X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustersplitcommand.cpp;h=34caf654124886f9cd23638a149b2b3487ca53e2;hb=8dd3c225255d7084e3aff8740aa4f1f1cabb367a;hp=e9b3077d18eb969114aebe881520760fb71e1d77;hpb=96f25c3c0f3ba2a1634094de146630dbc9ee0d03;p=mothur.git

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index e9b3077..34caf65 100644
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -201,7 +201,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 			else { distfile = fastafile;  splitmethod = "fasta";  m->setFastaFile(fastafile); }
 			
 			taxFile = validParameter.validFile(parameters, "taxonomy", true);
-			if (taxFile == "not open") { abort = true; }	
+			if (taxFile == "not open") { taxFile = ""; abort = true; }	
 			else if (taxFile == "not found") { taxFile = ""; }
 			else {  m->setTaxonomyFile(taxFile); }
 			
@@ -264,7 +264,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 			if (temp == "not found") { temp = "100"; }
 			//saves precision legnth for formatting below
 			length = temp.length();
-			convert(temp, precision); 
+			m->mothurConvert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
 			hard = m->isTrue(temp);
@@ -274,7 +274,7 @@ ClusterSplitCommand::ClusterSplitCommand(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, "splitmethod", false);	
 			if (splitmethod != "fasta") {
@@ -283,11 +283,11 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 			}
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);		if (temp == "not found")  { temp = "0.25"; }
-			convert(temp, cutoff); 
+			m->mothurConvert(temp, cutoff); 
 			cutoff += (5 / (precision * 10.0));  
 			
 			temp = validParameter.validFile(parameters, "taxlevel", false);		if (temp == "not found")  { temp = "3"; }
-			convert(temp, taxLevelCutoff); 
+			m->mothurConvert(temp, taxLevelCutoff); 
 			
 			method = validParameter.validFile(parameters, "method", false);		if (method == "not found") { method = "average"; }
 			
@@ -564,14 +564,14 @@ int ClusterSplitCommand::execute(){
 					listFileNames = cluster(distName, labels); //clusters individual files and returns names of list files
 				}else{
 					
-					cout << processors << '\t' << distName.size() << endl;
+					//cout << processors << '\t' << distName.size() << endl;
 					vector < vector < map<string, string> > > dividedNames; //distNames[1] = vector of filenames for process 1...
 					dividedNames.resize(processors);
 					
 					//for each file group figure out which process will complete it
 					//want to divide the load intelligently so the big files are spread between processes
 					for (int i = 0; i < distName.size(); i++) { 
-						cout << i << endl;
+						//cout << i << endl;
 						int processToAssign = (i+1) % processors; 
 						if (processToAssign == 0) { processToAssign = processors; }
 						
@@ -580,7 +580,7 @@ int ClusterSplitCommand::execute(){
 					
 					//not lets reverse the order of ever other process, so we balance big files running with little ones
 					for (int i = 0; i < processors; i++) {
-						cout << i << endl;
+						//cout << i << endl;
 						int remainder = ((i+1) % processors);
 						if (remainder) {  reverse(dividedNames[i].begin(), dividedNames[i].end());  }
 					}