X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=raredisplay.cpp;h=da22e74e90731d5294c6250d4c19f1a84045c06d;hp=b86312bc4411e8cdd2faca9934aab3abf5c96c52;hb=615301e57c25e241356a9c2380648d117709458d;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2

diff --git a/raredisplay.cpp b/raredisplay.cpp
index b86312b..da22e74 100644
--- a/raredisplay.cpp
+++ b/raredisplay.cpp
@@ -14,17 +14,9 @@
 void RareDisplay::init(string label){
 	try {
 		this->label = label;
-		if(nIters != 1){
-			tempInFile.clear();
-			openOutputFile(tempOutName, tempOutFile);
-			openInputFile(tempInName, tempInFile);
-		}
-		else{
-			openOutputFile(tempOutName, tempOutFile);
-		}
 	}
 	catch(exception& e) {
-		errorOut(e, "RareDisplay", "init");
+		m->errorOut(e, "RareDisplay", "init");
 		exit(1);
 	}
 }
@@ -36,26 +28,17 @@ void RareDisplay::update(SAbundVector* rank){
 		int newNSeqs = rank->getNumSeqs();
 		vector<double> data = estimate->getValues(rank);
 
-		if(nIters != 1){
-
-			double oldNSeqs, oldMean, oldVar;
-		
-			tempInFile >> oldNSeqs >> oldMean >> oldVar;
-		
-			double oldS = oldVar * ( nIters - 2 );
-			double delta = data[0] - oldMean;
-			double newMean = oldMean + delta / nIters;
-			double newS = oldS + delta * ( data[0] - newMean );
-			double newVar = newS / ( nIters - 1 );
-
-			tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl;
-		}
-		else{
-			tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl;
-		}
+		map<int, vector<double> >::iterator it = results.find(newNSeqs);
+        if (it == results.end()) { //first iter for this count
+            vector<double> temp;
+            temp.push_back(data[0]);
+            results[newNSeqs] = temp;
+        }else {
+            it->second.push_back(data[0]);
+        }
 	}
 	catch(exception& e) {
-		errorOut(e, "RareDisplay", "update");
+		m->errorOut(e, "RareDisplay", "update");
 		exit(1);
 	}
 }
@@ -64,27 +47,18 @@ void RareDisplay::update(SAbundVector* rank){
 void RareDisplay::update(vector<SharedRAbundVector*> shared, int numSeqs, int numGroupComb) {
 	try {
 		vector<double> data = estimate->getValues(shared); 
-		double newNSeqs = data[0];
-		
-		if(nIters != 1){
-			double oldNSeqs, oldMean, oldVar;
-		
-			tempInFile >> oldNSeqs >> oldMean >> oldVar;
 		
-			double oldS = oldVar * ( nIters - 2 );
-			double delta = data[0] - oldMean;
-			double newMean = oldMean + delta / nIters;
-			double newS = oldS + delta * ( data[0] - newMean );
-			double newVar = newS / ( nIters - 1 );
-
-			tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl;
-		}
-		else{
-			tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl;
-		}
+		map<int, vector<double> >::iterator it = results.find(numSeqs);
+        if (it == results.end()) { //first iter for this count
+            vector<double> temp;
+            temp.push_back(data[0]);
+            results[numSeqs] = temp;
+        }else {
+            it->second.push_back(data[0]);
+        }
 	}
 	catch(exception& e) {
-		errorOut(e, "RareDisplay", "update");
+		m->errorOut(e, "RareDisplay", "update");
 		exit(1);
 	}
 }
@@ -93,24 +67,10 @@ void RareDisplay::update(vector<SharedRAbundVector*> shared, int numSeqs, int nu
 
 void RareDisplay::reset(){
 	try {
-		if(nIters != 1){
-			tempOutFile.close();
-			tempInFile.close();
-		}
-		else{
-			tempOutFile.close();
-		}
-	
 		nIters++;
-	
-		remove(tempInName.c_str());
-		renameOk = rename(tempOutName.c_str(), tempInName.c_str());	
-		
-		//checks to make sure user was able to rename and remove successfully
-		if (renameOk != 0) { mothurOut("Unable to rename the necessary temp files."); mothurOutEndLine(); }
 	}
 	catch(exception& e) {
-		errorOut(e, "RareDisplay", "reset");
+		m->errorOut(e, "RareDisplay", "reset");
 		exit(1);
 	}
 }
@@ -119,42 +79,101 @@ void RareDisplay::reset(){
 
 void RareDisplay::close(){
 	try {
-		
 		output->initFile(label);
 	
-		openInputFile(tempInName, tempInFile);
-	
-		while(!tempInFile.eof()){
-			int nSeqs;
-			tempInFile >> nSeqs;
+		for (map<int, vector<double> >::iterator it = results.begin(); it != results.end(); it++) {
 		
 			vector<double> data(3,0);
-			double variance = 0;
+            
+            sort((it->second).begin(), (it->second).end());
+            
+            //lci=results[int(0.025*iter)] and hci=results[int(0.975*iter)]
+			data[0] = (it->second)[(int)(0.50*(nIters-1))];
+            //data[0] = m->getAverage(it->second);
+			data[1] = (it->second)[(int)(0.025*(nIters-1))];
+			data[2] = (it->second)[(int)(0.975*(nIters-1))];
+            //cout << nIters << '\t' << (int)(0.025*(nIters-1)) << '\t' << (int)(0.975*(nIters-1)) << endl;
+            
+            //cout << it->first << '\t' << data[1] << '\t' << data[2] << endl;
 		
-			tempInFile >> data[0];
-			tempInFile >> variance;
+			output->output(it->first, data);
+		}
 		
-			double ci = 1.96 * pow(variance, 0.5);
-			data[1] = data[0] - ci;
-			data[2] = data[0] + ci;
+		nIters = 1;
+        results.clear();
 		
-			output->output(nSeqs, data);
+		output->resetFile();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareDisplay", "close");
+		exit(1);
+	}
+}
+/***********************************************************************/
+
+void RareDisplay::inputTempFiles(string filename){
+	try {
+		ifstream in;
+		m->openInputFile(filename, in);
 		
-			gobble(tempInFile);
+		int thisIters, size;
+		in >> thisIters >> size; m->gobble(in);
+        nIters += thisIters;
+		
+		for (int i = 0; i < size; i++) {
+			int tempCount;
+            in >> tempCount; m->gobble(in);
+            map<int, vector<double> >::iterator it = results.find(tempCount);
+            if (it != results.end()) {
+                for (int j = 0; j < thisIters; j++) {
+                    double value;
+                    in >> value; m->gobble(in);
+                    (it->second).push_back(value);
+                }
+            }else {
+                vector<double> tempValues;
+                for (int j = 0; j < thisIters; j++) {
+                    double value;
+                    in >> value; m->gobble(in);
+                    tempValues.push_back(value);
+                }
+                results[tempCount] = tempValues;
+            }
 		}
-		tempInFile.close();
-	
-		remove(tempInName.c_str());
-		remove(tempOutName.c_str());
 		
-		nIters = 1;
-		output->resetFile();
+		in.close();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareDisplay", "inputTempFiles");
+		exit(1);
+	}
+}
+
+/***********************************************************************/
+
+void RareDisplay::outputTempFiles(string filename){
+	try {
+		ofstream out;
+		m->openOutputFile(filename, out);
+		
+		out << nIters-1 << '\t' << results.size() << endl;
+		
+		for (map<int, vector<double> >::iterator it = results.begin(); it != results.end(); it++) {
+            out << it->first << '\t';
+            for(int i = 0; i < (it->second).size(); i++) {
+                out << (it->second)[i] << '\t';
+            }
+            out << endl;
+		}
+		
+		out.close();
 	}
 	catch(exception& e) {
-		errorOut(e, "RareDisplay", "close");
+		m->errorOut(e, "RareDisplay", "outputTempFiles");
 		exit(1);
 	}
 }
 
+
 /***********************************************************************/