X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=indicatorcommand.h;h=61bd565a302e8e8ecbfd77b4d723215c7c9cb485;hp=1f46081dd464c32e599cf1d173d1eba60df3db46;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=1a5c2356c1b955c6ec024b2baf9f46377ee7c72e

diff --git a/indicatorcommand.h b/indicatorcommand.h
index 1f46081..61bd565 100644
--- a/indicatorcommand.h
+++ b/indicatorcommand.h
@@ -58,15 +58,144 @@ private:
 	map< vector<int>, vector<int> > randomizeGroupings(vector< vector<SharedRAbundVector*> >&, int);
 	map< vector<int>, vector<int> > randomizeGroupings(vector< vector<SharedRAbundFloatVector*> >&, int);
     
-	vector<float> driver(vector< vector<SharedRAbundFloatVector*> >&, map< vector<int>, vector<int> >, int, vector<float>, int);
-	vector<float> driver(vector< vector<SharedRAbundVector*> >&, map< vector<int>, vector<int> >, int, vector<float>, int);
+	vector<float> driver(vector< vector<SharedRAbundFloatVector*> >&, int, vector<float>, int);
+	vector<float> driver(vector< vector<SharedRAbundVector*> >&, int, vector<float>, int);
     
-	vector<float> getPValues(vector< vector<SharedRAbundFloatVector*> >&, map< vector<int>, vector<int> >, int, vector<float>);
-	vector<float> getPValues(vector< vector<SharedRAbundVector*> >&, map< vector<int>, vector<int> >, int, vector<float>);
+	vector<float> getPValues(vector< vector<SharedRAbundFloatVector*> >&, int, vector<float>);
+	vector<float> getPValues(vector< vector<SharedRAbundVector*> >&, int, vector<float>);
 
 	
 };
 
+/**************************************************************************************************/
+
+struct indicatorData {
+    vector< vector<SharedRAbundFloatVector*> > groupings;
+   	MothurOut* m;
+    int iters, num;
+    vector<float> indicatorValues;
+    vector<float> pvalues;
+	
+	indicatorData(){}
+	indicatorData(MothurOut* mout, int it, vector< vector<SharedRAbundFloatVector*> > ng, int n, vector<float> iv) {
+		m = mout;
+        iters = it;
+        groupings = ng;
+        indicatorValues = iv;
+        num = n;
+    }
+};
+/**************************************************************************************************/
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+static DWORD WINAPI MyIndicatorThreadFunction(LPVOID lpParam){
+	indicatorData* pDataArray;
+	pDataArray = (indicatorData*)lpParam;
+	
+	try {
+        
+		pDataArray->pvalues.resize(pDataArray->indicatorValues.size(), 0);
+		
+		for(int i=0;i<pDataArray->iters;i++){
+			if (pDataArray->m->control_pressed) { break; }
+            
+			//groupingsMap = randomizeGroupings(groupings, num);
+            ///////////////////////////////////////////////////////////////////////
+            map< vector<int>, vector<int> > randomGroupings;
+            
+            for (int j = 0; j < pDataArray->num; j++) {
+                
+                //get random groups to swap to switch with
+                //generate random int between 0 and groupings.size()-1
+                int z = pDataArray->m->getRandomIndex(pDataArray->groupings.size()-1);
+                int x = pDataArray->m->getRandomIndex(pDataArray->groupings.size()-1);
+                int a = pDataArray->m->getRandomIndex(pDataArray->groupings[z].size()-1);
+                int b = pDataArray->m->getRandomIndex(pDataArray->groupings[x].size()-1);
+                //cout << i << '\t' << z << '\t' << x << '\t' << a << '\t' << b << endl;
+                
+                vector<int> from;
+                vector<int> to;
+                
+                from.push_back(z); from.push_back(a);
+                to.push_back(x); to.push_back(b);
+                
+                randomGroupings[from] = to;
+            }
+            ///////////////////////////////////////////////////////////////////////
+            
+			//vector<float> randomIndicatorValues = getValues(groupings, notUsedGroupings, randomGroupings);
+            ///////////////////////////////////////////////////////////////////////
+            vector<float> randomIndicatorValues;
+            map< vector<int>, vector<int> >::iterator it;
+            
+            //for each otu
+            for (int i = 0; i < pDataArray->groupings[0][0]->getNumBins(); i++) {
+                
+                if (pDataArray->m->control_pressed) { return 0; }
+                
+                vector<float> terms;
+                float AijDenominator = 0.0;
+                vector<float> Bij;
+                
+                //get overall abundance of each grouping
+                for (int j = 0; j < pDataArray->groupings.size(); j++) {
+                    
+                    float totalAbund = 0;
+                    int numNotZero = 0;
+                    for (int k = 0; k < pDataArray->groupings[j].size(); k++) {
+                        vector<int> temp; temp.push_back(j); temp.push_back(k);
+                        it = randomGroupings.find(temp);
+                        
+                        if (it == randomGroupings.end()) { //this one didnt get moved
+                            totalAbund += pDataArray->groupings[j][k]->getAbundance(i);
+                            if (pDataArray->groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
+                        }else {
+                            totalAbund += pDataArray->groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i);
+                            if (pDataArray->groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i) != 0.0) { numNotZero++; }
+                        }
+                        
+                    }
+                    
+                    //mean abundance
+                    float Aij = (totalAbund / (float) pDataArray->groupings[j].size());
+                    terms.push_back(Aij);
+                    
+                    //percentage of sites represented
+                    Bij.push_back(numNotZero / (float) pDataArray->groupings[j].size());
+                    
+                    AijDenominator += Aij;
+                }
+                
+                float maxIndVal = 0.0;
+                for (int j = 0; j < terms.size(); j++) { 
+                    float thisAij = (terms[j] / AijDenominator); //relative abundance
+                    float thisValue = thisAij * Bij[j] * 100.0;
+                    
+                    //save largest
+                    if (thisValue > maxIndVal) { maxIndVal = thisValue; }
+                }
+                
+                randomIndicatorValues.push_back(maxIndVal);
+            }
+
+            ///////////////////////////////////////////////////////////////////////
+			
+			for (int j = 0; j < pDataArray->indicatorValues.size(); j++) {
+				if (randomIndicatorValues[j] >= pDataArray->indicatorValues[j]) { pDataArray->pvalues[j]++; }
+			}
+		}
+
+        return 0;
+		
+	}
+	catch(exception& e) {
+		pDataArray->m->errorOut(e, "IndicatorCommand", "MyIndicatorThreadFunction");
+		exit(1);
+	}
+}
+#endif
+
+
 
 #endif