X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.h;h=a7ccb573490135c10c6fdb7258bb46228047d98b;hb=fc1ed1ae1b022719176910ab71993bd6535810ad;hp=c0d368770cfa8df11560d2b89fee200231cb0dc3;hpb=c651c46022761aef61644f78462365d8f767ff0b;p=mothur.git

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index c0d3687..a7ccb57 100644
--- 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
+
+/**************************************************************************************************/
+
+