From: westcott <westcott>
Date: Mon, 8 Jun 2009 16:40:33 +0000 (+0000)
Subject: got rid of extra temp files in dist.seqs
X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=commitdiff_plain;h=bede5752eaeedb5a7e339439b6ba2f6670bca2b9

got rid of extra temp files in dist.seqs
---

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 9297909..67b87f1 100644
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -81,21 +81,21 @@ int DistanceCommand::execute(){
 		int numSeqs = seqDB->getNumSeqs();
 		cutoff += 0.005;
 		
-		string phylipFile = "";
-		string distFile = getRootName(globaldata->getFastaFile()) + "dist";
-		remove(distFile.c_str());
+		string outputFile;
 		
 		//doses the user want the phylip formatted file as well
 		if (isTrue(phylip) == true) {
-			phylipFile = getRootName(globaldata->getFastaFile()) + "phylip.dist";
-			remove(phylipFile.c_str());
+			outputFile = getRootName(globaldata->getFastaFile()) + "phylip.dist";
+			remove(outputFile.c_str());
 			
 			//output numSeqs to phylip formatted dist file
-			openOutputFile(phylipFile, phylipOut);
-			phylipOut << numSeqs << endl;
-			phylipOut.close();
+			openOutputFile(outputFile, outFile);
+			outFile << numSeqs << endl;
+			outFile.close();
+		}else { //user wants column format
+			outputFile = getRootName(globaldata->getFastaFile()) + "dist";
+			remove(outputFile.c_str());
 		}
-		
 				
 		//#	if defined (_WIN32)
 		//figure out how to implement the fork and wait commands in windows
@@ -106,12 +106,9 @@ int DistanceCommand::execute(){
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		//if you don't need to fork anything
 		if(processors == 1){
-			driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff);
-			
-			if (isTrue(phylip) == true) {
-				appendFiles((phylipFile + "tempPhylipA"), phylipFile);
-				remove((phylipFile + "tempPhylipA").c_str());
-			}
+			driver(distCalculator, seqDB, 0, numSeqs, outputFile + ".temp", cutoff);
+			appendFiles((outputFile + ".temp"), outputFile);
+			remove((outputFile + ".temp").c_str());
 		}else{ //you have multiple processors
 			
 			for (int i = 0; i < processors; i++) {
@@ -123,26 +120,18 @@ int DistanceCommand::execute(){
 			cout << lines[0]->start << '\t' << lines[0]->end << endl;
 			cout << lines[1]->start << '\t' << lines[1]->end << endl;
 
-			createProcesses(distFile, phylipFile); 
+			createProcesses(outputFile); 
 		
 			//append and remove temp files
 			for (it = processIDS.begin(); it != processIDS.end(); it++) {
-				appendFiles((distFile + toString(it->second) + ".temp"), distFile);
-				remove((distFile + toString(it->second) + ".temp").c_str());
-				
-				if (isTrue(phylip) == true) {
-					appendFiles((phylipFile + toString(it->second) + ".temp"), phylipFile);
-					remove((phylipFile + toString(it->second) + ".temp").c_str());
-				}
+				appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
+				remove((outputFile + toString(it->second) + ".temp").c_str());
 			}
 		}
 #else
-		driver(distCalculator, seqDB, 0, numSeqs, distFile, phylipFile + "tempPhylipA", cutoff);
-		
-		if (isTrue(phylip) = true) {
-			appendFiles((phylipFile + "tempPhylipA"), phylipFile);	
-			remove((phylipFile + "tempPhylipA").c_str());
-		}
+		driver(distCalculator, seqDB, 0, numSeqs, outputFile + ".temp", cutoff);
+		appendFiles((outputFile + ".temp"), outputFile);
+		remove((outputFile + ".temp").c_str());
 #endif
 		
 		delete distCalculator;
@@ -160,7 +149,7 @@ int DistanceCommand::execute(){
 	}	
 }
 /**************************************************************************************************/
-void DistanceCommand::createProcesses(string column, string phylip) {
+void DistanceCommand::createProcesses(string filename) {
 	try {
 		int process = 0;
 		processIDS.clear();
@@ -173,7 +162,7 @@ void DistanceCommand::createProcesses(string column, string phylip) {
 				processIDS[lines[process]->end] = pid;  //create map from line number to pid so you can append files in correct order later
 				process++;
 			}else if (pid == 0){
-				driver(distCalculator, seqDB, lines[process]->start, lines[process]->end, column + toString(getpid()) + ".temp", phylip + toString(getpid()) + ".temp", cutoff);
+				driver(distCalculator, seqDB, lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff);
 				exit(0);
 			}else { cout << "unable to spawn the necessary processes." << endl; exit(0); }
 		}
@@ -197,19 +186,15 @@ void DistanceCommand::createProcesses(string column, string phylip) {
 
 /**************************************************************************************************/
 /////// need to fix to work with calcs and sequencedb
-int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLine, int endLine, string dFileName, string pFilename, float cutoff){
+int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLine, int endLine, string dFileName, float cutoff){
 	try {
 
 		int startTime = time(NULL);
 		
 		//column file
-		ofstream distFile(dFileName.c_str(), ios::trunc);
-		distFile.setf(ios::fixed, ios::showpoint);
-		distFile << setprecision(4);
-		
-		ofstream philFile(pFilename.c_str(), ios::trunc);
-		philFile.setf(ios::fixed, ios::showpoint);
-		philFile << setprecision(4);
+		ofstream outFile(dFileName.c_str(), ios::trunc);
+		outFile.setf(ios::fixed, ios::showpoint);
+		outFile << setprecision(4);
 		
 		for(int i=startLine;i<endLine;i++){
 			
@@ -218,13 +203,13 @@ int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLi
 				double dist = distCalculator->getDist();
 				
 				if(dist <= cutoff){
-					distFile << align->get(i)->getName() << ' ' << align->get(j)->getName() << ' ' << dist << endl;
+					if (isTrue(phylip) != true) { outFile << align->get(i)->getName() << ' ' << align->get(j)->getName() << ' ' << dist << endl; }
 				}
-				if (isTrue(phylip) == true) {  philFile << dist << '\t'; }
+				if (isTrue(phylip) == true) {  outFile << dist << '\t'; }
 				
 			}
 			
-			if (isTrue(phylip) == true) { philFile << endl; }
+			if (isTrue(phylip) == true) { outFile << endl; }
 			
 			if(i % 100 == 0){
 				cout << i << '\t' << time(NULL) - startTime << endl;
@@ -233,8 +218,6 @@ int DistanceCommand::driver(Dist* distCalculator, SequenceDB* align, int startLi
 		}
 		cout << endLine-1 << '\t' << time(NULL) - startTime << endl;
 		
-		if (isTrue(phylip) != true) {  remove(pFilename.c_str());  }
-		
 		//philFile.close();
 		//distFile.close();
 		
diff --git a/distancecommand.h b/distancecommand.h
index 8322eee..2cb653f 100644
--- a/distancecommand.h
+++ b/distancecommand.h
@@ -34,9 +34,8 @@ private:
 	ValidCalculators* validCalculator;
 	Dist* distCalculator;
 	SequenceDB* seqDB;
-	ofstream out, phylipOut;
+	ofstream out, outFile;
 	ifstream in;
-	string outputFileName;
 	string countends, phylip;
 	int processors;
 	float cutoff;
@@ -45,8 +44,8 @@ private:
 	vector<linePair*> lines;
 	
 	void appendFiles(string, string);
-	void createProcesses(string, string);
-	int driver(Dist*, SequenceDB*, int, int, string, string, float);
+	void createProcesses(string);
+	int driver(Dist*, SequenceDB*, int, int, string, float);
 
 };