X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=raredisplay.cpp;h=b82127c51e6a64b50480a0f9b359cda3cd8e75f0;hb=70491a12902e89b85cfa6b44a7b7fbe066ee2ac1;hp=b86312bc4411e8cdd2faca9934aab3abf5c96c52;hpb=510b1cfc25cd79391d6973ca20c5ec25fb1bb3b2;p=mothur.git

diff --git a/raredisplay.cpp b/raredisplay.cpp
index b86312b..b82127c 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);
 	}
 }
@@ -38,24 +30,26 @@ void RareDisplay::update(SAbundVector* 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 oldS = var[index] * ( nIters - 2 );
+			double delta = data[0] - results[index];
+			double newMean = results[index] + delta / nIters;
 			double newS = oldS + delta * ( data[0] - newMean );
 			double newVar = newS / ( nIters - 1 );
 
-			tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl;
+			seqs[index] = newNSeqs;
+			results[index] = newMean; 
+			var[index] = newVar;
+			
+			index++;  
 		}
 		else{
-			tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl;
+			seqs.push_back(newNSeqs); 
+			results.push_back(data[0]);
+			var.push_back(0.0);
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "RareDisplay", "update");
+		m->errorOut(e, "RareDisplay", "update");
 		exit(1);
 	}
 }
@@ -67,24 +61,28 @@ void RareDisplay::update(vector<SharedRAbundVector*> shared, int numSeqs, int nu
 		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 oldS = var[index] * ( nIters - 2 );
+			double delta = data[0] - results[index];
+			double newMean = results[index] + delta / nIters;
 			double newS = oldS + delta * ( data[0] - newMean );
 			double newVar = newS / ( nIters - 1 );
-
-			tempOutFile << newNSeqs << '\t' << newMean << '\t' << newVar << endl;
+			seqs[index] = newNSeqs;
+			results[index] = newMean; 
+			var[index] = newVar;
+			
+			index++;  
 		}
 		else{
-			tempOutFile << newNSeqs << '\t' << data[0] << '\t' << 0 << endl;
+			
+			seqs.push_back(newNSeqs); 
+			results.push_back(data[0]);
+			var.push_back(0.0);
+
 		}
 	}
 	catch(exception& e) {
-		errorOut(e, "RareDisplay", "update");
+		m->errorOut(e, "RareDisplay", "update");
 		exit(1);
 	}
 }
@@ -93,24 +91,11 @@ 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(); }
+		index = 0;
 	}
 	catch(exception& e) {
-		errorOut(e, "RareDisplay", "reset");
+		m->errorOut(e, "RareDisplay", "reset");
 		exit(1);
 	}
 }
@@ -122,39 +107,83 @@ void RareDisplay::close(){
 		
 		output->initFile(label);
 	
-		openInputFile(tempInName, tempInFile);
-	
-		while(!tempInFile.eof()){
-			int nSeqs;
-			tempInFile >> nSeqs;
+		for (int i = 0; i < seqs.size(); i++) {
 		
 			vector<double> data(3,0);
-			double variance = 0;
-		
-			tempInFile >> data[0];
-			tempInFile >> variance;
-		
+			double variance = var[i];
+			
+			data[0] = results[i];
+			
 			double ci = 1.96 * pow(variance, 0.5);
 			data[1] = data[0] - ci;
 			data[2] = data[0] + ci;
 		
-			output->output(nSeqs, data);
-		
-			gobble(tempInFile);
+			output->output(seqs[i], data);
 		}
-		tempInFile.close();
-	
-		remove(tempInName.c_str());
-		remove(tempOutName.c_str());
 		
 		nIters = 1;
+		index = 0;
+		
+		seqs.clear();
+		results.clear();
+		var.clear();
+		
 		output->resetFile();
 	}
 	catch(exception& e) {
-		errorOut(e, "RareDisplay", "close");
+		m->errorOut(e, "RareDisplay", "close");
 		exit(1);
 	}
 }
+/***********************************************************************/
+
+void RareDisplay::inputTempFiles(string filename){
+	try {
+		ifstream in;
+		m->openInputFile(filename, in);
+		
+		int thisIters;
+		in >> thisIters; m->gobble(in);
+		
+		for (int i = 0; i < seqs.size(); i++) {
+			double tempresult, tempvar;
+			in >> tempresult >> tempvar; m->gobble(in);
+			
+			//find weighted result
+			results[i] = ((nIters * results[i]) + (thisIters * tempresult)) / (float)(nIters + thisIters);
+			
+			var[i] = ((nIters * var[i]) + (thisIters * tempvar)) / (float)(nIters + thisIters);
+		}
+		
+		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 << endl;
+		
+		for (int i = 0; i < seqs.size(); i++) {
+			out << results[i] << '\t' << var[i] << endl;
+		}
+		
+		out.close();
+	}
+	catch(exception& e) {
+		m->errorOut(e, "RareDisplay", "outputTempFiles");
+		exit(1);
+	}
+}
+
 
 /***********************************************************************/