X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=seqsummarycommand.h;h=552f4a08bee284bf914e6a50cd51176864b8b1d8;hp=01dd450194c2f454ddd1b6c44de3fda99cde0798;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=faf4e99552d6fb4595ff348b1f909ddc74536da2

diff --git a/seqsummarycommand.h b/seqsummarycommand.h
index 01dd450..552f4a0 100644
--- a/seqsummarycommand.h
+++ b/seqsummarycommand.h
@@ -12,19 +12,161 @@
 
 #include "mothur.h"
 #include "command.hpp"
-#include "globaldata.hpp"
-
+#include "sequence.hpp"
 
+/**************************************************************************************************/
 
 class SeqSummaryCommand : public Command {
 public:
+	SeqSummaryCommand(string);
 	SeqSummaryCommand();
-	~SeqSummaryCommand();
-	int execute();
+	~SeqSummaryCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "summary.seqs";			}
+	string getCommandCategory()		{ return "Sequence Processing";		}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Summary.seqs"; }
+	string getDescription()		{ return "summarize the quality of sequences in an unaligned or aligned fasta file"; }
 	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }		
 private:
-	GlobalData* globaldata;	
+	bool abort;
+	string fastafile, outputDir, namefile, countfile;
+	int processors;
+	vector<string> outputNames;
+	map<string, int> nameMap;
+	
+	struct linePair {
+		unsigned long long start;
+		unsigned long long end;
+		linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
+	};
+
+	vector<linePair*> lines;
+	vector<int> processIDS;
+	
+	int createProcessesCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string);
+	int driverCreateSummary(vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, string, string, linePair*);	
 
+	#ifdef USE_MPI
+	int MPICreateSummary(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, MPI_File&, MPI_File&, vector<unsigned long long>&);	
+	#endif
+
+
+};
+
+/**************************************************************************************************/
+//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).
+struct seqSumData {
+	vector<int> startPosition;
+	vector<int> endPosition;
+	vector<int> seqLength; 
+	vector<int> ambigBases; 
+	vector<int> longHomoPolymer; 
+	string filename; 
+	string sumFile; 
+	unsigned long long start;
+	unsigned long long end;
+	int count;
+	MothurOut* m;
+	bool hasNameMap;
+	map<string, int> nameMap;
+	
+	
+	seqSumData(){}
+	seqSumData(string f, string sf, MothurOut* mout, unsigned long long st, unsigned long long en, bool na, map<string, int> nam) {
+		filename = f;
+		sumFile = sf;
+		m = mout;
+		start = st;
+		end = en;
+		hasNameMap = na;
+		nameMap = nam;
+		count = 0;
+	}
 };
 
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#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); 
+		}
+		
+		for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+			
+            pDataArray->count++;
+            
+			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->hasNameMap){
+					//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 name or count file, 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
+
+/**************************************************************************************************/
+
+