added phylip as output file type for commands that output distance matrices. added...

[mothur.git] / amovacommand.cpp

diff --git a/amovacommand.cpp b/amovacommand.cpp
index af867de3bf4811e00f98904f06935ac95a8313f3..c4260fb096dd8b0b253f5239f7ce265376d24ed5 100644 (file)
--- a/amovacommand.cpp
+++ b/amovacommand.cpp
@@ -50,7 +50,26 @@ string AmovaCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string AmovaCommand::getOutputFileNameTag(string type, string inputName=""){   
+       try {
+        string tag = "";
+               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 == "amova") {  tag = "amova"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file.\n");  }
+        }
+        return tag;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "AmovaCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 //**********************************************************************************************************************
 AmovaCommand::AmovaCommand(){  
        try {
@@ -71,6 +90,7 @@ AmovaCommand::AmovaCommand(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();
@@ -122,25 +142,25 @@ AmovaCommand::AmovaCommand(string option) {
                                phylipFileName = m->getPhylipFile(); 
                                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);
-                       if (designFileName == "not open") { abort = true; }
+                       if (designFileName == "not open") { designFileName = ""; abort = true; }
                        else if (designFileName == "not found") {
                                //if there is a current design file, use it
                                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); 
                }
        }
        catch(exception& e) {
@@ -174,13 +194,20 @@ 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";                         
+               string AMOVAFileName = outputDir + m->getRootName(m->getSimpleName(phylipFileName)) + getOutputFileNameTag("amova");                            
                m->openOutputFile(AMOVAFileName, AMOVAFile);
                outputNames.push_back(AMOVAFileName); outputTypes["amova"].push_back(AMOVAFileName);
                
@@ -282,7 +309,7 @@ double AmovaCommand::runAMOVA(ofstream& AMOVAFile, map<string, vector<int> > gro
                m->mothurOut("df\t" + toString(dfAmong) + '\t' + toString(dfWithin) + '\t' + toString(dfTotal) + '\n');
 
                AMOVAFile << "MS\t" << MSAmong << '\t' << MSWithin << endl << endl;
-               m->mothurOut("MS\t" + toString(MSAmong) + '\t' + toString(MSWithin) + "\n");
+               m->mothurOut("MS\t" + toString(MSAmong) + '\t' + toString(MSWithin) + "\n\n");
 
                AMOVAFile << "Fs:\t" << Fs << endl;
                m->mothurOut("Fs:\t" + toString(Fs) + '\n');