X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtreecommand.cpp;h=edfdf3b77e0d85ff51afce83323d0204ab987a66;hb=89f19f9c6ab89c2f6c7c6921a328ae87bce6f8e3;hp=60654489ce6a1a848eb0dc9743f43e64b832a639;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 6065448..edfdf3b 100644
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -9,6 +9,41 @@
 
 #include "readtreecommand.h"
 
+//**********************************************************************************************************************
+vector<string> ReadTreeCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"tree","group","name","outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ReadTreeCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> ReadTreeCommand::getRequiredParameters(){	
+	try {
+		string Array[] =  {"tree"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ReadTreeCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> ReadTreeCommand::getRequiredFiles(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ReadTreeCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 ReadTreeCommand::ReadTreeCommand(string option)  {
 	try {
@@ -44,7 +79,7 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
 				it = parameters.find("tree");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["tree"] = inputDir + it->second;		}
 				}
@@ -52,7 +87,7 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
 				it = parameters.find("group");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["group"] = inputDir + it->second;		}
 				}
@@ -60,7 +95,7 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
 				it = parameters.find("name");
 				//user has given a template file
 				if(it != parameters.end()){ 
-					path = hasPath(it->second);
+					path = m->hasPath(it->second);
 					//if the user has not given a path then, add inputdir. else leave path alone.
 					if (path == "") {	parameters["name"] = inputDir + it->second;		}
 				}
@@ -76,8 +111,20 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
 			
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }	
-			else if (groupfile == "not found") { groupfile = ""; m->mothurOut("group is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true;	}
-			else {  
+			else if (groupfile == "not found") { 
+				groupfile = ""; 
+				
+				m->mothurOut("You have not provided a group file. I am assumming all sequence are from the same group."); m->mothurOutEndLine(); 	
+				
+				if (treefile != "") {  Tree* tree = new Tree(treefile); delete tree;  } //extracts names from tree to make faked out groupmap
+				
+				globaldata->setGroupFile(groupfile); 
+				//read in group map info.
+				treeMap = new TreeMap();
+				for (int i = 0; i < globaldata->Treenames.size(); i++) { treeMap->addSeq(globaldata->Treenames[i], "Group1"); }
+				globaldata->gTreemap = treeMap;
+					
+			}else {  
 				globaldata->setGroupFile(groupfile); 
 				//read in group map info.
 				treeMap = new TreeMap(groupfile);
@@ -108,8 +155,10 @@ void ReadTreeCommand::help(){
 	try {
 		m->mothurOut("The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. \n");
 		m->mothurOut("It also must be run before using the parsimony command, unless you are using the randomtree parameter.\n");
+		m->mothurOut("The read.tree command parameters are tree, group and name.\n");
 		m->mothurOut("The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile).\n");
-		m->mothurOut("The tree and group parameters are both required.\n");
+		m->mothurOut("The tree and group parameters are both required, if no group file is given then one group is assumed.\n");
+		m->mothurOut("The name parameter allows you to enter a namefile.\n");
 		m->mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
 	}
 	catch(exception& e) {
@@ -147,12 +196,21 @@ int ReadTreeCommand::execute(){
 				delete globaldata->gTreemap;
 				return 0;
 			}
-			
+	
 			T[i]->assembleTree();
 		}
 
+		
+		//if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
+		int numNamesInTree;
+		if (namefile != "")  {  
+			if (numUniquesInName == globaldata->Treenames.size()) {  numNamesInTree = nameMap.size();  }
+			else {   numNamesInTree = globaldata->Treenames.size();  }
+		}else {  numNamesInTree = globaldata->Treenames.size();  }
+		
+		
 		//output any names that are in group file but not in tree
-		if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
+		if (numNamesInTree < treeMap->getNumSeqs()) {
 			for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
 				//is that name in the tree?
 				int count = 0;
@@ -180,8 +238,10 @@ int ReadTreeCommand::execute(){
 					}
 				}
 			}
+			
+			globaldata->gTreemap = treeMap;
 		}
-		
+
 		return 0;
 	}
 	catch(exception& e) {
@@ -193,26 +253,29 @@ int ReadTreeCommand::execute(){
 int ReadTreeCommand::readNamesFile() {
 	try {
 		globaldata->names.clear();
+		numUniquesInName = 0;
 		
 		ifstream in;
-		openInputFile(namefile, in);
+		m->openInputFile(namefile, in);
 		
 		string first, second;
 		map<string, string>::iterator itNames;
 		
 		while(!in.eof()) {
-			in >> first >> second; gobble(in);
+			in >> first >> second; m->gobble(in);
 			
+			numUniquesInName++;
+
 			itNames = globaldata->names.find(first);
 			if (itNames == globaldata->names.end()) {  
 				globaldata->names[first] = second; 
 				
 				//we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
 				vector<string> dupNames;
-				splitAtComma(second, dupNames);
+				m->splitAtComma(second, dupNames);
 				
-				for (int i = 0; i < dupNames.size(); i++) {	nameMap[dupNames[i]] = dupNames[i];  }
-			}else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); return 1; }			
+				for (int i = 0; i < dupNames.size(); i++) {	nameMap[dupNames[i]] = dupNames[i];  if ((groupfile == "") && (i != 0)) { globaldata->gTreemap->addSeq(dupNames[i], "Group1"); }  }
+			}else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); namefile = ""; return 1; }			
 		}
 		in.close();