X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=filterseqscommand.cpp;h=cb0b131f58e039f5eea76b784334715e1e7481e3;hb=348de0f8b17d84ede77081dcf67bd6ef43496677;hp=c463cd294d04dcdc31e1a6891db1659db45dc05e;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281;p=mothur.git

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index c463cd2..cb0b131 100644
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -25,7 +25,7 @@ vector<string> FilterSeqsCommand::getValidParameters(){
 //**********************************************************************************************************************
 FilterSeqsCommand::FilterSeqsCommand(){	
 	try {
-		//initialize outputTypes
+		abort = true; calledHelp = true; 
 		vector<string> tempOutNames;
 		outputTypes["fasta"] = tempOutNames;
 		outputTypes["filter"] = tempOutNames;
@@ -61,11 +61,11 @@ vector<string> FilterSeqsCommand::getRequiredFiles(){
 /**************************************************************************************/
 FilterSeqsCommand::FilterSeqsCommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		filterFileName = "";
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
 			//valid paramters for this command
@@ -132,7 +132,9 @@ FilterSeqsCommand::FilterSeqsCommand(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;
 						}
 					}
@@ -142,7 +144,9 @@ FilterSeqsCommand::FilterSeqsCommand(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;
 						}
 					}
@@ -235,7 +239,7 @@ void FilterSeqsCommand::help(){
 int FilterSeqsCommand::execute() {	
 	try {
 	
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		
 		ifstream inFASTA;
 		m->openInputFile(fastafileNames[0], inFASTA);
@@ -298,6 +302,12 @@ int FilterSeqsCommand::execute() {
 		m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 		m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 		
+		//set fasta file as new current fastafile
+		string current = "";
+		itTypes = outputTypes.find("fasta");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+		}
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -324,7 +334,7 @@ int FilterSeqsCommand::filterSequences() {
 				
 				string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
 #ifdef USE_MPI	
-				int pid, start, end, numSeqsPerProcessor, num; 
+				int pid, numSeqsPerProcessor, num; 
 				int tag = 2001;
 				vector<unsigned long int>MPIPos;
 						
@@ -333,7 +343,6 @@ int FilterSeqsCommand::filterSequences() {
 				MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 				
 				MPI_File outMPI;
-				MPI_File tempMPI;
 				MPI_File inMPI;
 				int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
 				int inMode=MPI_MODE_RDONLY; 
@@ -605,7 +614,11 @@ int FilterSeqsCommand::createProcessesRunFilter(string F, string filename) {
 				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);
+			}
 		}
 		
 		//force parent to wait until all the processes are done
@@ -969,7 +982,11 @@ int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename)
 				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 do your part