added count parameter to chimera.slayer command

[mothur.git] / homovacommand.cpp

diff --git a/homovacommand.cpp b/homovacommand.cpp
index f9d259d2e817d9d4458dc4b54adc218aea6ab5b3..006f1e4d5ee0b046e3216b0f470ce5d5c6200aa0 100644 (file)
--- a/homovacommand.cpp
+++ b/homovacommand.cpp
@@ -49,9 +49,27 @@ string HomovaCommand::getHelpString(){
                exit(1);
        }
 }
-
 //**********************************************************************************************************************
-
+string HomovaCommand::getOutputFileNameTag(string type, string inputName=""){  
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "homova")            {   outputFileName =  "homova";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "HomovaCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 HomovaCommand::HomovaCommand(){        
        try {
                abort = true; calledHelp = true; 
@@ -72,6 +90,7 @@ HomovaCommand::HomovaCommand(string option) {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -124,7 +143,7 @@ HomovaCommand::HomovaCommand(string option) {
                                if (phylipFileName != "") { m->mothurOut("Using " + phylipFileName + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
                                
-                       }       
+                       }else { m->setPhylipFile(phylipFileName); }     
                        
                        //check for required parameters
                        designFileName = validParameter.validFile(parameters, "design", true);
@@ -134,15 +153,15 @@ HomovaCommand::HomovaCommand(string option) {
                                designFileName = m->getDesignFile(); 
                                if (designFileName != "") { m->mothurOut("Using " + designFileName + " as input file for the design parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current design file and the design parameter is required."); m->mothurOutEndLine(); abort = true; }                                                           
-                       }       
+                       }else { m->setDesignFile(designFileName); }     
                        
                        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); 
                }
                
        }
@@ -177,13 +196,19 @@ int HomovaCommand::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 HOMOVAFile;
-               string HOMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName))  + "homova";                               
+               string HOMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + getOutputFileNameTag("homova");                          
                m->openOutputFile(HOMOVAFileName, HOMOVAFile);
                outputNames.push_back(HOMOVAFileName); outputTypes["homova"].push_back(HOMOVAFileName);