added otu.association command. added calcSpearman, calcKendall and calcPearson functi...

[mothur.git] / clustersplitcommand.cpp

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 7505ae66e453fff787d807117ed2e026f658e6a0..34caf654124886f9cd23638a149b2b3487ca53e2 100644 (file)
--- 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"; }