+ 
    sprintf(pepXmlPath_, "%s.xml", outpath_);
+   sprintf(mzXmlPath_, "%s.mzXML", outpath_);
    sprintf(paramsPath_, "%s/sequest.params", outpath_);
!   sprintf(baseName_, "%s", outpath_);
  }
  
***************
*** 359,369 ****
              }
  	  
! 	  sprintf(baseName_, "%s", pathName);
  	  sprintf(baseDir_, "%s", pathName);
  	  
! 	  baseName_[strlen(baseName_)-1] = '\0';
  
! 	  //sprintf(pepXmlPath_, "%s.xml", baseName_);
! 	  sprintf(mzXmlPath_, "%s.mzXML", baseName_);
  
  	  //TODO: need an option for this 
--- 385,395 ----
              }
  	  
! 	  // sprintf(baseName_, "%s", pathName);
  	  sprintf(baseDir_, "%s", pathName);
  	  
! 	  // baseName_[strlen(baseName_)-1] = '\0';
  
! 	  // sprintf(pepXmlPath_, "%s.xml", baseName_);
! 	  // sprintf(mzXmlPath_, "%s.mzXML", baseName_);
  
  	  //TODO: need an option for this 
***************
*** 407,408 ****
--- 433,491 ----
    delete [] paramsFile;
  }
+ 
+ 
+ void  CombineOut::readTgzFile(char* path, hash_map<const char*, SequestOut*, hash<const char*>, eqstr>& outFiles, SequestParams*& seqParam) 
+ {
+   struct stat fileStat;
+   FILE *tgzpipe, *outpipe;
+ #ifdef WINDOWS_CYGWIN
+   char SEP = '\\';
+ #else
+   char SEP = '/';
+ #endif
+   char * pathName = new char [4086];
+   char * fileName = new char [4086];
+   char * paramsFile = new char [4086];
+   char * command = new char [4086];
+   char * next = new char [4086];
+   if (!stat(path, &fileStat))
+     {
+       if (S_ISREG(fileStat.st_mode))
+ 	{
+ 	  sprintf(command, "tar tfz %s *.out", path);
+ 	  if ((tgzpipe = popen(command, "r"))!=NULL) {
+ 	    while (fgets(next, 4086, tgzpipe)!=NULL) {
+ 	      next[strlen(next)-1] = '\0';
+ 	      sprintf(command, "tar Oxfz %s %s", path, next);
+ 	      if ((outpipe = popen(command, "r"))!=NULL) {
+ 		SequestOut* tmp = new SequestOut();
+ 		struct HeaderStruct * hdr = (HeaderStruct *)malloc(sizeof(HeaderStruct));
+ 		this->readOutFile(outpipe, tmp, hdr, seqParam);
+ 		char* key = new char[4086];
+ 		sprintf(key, "%s", next);
+ 		hash_map<const char*, SequestOut*, hash<const char*>, eqstr>::iterator curr; 
+ 		hash_map<const char*, SequestOut*, hash<const char*>, eqstr>::iterator end = outFiles.end();
+ 		outFiles.insert(pair<const char*, SequestOut*>(key, tmp));
+ 	      }
+ 	      pclose(outpipe);
+ 	    }
+ 	  }
+ 	  else
+ 	    {
+ 	      //Do nothing right now
+ 	      //TODO: do something meaningful
+ 	    }	
+ 	}    
+       else 
+ 	{
+ 	  //Do nothing right now
+ 	  //TODO: do something meaningful
+ 	}
+       
+     }
+   delete [] next;
+   delete [] command;
+   delete [] pathName;
+   delete [] fileName;
+   delete [] paramsFile;
+ }