test on laptop setup

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 7a1af627a5e290c6d348e4a3783c645ba575982c..77dacfe711ea694d7d81cb7536fd15d14cb0ec97 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -17,8 +17,8 @@ vector<string> TrimFlowsCommand::setParameters(){
                CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pflow);
                CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
                CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "",false,false); parameters.push_back(pmaxhomop);
-               CommandParameter pmaxflows("maxflows", "Number", "", "720", "", "", "",false,false); parameters.push_back(pmaxflows);
-               CommandParameter pminflows("minflows", "Number", "", "360", "", "", "",false,false); parameters.push_back(pminflows);
+               CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pmaxflows);
+               CommandParameter pminflows("minflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pminflows);
                CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
                CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
                CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
@@ -149,10 +149,10 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
-                       convert(temp, minFlows);  
+                       m->mothurConvert(temp, minFlows);  
 
                        temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
-                       convert(temp, maxFlows);  
+                       m->mothurConvert(temp, maxFlows);  
                        
                        
                        temp = validParameter.validFile(parameters, "oligos", true);
@@ -164,28 +164,28 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                        else if(m->isTrue(temp))        {       fasta = 1;      }
                        
                        temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found"){       temp = "9";             }
-                       convert(temp, maxHomoP);  
+                       m->mothurConvert(temp, maxHomoP);  
 
                        temp = validParameter.validFile(parameters, "signal", false);           if (temp == "not found"){       temp = "0.50";  }
-                       convert(temp, signal);  
+                       m->mothurConvert(temp, signal);  
 
                        temp = validParameter.validFile(parameters, "noise", false);            if (temp == "not found"){       temp = "0.70";  }
-                       convert(temp, noise);  
+                       m->mothurConvert(temp, noise);  
        
                        temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found"){       temp = "0";             }
-                       convert(temp, bdiffs);
+                       m->mothurConvert(temp, bdiffs);
                        
                        temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found"){       temp = "0";             }
-                       convert(temp, pdiffs);
+                       m->mothurConvert(temp, pdiffs);
                        
                        temp = validParameter.validFile(parameters, "tdiffs", false);
                        if (temp == "not found"){ int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
-                       convert(temp, tdiffs);
+                       m->mothurConvert(temp, tdiffs);
                        if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors);
+                       m->mothurConvert(temp, processors);
        
                        flowOrder = validParameter.validFile(parameters, "order", false);
                        if (flowOrder == "not found"){ flowOrder = "TACG";              }
@@ -202,7 +202,7 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
                
        }
        catch(exception& e) {
-               m->errorOut(e, "TrimFlowsCommand", "TrimSeqsCommand");
+               m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
                exit(1);
        }
 }