added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index 7904425caf46918ef8e79aa34abea972b77b2cd5..dcb026c310ef7052116bb61f5b3517e24ae1e39e 100644 (file)
--- a/mothur.h
+++ b/mothur.h
@@ -941,6 +941,78 @@ inline string sortFile(string distFile){
                exit(1);
        }       
 }
+/**************************************************************************************************/
+inline vector<long> setFilePosFasta(string filename, int& num) {
+
+                       vector<long> positions;
+                       ifstream inFASTA;
+                       openInputFile(filename, inFASTA);
+                               
+                       string input;
+                       while(!inFASTA.eof()){
+                               input = getline(inFASTA); gobble(inFASTA);
+                               if (input.length() != 0) {
+                                       if(input[0] == '>'){    long pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);      }
+                               }
+                       }
+                       inFASTA.close();
+               
+                       num = positions.size();
+               
+                       FILE * pFile;
+                       long size;
+               
+                       //get num bytes in file
+                       pFile = fopen (filename.c_str(),"rb");
+                       if (pFile==NULL) perror ("Error opening file");
+                       else{
+                               fseek (pFile, 0, SEEK_END);
+                               size=ftell (pFile);
+                               fclose (pFile);
+                       }
+               
+                       positions.push_back(size);
+               
+                       return positions;
+}
+/**************************************************************************************************/
+inline vector<long> setFilePosEachLine(string filename, int& num) {
+
+                       vector<long> positions;
+                       ifstream in;
+                       openInputFile(filename, in);
+                               
+                       string input;
+                       while(!in.eof()){
+                               long lastpos = in.tellg();
+                               input = getline(in); gobble(in);
+                               if (input.length() != 0) {
+                                       long pos = in.tellg(); 
+                                       if (pos != -1) { positions.push_back(pos - input.length() - 1); }
+                                       else {  positions.push_back(lastpos);  }
+                               }
+                       }
+                       in.close();
+               
+                       num = positions.size();
+               
+                       FILE * pFile;
+                       long size;
+               
+                       //get num bytes in file
+                       pFile = fopen (filename.c_str(),"rb");
+                       if (pFile==NULL) perror ("Error opening file");
+                       else{
+                               fseek (pFile, 0, SEEK_END);
+                               size=ftell (pFile);
+                               fclose (pFile);
+                       }
+               
+                       positions.push_back(size);
+               
+                       return positions;
+}
+
 /**************************************************************************************************/
 #endif