X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtreecommand.cpp;h=c476f5a89928cf131593178b40eb50d60130a7bd;hb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;hp=deae495a2171c6af3d117436920558f2e10e7a27;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index deae495..c476f5a 100644
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -9,16 +9,17 @@
 
 #include "readtreecommand.h"
 
+
 //**********************************************************************************************************************
 ReadTreeCommand::ReadTreeCommand(string option)  {
 	try {
-		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
 				
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
 		
 		else {
+			/*
 			//valid paramters for this command
 			string Array[] =  {"tree","group","name","outputdir","inputdir"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
@@ -72,17 +73,24 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
 			treefile = validParameter.validFile(parameters, "tree", true);
 			if (treefile == "not open") { abort = true; }
 			else if (treefile == "not found") { treefile = ""; m->mothurOut("tree is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true;  }	
-			else {  globaldata->setTreeFile(treefile);  globaldata->setFormat("tree"); 	}
 			
 			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 {  
-				globaldata->setGroupFile(groupfile); 
+			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
+				
+				//read in group map info.
+				treeMap = new TreeMap();
+				for (int i = 0; i < m->Treenames.size(); i++) { treeMap->addSeq(m->Treenames[i], "Group1"); }
+					
+			}else {  
 				//read in group map info.
 				treeMap = new TreeMap(groupfile);
 				treeMap->readMap();
-				globaldata->gTreemap = treeMap;
 			}
 			
 			namefile = validParameter.validFile(parameters, "name", true);
@@ -94,7 +102,7 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
 				filename = treefile;
 				read = new ReadNewickTree(filename);
 			}
-						
+			*/			
 		}
 	}
 	catch(exception& e) {
@@ -104,42 +112,19 @@ ReadTreeCommand::ReadTreeCommand(string option)  {
 }
 //**********************************************************************************************************************
 
-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 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) {
-		m->errorOut(e, "ReadTreeCommand", "help");	
-		exit(1);
-	}
-}
-
-//**********************************************************************************************************************
-
-ReadTreeCommand::~ReadTreeCommand(){
-	if (abort == false) { delete read; }
-}
-
-//**********************************************************************************************************************
-
 int ReadTreeCommand::execute(){
 	try {
 	
-		if (abort == true) { return 0; }
-		
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+		m->mothurOut(getHelpString()); m->mothurOutEndLine();
+		/*
 		int readOk;
 		
-		readOk = read->read(); 
+		readOk = read->read(treeMap); 
 		
 		if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
 		
-		vector<Tree*> T = globaldata->gTree;
+		vector<Tree*> T = read->gTree;
 
 		//assemble users trees
 		for (int i = 0; i < T.size(); i++) {
@@ -153,8 +138,17 @@ int ReadTreeCommand::execute(){
 			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;
@@ -185,7 +179,7 @@ int ReadTreeCommand::execute(){
 			
 			globaldata->gTreemap = treeMap;
 		}
-		
+		 */
 		return 0;
 	}
 	catch(exception& e) {
@@ -196,7 +190,9 @@ int ReadTreeCommand::execute(){
 /*****************************************************************/
 int ReadTreeCommand::readNamesFile() {
 	try {
-		globaldata->names.clear();
+		/*
+		m->names.clear();
+		numUniquesInName = 0;
 		
 		ifstream in;
 		m->openInputFile(namefile, in);
@@ -207,7 +203,9 @@ int ReadTreeCommand::readNamesFile() {
 		while(!in.eof()) {
 			in >> first >> second; m->gobble(in);
 			
-			itNames = globaldata->names.find(first);
+			numUniquesInName++;
+
+			itNames = m->names.find(first);
 			if (itNames == globaldata->names.end()) {  
 				globaldata->names[first] = second; 
 				
@@ -215,11 +213,11 @@ int ReadTreeCommand::readNamesFile() {
 				vector<string> 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();
-		
+		*/
 		return 0;
 	}
 	catch(exception& e) {