X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=classifyseqscommand.cpp;h=0a1ef8823e35f687529c70de5ef29e7d33eb91fe;hb=dfa69e4bbb18b2313495822f36b80cb475b7fb08;hp=9f05eda2704c179ca3eb4f120d83862aeb4eb6e4;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 9f05eda..0a1ef88 100644
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -30,6 +30,7 @@ vector<string> ClassifySeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 ClassifySeqsCommand::ClassifySeqsCommand(){	
 	try {
+		abort = true;
 		//initialize outputTypes
 		vector<string> tempOutNames;
 		outputTypes["taxonomy"] = tempOutNames;
@@ -161,7 +162,9 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 						if (m->getDefaultPath() != "") { //default path is set
 							string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 							m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-							ableToOpen = m->openInputFile(tryPath, in, "noerror");
+							ifstream in2;
+							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+							in2.close();
 							fastaFileNames[i] = tryPath;
 						}
 					}
@@ -170,7 +173,9 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 						if (m->getOutputDir() != "") { //default path is set
 							string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 							m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
-							ableToOpen = m->openInputFile(tryPath, in, "noerror");
+							ifstream in2;
+							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+							in2.close();
 							fastaFileNames[i] = tryPath;
 						}
 					}
@@ -223,7 +228,9 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 						if (m->getDefaultPath() != "") { //default path is set
 							string tryPath = m->getDefaultPath() + m->getSimpleName(namefileNames[i]);
 							m->mothurOut("Unable to open " + namefileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-							ableToOpen = m->openInputFile(tryPath, in, "noerror");
+							ifstream in2;
+							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+							in2.close();
 							namefileNames[i] = tryPath;
 						}
 					}
@@ -232,7 +239,9 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 						if (m->getOutputDir() != "") { //default path is set
 							string tryPath = m->getOutputDir() + m->getSimpleName(namefileNames[i]);
 							m->mothurOut("Unable to open " + namefileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
-							ableToOpen = m->openInputFile(tryPath, in, "noerror");
+							ifstream in2;
+							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+							in2.close();
 							namefileNames[i] = tryPath;
 						}
 					}
@@ -274,7 +283,9 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 						if (m->getDefaultPath() != "") { //default path is set
 							string tryPath = m->getDefaultPath() + m->getSimpleName(groupfileNames[i]);
 							m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
-							ableToOpen = m->openInputFile(tryPath, in, "noerror");
+							ifstream in2;
+							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+							in2.close();
 							groupfileNames[i] = tryPath;
 						}
 					}
@@ -283,7 +294,9 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
 						if (m->getOutputDir() != "") { //default path is set
 							string tryPath = m->getOutputDir() + m->getSimpleName(groupfileNames[i]);
 							m->mothurOut("Unable to open " + groupfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
-							ableToOpen = m->openInputFile(tryPath, in, "noerror");
+							ifstream in2;
+							ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+							in2.close();
 							groupfileNames[i] = tryPath;
 						}
 					}
@@ -448,7 +461,7 @@ int ClassifySeqsCommand::execute(){
 			for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 			
 #ifdef USE_MPI	
-				int pid, end, numSeqsPerProcessor; 
+				int pid, numSeqsPerProcessor; 
 				int tag = 2001;
 				vector<unsigned long int> MPIPos;
 				
@@ -546,16 +559,6 @@ int ClassifySeqsCommand::execute(){
 				
 				numFastaSeqs = createProcesses(newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]); 
 				
-				rename((newTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), newTaxonomyFile.c_str());
-				rename((tempTaxonomyFile + toString(processIDS[0]) + ".temp").c_str(), tempTaxonomyFile.c_str());
-				
-				for(int i=1;i<processors;i++){
-					appendTaxFiles((newTaxonomyFile + toString(processIDS[i]) + ".temp"), newTaxonomyFile);
-					appendTaxFiles((tempTaxonomyFile + toString(processIDS[i]) + ".temp"), tempTaxonomyFile);
-					remove((newTaxonomyFile + toString(processIDS[i]) + ".temp").c_str());
-					remove((tempTaxonomyFile + toString(processIDS[i]) + ".temp").c_str());
-				}
-				
 			}
 	#else
 			numFastaSeqs = driver(lines[0], newTaxonomyFile, tempTaxonomyFile, fastaFileNames[s]);
@@ -649,7 +652,7 @@ int ClassifySeqsCommand::execute(){
 			
 			//get maxLevel from phylotree so you know how many 'unclassified's to add
 			int maxLevel = taxaSum.getMaxLevel();
-			
+							
 			//read taxfile - this reading and rewriting is done to preserve the confidence scores.
 			string name, taxon;
 			while (!inTax.eof()) {
@@ -723,7 +726,7 @@ string ClassifySeqsCommand::addUnclassifieds(string tax, int maxlevel) {
 int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile, string filename) {
 	try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
-		int process = 0;
+		int process = 1;
 		int num = 0;
 		
 		//loop through and create all the processes you want
@@ -744,11 +747,18 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
 				out.close();
 
 				exit(0);
-			}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+			}else { 
+				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+				for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+				exit(0);
+			}
 		}
 		
+		//parent does its part
+		num = driver(lines[0], taxFileName, tempTaxFile, filename);
+		
 		//force parent to wait until all the processes are done
-		for (int i=0;i<processors;i++) { 
+		for (int i=0;i<processIDS.size();i++) { 
 			int temp = processIDS[i];
 			wait(&temp);
 		}
@@ -761,6 +771,13 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
 			in.close(); remove(tempFile.c_str());
 		}
 		
+		for(int i=0;i<processIDS.size();i++){
+			appendTaxFiles((taxFileName + toString(processIDS[i]) + ".temp"), taxFileName);
+			appendTaxFiles((tempTaxFile + toString(processIDS[i]) + ".temp"), tempTaxFile);
+			remove((taxFileName + toString(processIDS[i]) + ".temp").c_str());
+			remove((tempTaxFile + toString(processIDS[i]) + ".temp").c_str());
+		}
+		
 		return num;
 #endif		
 	}
@@ -812,13 +829,14 @@ int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempT
 
 		bool done = false;
 		int count = 0;
-	
+		
 		while (!done) {
 			if (m->control_pressed) { return 0; }
 		
 			Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
-		
+			
 			if (candidateSeq->getName() != "") {
+			
 				taxonomy = classify->getTaxonomy(candidateSeq);
 				
 				if (m->control_pressed) { delete candidateSeq; return 0; }
@@ -846,10 +864,11 @@ int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempT
 			
 			//report progress
 			if((count) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
+			
 		}
 		//report progress
 		if((count) % 100 != 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
-				
+			
 		inFASTA.close();
 		outTax.close();
 		outTaxSimple.close();