X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=626659501a531db80f5193bef33e88793414a874;hb=d04f948b1a2a1a2984fc4a45d04403b8c121c5bc;hp=3403b9934dfb9366d066a64ed5552484b2e4275c;hpb=15bc21bb4281af0f3ea7b29d9b9363f4635ef939;p=mothur.git

diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp
index 3403b99..6266595 100644
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -19,7 +19,55 @@
 #include "sharedmorisitahorn.h"
 #include "sharedbraycurtis.h"
 
-
+//**********************************************************************************************************************
+vector<string> TreeGroupCommand::getValidParameters(){	
+	try {
+		string Array[] =  {"label","calc","groups", "phylip", "column", "name", "precision","cutoff","outputdir","inputdir"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TreeGroupCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+TreeGroupCommand::TreeGroupCommand(){	
+	try {
+		abort = true;
+		globaldata = GlobalData::getInstance();
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["tree"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> TreeGroupCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray;
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TreeGroupCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> TreeGroupCommand::getRequiredFiles(){	
+	try {
+		string Array[] =  {"phylip","column","shared","or"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "TreeGroupCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
 TreeGroupCommand::TreeGroupCommand(string option)  {
@@ -50,6 +98,10 @@ TreeGroupCommand::TreeGroupCommand(string option)  {
 				if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["tree"] = tempOutNames;
+			
 			//if the user changes the input directory command factory will send this info to us in the output parameter 
 			string inputDir = validParameter.validFile(parameters, "inputdir", false);		
 			if (inputDir == "not found"){	inputDir = "";		}
@@ -324,7 +376,7 @@ int TreeGroupCommand::execute(){
 
 			//create a new filename
 			outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "tre";	
-			outputNames.push_back(outputFile);
+			outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 				
 			createTree();
 			
@@ -595,7 +647,7 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 		
 					//create a new filename
 					outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre";				
-					outputNames.push_back(outputFile);
+					outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); 
 												
 					for (int k = 0; k < thisLookup.size(); k++) { 
 						for (int l = k; l < thisLookup.size(); l++) {
@@ -617,6 +669,21 @@ int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
 						}
 					}
 					
+					//createdistance file from simMatrix
+					/*string o = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
+					ofstream outDist;
+					m->openOutputFile(o, outDist);
+					outDist << simMatrix.size() << endl;
+					for (int k = 0; k < simMatrix.size(); k++) {
+						outDist << thisLookup[k]->getGroup() << '\t';
+						for (int l = 0; l < k; l++) {
+							outDist << (1.0-simMatrix[k][l]) << '\t';
+						}
+						outDist << endl;
+					}
+					outDist.close();*/
+
+					
 					if (m->control_pressed) { return 1; }
 					//creates tree from similarity matrix and write out file
 					createTree();