X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensuscommand.cpp;h=9b72638662e4001963b9219f4c5f313010774797;hb=5d6d303e481489e226fdf8d6c5385b99b50718bc;hp=2fef5b16a062ed99cd90c2fc43e7617c25d5ee13;hpb=e0fbf58358a72f20352cf2a43922ab6b5bdf0cf8;p=mothur.git

diff --git a/consensuscommand.cpp b/consensuscommand.cpp
index 2fef5b1..9b72638 100644
--- a/consensuscommand.cpp
+++ b/consensuscommand.cpp
@@ -9,6 +9,54 @@
 
 #include "consensuscommand.h"
 
+//**********************************************************************************************************************
+vector<string> ConcensusCommand::getValidParameters(){	
+	try {
+		vector<string> myArray; 
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ConcensusCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> ConcensusCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray; 
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ConcensusCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> ConcensusCommand::getRequiredFiles(){	
+	try {
+		string AlignArray[] =  {"tree","group"};
+		vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ConcensusCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+ConcensusCommand::ConcensusCommand(){	
+	try {
+		abort = true;
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["tree"] = tempOutNames;
+		outputTypes["nodepairs"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ConcensusCommand", "ConcensusCommand");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
 ConcensusCommand::ConcensusCommand(string fileroot)  {
@@ -16,6 +64,11 @@ ConcensusCommand::ConcensusCommand(string fileroot)  {
 		globaldata = GlobalData::getInstance();
 		abort = false;
 		
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["tree"] = tempOutNames;
+		outputTypes["nodepairs"] = tempOutNames;
+		
 		filename = fileroot;
 		
 		t = globaldata->gTree;
@@ -67,8 +120,8 @@ int ConcensusCommand::execute(){
 		if (m->control_pressed) { return 0; }
 		
 		//open file for pairing not included in the tree
-		notIncluded = filename + ".cons.pairs";
-		openOutputFile(notIncluded, out2);
+		notIncluded = filename + ".cons.pairs"; outputNames.push_back(notIncluded);  outputTypes["nodepairs"].push_back(notIncluded);
+		m->openOutputFile(notIncluded, out2);
 		
 		consensusTree = new Tree();
 		
@@ -150,10 +203,10 @@ int ConcensusCommand::execute(){
 			out2 << '\t' << it2->second << endl;
 		}
 		
-		outputFile = filename + ".cons.tre";
-		openOutputFile(outputFile, out);
+		outputFile = filename + ".cons.tre";  outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
+		m->openOutputFile(outputFile, out);
 		
-		consensusTree->printForBoot(out);
+		consensusTree->print(out, "boot");
 		
 		out.close(); out2.close();