--- /dev/null
+#ifndef SUMMARYQUALCOMMAND_H
+#define SUMMARYQUALCOMMAND_H
+
+/*
+ * summaryqualcommand.h
+ * Mothur
+ *
+ * Created by westcott on 11/28/11.
+ * Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "qualityscores.h"
+
+/**************************************************************************************************/
+
+class SummaryQualCommand : public Command {
+public:
+ SummaryQualCommand(string);
+ SummaryQualCommand();
+ ~SummaryQualCommand(){}
+
+ vector<string> setParameters();
+ string getCommandName() { return "summary.qual"; }
+ string getCommandCategory() { return "Sequence Processing"; }
+ string getHelpString();
+ string getCitation() { return "http://www.mothur.org/wiki/Summary.qual"; }
+ string getDescription() { return "summarize the quality of a set of sequences"; }
+
+ int execute();
+ void help() { m->mothurOut(getHelpString()); }
+
+private:
+ bool abort;
+ string qualfile, outputDir, namefile;
+ vector<string> outputNames;
+ map<string, int> nameMap;
+ int processors;
+
+ 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< vector<int> >&, string);
+ int driverCreateSummary(vector<int>&, vector<int>&, vector< vector<int> >&, string, linePair);
+ int printQual(string, vector<int>&, vector<int>&, vector< vector<int> >&);
+};
+
+/**************************************************************************************************/
+//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 seqSumQualData {
+ vector<int>* position;
+ vector<int>* averageQ;
+ vector< vector<int> >* scores;
+ string filename, namefile;
+ unsigned long long start;
+ unsigned long long end;
+ int count;
+ MothurOut* m;
+ map<string, int> nameMap;
+
+ ~seqSumQualData(){}
+ seqSumQualData(vector<int>* p, vector<int>* a, vector< vector<int> >* s, string f, MothurOut* mout, unsigned long long st, unsigned long long en, string n, map<string, int> nam) {
+ position = p;
+ averageQ = a;
+ scores = s;
+ filename = f;
+ m = mout;
+ start = st;
+ end = en;
+ namefile = n;
+ nameMap = nam;
+ count = 0;
+ }
+};
+
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#else
+static DWORD WINAPI MySeqSumQualThreadFunction(LPVOID lpParam){
+ seqSumQualData* pDataArray;
+ pDataArray = (seqSumQualData*)lpParam;
+
+ try {
+ ifstream in;
+ pDataArray->m->openInputFile(pDataArray->filename, in);
+
+ //print header if you are process 0
+ if ((pDataArray->start == 0) || (pDataArray->start == 1)) {
+ in.seekg(0);
+ }else { //this accounts for the difference in line endings.
+ in.seekg(pDataArray->start-1); pDataArray->m->gobble(in);
+ }
+
+ int count = 0;
+ for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
+
+ if (pDataArray->m->control_pressed) { in.close(); pDataArray->count = 1; return 1; }
+
+ QualityScores 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; }
+ }
+
+ vector<int> thisScores = current.getQualityScores();
+
+ //resize to num of positions setting number of seqs with that size to 1
+ if (pDataArray->position->size() < thisScores.size()) { pDataArray->position->resize(thisScores.size(), 0); }
+ if (pDataArray->averageQ->size() < thisScores.size()) { pDataArray->averageQ->resize(thisScores.size(), 0); }
+ if (pDataArray->scores->size() < thisScores.size()) {
+ pDataArray->scores->resize(thisScores.size());
+ for (int i = 0; i < pDataArray->scores->size(); i++) { pDataArray->scores->at(i).resize(41, 0); }
+ }
+
+ //increase counts of number of seqs with this position
+ //average is really the total, we will average in execute
+ for (int i = 0; i < thisScores.size(); i++) {
+ pDataArray->position->at(i) += num;
+ pDataArray->averageQ->at(i) += (thisScores[i] * num); //weighting for namesfile
+ if (thisScores[i] > 40) { pDataArray->m->mothurOut("[ERROR]: " + current.getName() + " has a quality scores of " + toString(thisScores[i]) + ", expecting values to be less than 40."); pDataArray->m->mothurOutEndLine(); pDataArray->m->control_pressed = true; }
+ else { pDataArray->scores->at(i)[thisScores[i]] += num; }
+ }
+
+ count += num;
+ }
+ }
+
+ pDataArray->count = count;
+ in.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ pDataArray->m->errorOut(e, "SummaryQualCommand", "MySeqSumQualThreadFunction");
+ exit(1);
+ }
+}
+#endif
+
+
+/**************************************************************************************************/
+
+
+#endif
+
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