X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=readtreecommand.cpp;h=88e34ff5c7e3f2c243eb7e0dac56b7d11fcb39b4;hb=786d5631d9cd5baa6ed6ef16f8b4b384cbc7470f;hp=7cca943274aa929e6bfb5acf29f4c12988b8e965;hpb=58cf1d08fee8c64334979075fa57bcafb035a2ed;p=mothur.git

diff --git a/readtreecommand.cpp b/readtreecommand.cpp
index 7cca943..88e34ff 100644
--- a/readtreecommand.cpp
+++ b/readtreecommand.cpp
@@ -10,18 +10,55 @@
 #include "readtreecommand.h"
 
 //**********************************************************************************************************************
-ReadTreeCommand::ReadTreeCommand(){
+ReadTreeCommand::ReadTreeCommand(string option){
 	try {
 		globaldata = GlobalData::getInstance();
-		filename = globaldata->inputFileName;
+		abort = false;
 		
-		//read in group map info.
-		treeMap = new TreeMap(globaldata->getGroupFile());
-		treeMap->readMap();
-		globaldata->gTreemap = treeMap;
-
-		read = new ReadNewickTree(filename);
+		//allow user to run help
+		if(option == "help") { help(); abort = true; }
+		
+		else {
+			//valid paramters for this command
+			string Array[] =  {"tree","group"};
+			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+			
+			OptionParser parser(option);
+			map<string, string> parameters = parser.getParameters();
+			
+			ValidParameters validParameter;
 		
+			//check to make sure all parameters are valid for command
+			for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) { 
+				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
+			}
+			
+			globaldata->runParse = true;
+			globaldata->newRead();
+			
+			//check for required parameters
+			treefile = validParameter.validFile(parameters, "tree", true);
+			if (treefile == "not open") { abort = true; }
+			else if (treefile == "not found") { treefile = ""; cout << "tree is a required parameter for the read.tree command." << endl; 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 = ""; cout << "group is a required parameter for the read.tree command." << endl; abort = true;	}
+			else {  
+				globaldata->setGroupFile(groupfile); 
+				//read in group map info.
+				treeMap = new TreeMap(groupfile);
+				treeMap->readMap();
+				globaldata->gTreemap = treeMap;
+			}
+			
+			if (abort == false) {
+				filename = treefile;
+				read = new ReadNewickTree(filename);
+			}
+						
+		}
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function ReadTreeCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -32,6 +69,25 @@ ReadTreeCommand::ReadTreeCommand(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+
+void ReadTreeCommand::help(){
+	try {
+		cout << "The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. " << "\n";
+		cout << "It also must be run before using the parsimony command, unless you are using the randomtree parameter." << "\n";
+		cout << "The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile)." << "\n";
+		cout << "The tree and group parameters are both required." << "\n";
+		cout << "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile)." << "\n" << "\n";
+	}
+	catch(exception& e) {
+		cout << "Standard Error: " << e.what() << " has occurred in the ReadTreeCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}
+	catch(...) {
+		cout << "An unknown error has occurred in the ReadTreeCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+		exit(1);
+	}	
+}
 
 //**********************************************************************************************************************
 
@@ -44,10 +100,37 @@ ReadTreeCommand::~ReadTreeCommand(){
 int ReadTreeCommand::execute(){
 	try {
 	
-		read->read(); 
+		if (abort == true) { return 0; }
+		
+		int readOk;
 		
-		Tree* T = globaldata->gTree;
-//		T->createNewickFile();
+		readOk = read->read(); 
+		
+		if (readOk != 0) { cout << "Read Terminated." << endl; globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
+		
+		vector<Tree*> T = globaldata->gTree;
+		
+		//assemble users trees
+		for (int i = 0; i < T.size(); i++) {
+			T[i]->assembleTree();
+		}
+
+		//output any names that are in names file but not in tree
+		if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
+			for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
+				//is that name in the tree?
+				int count = 0;
+				for (int j = 0; j < globaldata->Treenames.size(); j++) {
+					if (treeMap->namesOfSeqs[i] == globaldata->Treenames[j]) { break; } //found it
+					count++;
+				}
+				
+				//then you did not find it so report it 
+				if (count == globaldata->Treenames.size()) { 
+					cout << treeMap->namesOfSeqs[i] << " is in your namefile and not in your tree. It will be disregarded." << endl;
+				}
+			}
+		}
 		
 		return 0;
 	}