added forward and reverse barcodes to trim.seqs to process illumina seqs

[mothur.git] / amovacommand.cpp

diff --git a/amovacommand.cpp b/amovacommand.cpp
index 141673375fb8bb1a37e67980df9708fe6d2da126..3ec14bf7c06af5883e7eb6d9b3b38449ceac83be 100644 (file)
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -136,11 +136,11 @@ AmovaCommand::AmovaCommand(string option) {
 
                        string temp = validParameter.validFile(parameters, "iters", false);
                        if (temp == "not found") { temp = "1000"; }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                        
                        temp = validParameter.validFile(parameters, "alpha", false);
                        if (temp == "not found") { temp = "0.05"; }
-                       convert(temp, experimentwiseAlpha); 
+                       m->mothurConvert(temp, experimentwiseAlpha); 
                }
        }
        catch(exception& e) {
@@ -174,10 +174,17 @@ int AmovaCommand::execute(){
                //link designMap to rows/columns in distance matrix
                map<string, vector<int> > origGroupSampleMap;
                for(int i=0;i<sampleNames.size();i++){
-                       origGroupSampleMap[designMap->getGroup(sampleNames[i])].push_back(i);
+                       string group = designMap->getGroup(sampleNames[i]);
+                       
+                       if (group == "not found") {
+                               m->mothurOut("[ERROR]: " + sampleNames[i] + " is not in your design file, please correct."); m->mothurOutEndLine(); m->control_pressed = true;
+                       }else { origGroupSampleMap[group].push_back(i); }
+                       
                }
                int numGroups = origGroupSampleMap.size();
                
+               if (m->control_pressed) { delete designMap; return 0; }
+               
                //create a new filename
                ofstream AMOVAFile;
                string AMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName))  + "amova";