X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=anosimcommand.cpp;h=2a688f59b72c4ba9779ea921149254b3e554b788;hp=2ee691ea9cb0db6f3a98ff299d0a1f9c6f60bbaf;hb=cf9987b67aa49777a4c91c2d21f96e58bf17aa82;hpb=1d898dc6edaf9e9f287fab53bf1f21fb29757a17

diff --git a/anosimcommand.cpp b/anosimcommand.cpp
index 2ee691e..2a688f5 100644
--- a/anosimcommand.cpp
+++ b/anosimcommand.cpp
@@ -14,12 +14,12 @@
 //**********************************************************************************************************************
 vector<string> AnosimCommand::setParameters(){	
 	try {
-		CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pdesign);
-		CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
-		CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
-		CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "",false,false); parameters.push_back(palpha);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pdesign("design", "InputTypes", "", "", "none", "none", "none","anosim",false,true,true); parameters.push_back(pdesign);
+		CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","anosim",false,true,true); parameters.push_back(pphylip);
+		CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+		CommandParameter palpha("alpha", "Number", "", "0.05", "", "", "","",false,false); parameters.push_back(palpha);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -49,7 +49,21 @@ string AnosimCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string AnosimCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "anosim") {  pattern = "[filename],anosim"; } //makes file like: amazon.align
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "AnosimCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 //**********************************************************************************************************************
 AnosimCommand::AnosimCommand(){	
 	try {
@@ -71,6 +85,7 @@ AnosimCommand::AnosimCommand(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();
@@ -123,25 +138,25 @@ AnosimCommand::AnosimCommand(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);
-			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); 
 		}
 		
 	}
@@ -175,13 +190,21 @@ 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";				
+        map<string, string> variables; variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipFileName));
+		string ANOSIMFileName = getOutputFileName("anosim", variables);	
+        
 		m->openOutputFile(ANOSIMFileName, ANOSIMFile);
 		outputNames.push_back(ANOSIMFileName); outputTypes["anosim"].push_back(ANOSIMFileName);
 		m->mothurOut("\ncomparison\tR-value\tP-value\n");