X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=shhhercommand.cpp;h=40a4c8499a599207b56831c91e6f0f41c023eb2c;hb=116bbb1533575666a682910a10ae1fa2fc5b605c;hp=13e7ccfd496d035c151eaade308f9832af76b511;hpb=5eca3348fe3962b8965236ca877ef6f52e8fb104;p=mothur.git

diff --git a/shhhercommand.cpp b/shhhercommand.cpp
index 13e7ccf..40a4c84 100644
--- a/shhhercommand.cpp
+++ b/shhhercommand.cpp
@@ -251,19 +251,19 @@ ShhherCommand::ShhherCommand(string option) {
 			
 			temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 
 			temp = validParameter.validFile(parameters, "cutoff", false);	if (temp == "not found"){	temp = "0.01";		}
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			
 			temp = validParameter.validFile(parameters, "mindelta", false);	if (temp == "not found"){	temp = "0.000001";	}
-			convert(temp, minDelta); 
+			m->mothurConvert(temp, minDelta); 
 
 			temp = validParameter.validFile(parameters, "maxiter", false);	if (temp == "not found"){	temp = "1000";		}
-			convert(temp, maxIters); 
+			m->mothurConvert(temp, maxIters); 
 
 			temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found")	{	temp = "60";		}
-			convert(temp, sigma); 
+			m->mothurConvert(temp, sigma); 
 			
 			flowOrder = validParameter.validFile(parameters, "order", false);
 			if (flowOrder == "not found"){ flowOrder = "TACG";		}
@@ -2150,7 +2150,9 @@ void ShhherCommand::setOTUs(){
 void ShhherCommand::writeQualities(vector<int> otuCounts){
 	
 	try {
-		string qualityFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.qual";
+		string thisOutputDir = outputDir;
+		if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+		string qualityFileName = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.qual";
 
 		ofstream qualityFile;
 		m->openOutputFile(qualityFileName, qualityFile);
@@ -2255,8 +2257,9 @@ void ShhherCommand::writeQualities(vector<int> otuCounts){
 
 void ShhherCommand::writeSequences(vector<int> otuCounts){
 	try {
-		
-		string fastaFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.fasta";
+		string thisOutputDir = outputDir;
+		if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+		string fastaFileName = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.fasta";
 		ofstream fastaFile;
 		m->openOutputFile(fastaFileName, fastaFile);
 		
@@ -2302,7 +2305,9 @@ void ShhherCommand::writeSequences(vector<int> otuCounts){
 
 void ShhherCommand::writeNames(vector<int> otuCounts){
 	try {
-		string nameFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
+		string thisOutputDir = outputDir;
+		if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+		string nameFileName = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.names";
 		ofstream nameFile;
 		m->openOutputFile(nameFileName, nameFile);
 		
@@ -2338,7 +2343,9 @@ void ShhherCommand::writeNames(vector<int> otuCounts){
 
 void ShhherCommand::writeGroups(){
 	try {
-		string fileRoot = flowFileName.substr(0,flowFileName.find_last_of('.'));
+		string thisOutputDir = outputDir;
+		if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+		string fileRoot = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.'));
 		string groupFileName = fileRoot + ".shhh.groups";
 		ofstream groupFile;
 		m->openOutputFile(groupFileName, groupFile);
@@ -2361,7 +2368,9 @@ void ShhherCommand::writeGroups(){
 
 void ShhherCommand::writeClusters(vector<int> otuCounts){
 	try {
-		string otuCountsFileName = flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.counts";
+		string thisOutputDir = outputDir;
+		if (outputDir == "") {  thisOutputDir += m->hasPath(flowFileName);  }
+		string otuCountsFileName = thisOutputDir + flowFileName.substr(0,flowFileName.find_last_of('.')) + ".shhh.counts";
 		ofstream otuCountsFile;
 		m->openOutputFile(otuCountsFileName, otuCountsFile);