added paralellization for windows to dist.seqs and summary.seqs

[mothur.git] / seqsummarycommand.h

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index c0d368770cfa8df11560d2b89fee200231cb0dc3..a7ccb573490135c10c6fdb7258bb46228047d98b 100644 (file)
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -12,6 +12,9 @@
 
 #include "mothur.h"
 #include "command.hpp"
+#include "sequence.hpp"
+
+/**************************************************************************************************/
 
 class SeqSummaryCommand : public Command {
 public:
@@ -54,4 +57,118 @@ private:
 
 };
 
+/**************************************************************************************************/
+//custom data structure for threads to use.
+// This is passed by void pointer so it can be any data type
+// that can be passed using a single void pointer (LPVOID).
+typedef struct seqSumData {
+       vector<int>* startPosition;
+       vector<int>* endPosition;
+       vector<int>* seqLength; 
+       vector<int>* ambigBases; 
+       vector<int>* longHomoPolymer; 
+       string filename; 
+       string sumFile; 
+       unsigned long int start;
+       unsigned long int end;
+       int count;
+       MothurOut* m;
+       string namefile;
+       map<string, int> nameMap;
+       
+       
+       seqSumData(){}
+       seqSumData(vector<int>* s, vector<int>* e, vector<int>* l, vector<int>* a, vector<int>* h, string f, string sf, MothurOut* mout, unsigned long int st, unsigned long int en, string na, map<string, int> nam) {
+               startPosition = s;
+               endPosition = e;
+               seqLength = l;
+               ambigBases = a;
+               longHomoPolymer = h;
+               filename = f;
+               sumFile = sf;
+               m = mout;
+               start = st;
+               end = en;
+               namefile = na;
+               nameMap = nam;
+               count = 0;
+       }
+};
+
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+static DWORD WINAPI MySeqSumThreadFunction(LPVOID lpParam){ 
+       seqSumData* pDataArray;
+       pDataArray = (seqSumData*)lpParam;
+       
+       try {
+               ofstream outSummary;
+               pDataArray->m->openOutputFile(pDataArray->sumFile, outSummary);
+               
+               ifstream in;
+               pDataArray->m->openInputFile(pDataArray->filename, in);
+
+               //print header if you are process 0
+               if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+                       outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer\tnumSeqs" << endl;  
+                       in.seekg(0);
+               }else { //this accounts for the difference in line endings. 
+                       in.seekg(pDataArray->start-1); pDataArray->m->gobble(in); 
+               }
+               
+               pDataArray->count = pDataArray->end;
+               for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+                       
+                       if (pDataArray->m->control_pressed) { in.close(); outSummary.close(); pDataArray->count = 1; return 1; }
+                       
+                       Sequence current(in); pDataArray->m->gobble(in); 
+                       
+                       if (current.getName() != "") {
+                               
+                               int num = 1;
+                               if (pDataArray->namefile != "") {
+                                       //make sure this sequence is in the namefile, else error 
+                                       map<string, int>::iterator it = pDataArray->nameMap.find(current.getName());
+                                       
+                                       if (it == pDataArray->nameMap.end()) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
+                                       else { num = it->second; }
+                               }
+                               
+                               //for each sequence this sequence represents
+                               for (int i = 0; i < num; i++) {
+                                       pDataArray->startPosition->push_back(current.getStartPos());
+                                       pDataArray->endPosition->push_back(current.getEndPos());
+                                       pDataArray->seqLength->push_back(current.getNumBases());
+                                       pDataArray->ambigBases->push_back(current.getAmbigBases());
+                                       pDataArray->longHomoPolymer->push_back(current.getLongHomoPolymer());
+                               }
+                               
+                               outSummary << current.getName() << '\t';
+                               outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
+                               outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
+                               outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
+                       }
+               }
+               
+               in.close();
+               outSummary.close();
+               
+               return 0;
+               
+       }
+       catch(exception& e) {
+               pDataArray->m->errorOut(e, "SeqSummaryCommand", "MySeqSumThreadFunction");
+               exit(1);
+       }
+} 
 #endif
+
+
+
+
+#endif
+
+/**************************************************************************************************/
+
+