X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=metastatscommand.h;h=12e0aebbe2d6a61409f5f749aba4a23db2841b31;hp=8c633b5417cbe07dc96827cf80c8e0b5522c0fad;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=37eac2026d91179acda0494c4dcca22f176551b9

diff --git a/metastatscommand.h b/metastatscommand.h
index 8c633b5..12e0aeb 100644
--- a/metastatscommand.h
+++ b/metastatscommand.h
@@ -12,23 +12,27 @@
  
 #include "command.hpp"
 #include "inputdata.h"
-#include "readotu.h"
 #include "sharedrabundvector.h"
-
-class GlobalData;
+#include "mothurmetastats.h"
 
 class MetaStatsCommand : public Command {
 
 public:
 	MetaStatsCommand(string);
 	MetaStatsCommand();
-	~MetaStatsCommand();
-	vector<string> getRequiredParameters();
-	vector<string> getValidParameters();
-	vector<string> getRequiredFiles();
-	map<string, vector<string> > getOutputFiles() { return outputTypes; }
-	int execute();
-	void help();
+	~MetaStatsCommand() {}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "metastats";				}
+	string getCommandCategory()		{ return "OTU-Based Approaches";	}
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "White JR, Nagarajan N, Pop M (2009). Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352. \nhttp://www.mothur.org/wiki/Metastats"; }
+	string getDescription()		{ return "detects differentially abundant features in clinical metagenomic samples"; }
+
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
 	struct linePair {
@@ -38,16 +42,13 @@ private:
 	};
 	vector<linePair> lines;
 	
-	GlobalData* globaldata;
 	GroupMap* designMap;
-	ReadOTUFile* read;
 	InputData* input;
 	vector<SharedRAbundVector*> lookup;
-	map<string, vector<string> > outputTypes;
-	
+		
 	bool abort, allLines, pickedGroups;
 	set<string> labels; //holds labels to be used
-	string groups, label, outputDir, inputDir, designfile, sets;
+	string groups, label, outputDir, inputDir, designfile, sets, sharedfile;
 	vector<string> Groups, outputNames, Sets;
 	vector< vector<string> > namesOfGroupCombos;
 	int iters, processors;
@@ -57,5 +58,107 @@ private:
 	int driver(int, int, vector<SharedRAbundVector*>&);
 };
 
+/**************************************************************************************************/
+//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 metastatsData {
+    vector<SharedRAbundVector*> thisLookUp;
+    vector< vector<string> > namesOfGroupCombos;
+    vector<string> designMapGroups;
+    vector<string> outputNames;
+	int start;
+	int num, iters, count;
+	float threshold;
+	MothurOut* m;
+	string sharedfile;
+    string outputDir;
+	
+	metastatsData(){}
+	metastatsData(string sf, string oDir, MothurOut* mout, int st, int en, vector< vector<string> > ns, vector<SharedRAbundVector*> lu, vector<string> dg, int i, float thr) {
+		sharedfile = sf;
+        outputDir = oDir;
+		m = mout;
+		start = st;
+		num = en;
+        namesOfGroupCombos = ns;
+        thisLookUp = lu;
+        designMapGroups = dg;
+        iters = i;
+        threshold = thr;
+        count=0;
+	}
+};
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MyMetastatsThreadFunction(LPVOID lpParam){ 
+	metastatsData* pDataArray;
+	pDataArray = (metastatsData*)lpParam;
+	
+	try {
+		
+        //for each combo
+		for (int c = pDataArray->start; c < (pDataArray->start+pDataArray->num); c++) {
+			pDataArray->count++;
+			//get set names
+			string setA = pDataArray->namesOfGroupCombos[c][0]; 
+			string setB = pDataArray->namesOfGroupCombos[c][1];
+            
+			//get filename
+			string outputFileName = pDataArray->outputDir +  pDataArray->m->getRootName(pDataArray->m->getSimpleName(pDataArray->sharedfile)) + pDataArray->thisLookUp[0]->getLabel() + "." + setA + "-" + setB + ".metastats";
+			pDataArray->outputNames.push_back(outputFileName); 
+			
+			vector< vector<double> > data2; data2.resize(pDataArray->thisLookUp[0]->getNumBins());
+			
+			vector<SharedRAbundVector*> subset;
+			int setACount = 0;
+			int setBCount = 0;
+			for (int i = 0; i < pDataArray->thisLookUp.size(); i++) {
+				//is this group for a set we want to compare??
+				//sorting the sets by putting setB at the back and setA in the front
+				if (pDataArray->designMapGroups[i] == setB) {  
+					subset.push_back(pDataArray->thisLookUp[i]);
+					setBCount++;
+				}else if (pDataArray->designMapGroups[i] == setA) {
+					subset.insert(subset.begin()+setACount, pDataArray->thisLookUp[i]);
+					setACount++;
+				}
+			}
+            
+			if ((setACount == 0) || (setBCount == 0))  { 
+				pDataArray->m->mothurOut("Missing shared info for " + setA + " or " + setB + ". Skipping comparison."); pDataArray->m->mothurOutEndLine(); 
+				pDataArray->outputNames.pop_back();
+			}else {
+				//fill data
+				for (int j = 0; j < pDataArray->thisLookUp[0]->getNumBins(); j++) {
+					data2[j].resize(subset.size(), 0.0);
+					for (int i = 0; i < subset.size(); i++) {
+						data2[j][i] = (subset[i]->getAbundance(j));
+					}
+				}
+				
+				pDataArray->m->mothurOut("Comparing " + setA + " and " + setB + "..."); pDataArray->m->mothurOutEndLine(); 
+				
+				pDataArray->m->mothurOutEndLine();
+				MothurMetastats mothurMeta(pDataArray->threshold, pDataArray->iters);
+				mothurMeta.runMetastats(outputFileName, data2, setACount);
+				pDataArray->m->mothurOutEndLine();
+				pDataArray->m->mothurOutEndLine(); 
+			}
+        }
+		
+		return 0;
+		
+	}
+	catch(exception& e) {
+		pDataArray->m->errorOut(e, "MetaStatsCommand", "MyMetastatsThreadFunction");
+		exit(1);
+	}
+} 
+#endif
+
+
+
 #endif