forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / anosimcommand.cpp

diff --git a/anosimcommand.cpp b/anosimcommand.cpp
index c5cb4d60c751d6614b82cd961c29d9e645fcbaa8..1b6afe35b760ed140b6747d02a41ce5d4424fca1 100644 (file)
--- a/anosimcommand.cpp
+++ b/anosimcommand.cpp
@@ -138,11 +138,11 @@ AnosimCommand::AnosimCommand(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); 
                }
                
        }
@@ -176,10 +176,16 @@ int AnosimCommand::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 ANOSIMFile;
                string ANOSIMFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName))  + "anosim";