X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensuscommand.cpp;h=e522b098f0703d6909f1906c3039fb4459e99854;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=a65d56fb86c2a8a91ac2915def73d05c7e53b6d6;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/consensuscommand.cpp b/consensuscommand.cpp
index a65d56f..e522b09 100644
--- a/consensuscommand.cpp
+++ b/consensuscommand.cpp
@@ -10,56 +10,85 @@
 #include "consensuscommand.h"
 
 //**********************************************************************************************************************
-
-ConcensusCommand::ConcensusCommand(string fileroot)  {
+vector<string> ConcensusCommand::setParameters(){	
 	try {
-		globaldata = GlobalData::getInstance();
-		abort = false;
-		
-		filename = fileroot;
-		
-		t = globaldata->gTree;
-	
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
+		return myArray;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "ConcensusCommand", "ConcensusCommand");
+		m->errorOut(e, "ConcensusCommand", "setParameters");
 		exit(1);
 	}
 }
-
 //**********************************************************************************************************************
-
-void ConcensusCommand::help(){
+string ConcensusCommand::getHelpString(){	
 	try {
-		m->mothurOut("The consensus command can only be executed after a successful read.tree command.\n");
-		m->mothurOut("The consensus command has no parameters.\n");
-		m->mothurOut("The consensus command should be in the following format: consensus().\n");
-		m->mothurOut("The consensus command output two files: .consensus.tre and .consensuspairs.\n");
-		m->mothurOut("The .consensus.tre file contains the consensus tree of the trees in your input file.\n");
-		m->mothurOut("The branch lengths are the percentage of trees in your input file that had the given pair.\n");
-		m->mothurOut("The .consensuspairs file contains a list of the internal nodes in your tree.  For each node, the pair that was used in the consensus tree \n");
-		m->mothurOut("is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages.\n\n");		
+		string helpString = "";
+		helpString += "The consensus command can only be executed after a successful read.tree command.\n";
+		helpString += "The consensus command has no parameters.\n";
+		helpString += "The consensus command should be in the following format: consensus().\n";
+		helpString += "The consensus command output two files: .consensus.tre and .consensuspairs.\n";
+		helpString += "The .consensus.tre file contains the consensus tree of the trees in your input file.\n";
+		helpString += "The branch lengths are the percentage of trees in your input file that had the given pair.\n";
+		helpString += "The .consensuspairs file contains a list of the internal nodes in your tree.  For each node, the pair that was used in the consensus tree \n";
+		helpString += "is reported with its percentage, as well as the other pairs that were seen for that node but not used and their percentages.\n";		
+		return helpString;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "ConcensusCommand", "help");
+		m->errorOut(e, "ConcensusCommand", "getHelpString");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+ConcensusCommand::ConcensusCommand(){	
+	try {
+		abort = true; calledHelp = true; 
+		setParameters();
+		vector<string> tempOutNames;
+		outputTypes["tree"] = tempOutNames;
+		outputTypes["nodepairs"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ConcensusCommand", "ConcensusCommand");
 		exit(1);
 	}
 }
-
 //**********************************************************************************************************************
 
-ConcensusCommand::~ConcensusCommand(){}
-
+ConcensusCommand::ConcensusCommand(string fileroot)  {
+	try {
+		abort = false; calledHelp = false;   
+		
+		setParameters();
+		
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["tree"] = tempOutNames;
+		outputTypes["nodepairs"] = tempOutNames;
+		
+		filename = fileroot;
+	
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ConcensusCommand", "ConcensusCommand");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
 int ConcensusCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
-		else {  
-			numNodes = t[0]->getNumNodes();
-			numLeaves = t[0]->getNumLeaves();
-		}
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+		
+		
+		m->mothurOut("This command is not currently in use."); m->mothurOutEndLine();
+	/*	
+		t = globaldata->gTree;
+		numNodes = t[0]->getNumNodes();
+		numLeaves = t[0]->getNumLeaves();
+		
 		
 		//get the possible pairings
 		getSets();	
@@ -67,7 +96,7 @@ int ConcensusCommand::execute(){
 		if (m->control_pressed) { return 0; }
 		
 		//open file for pairing not included in the tree
-		notIncluded = filename + ".cons.pairs";
+		notIncluded = filename + ".cons.pairs"; outputNames.push_back(notIncluded);  outputTypes["nodepairs"].push_back(notIncluded);
 		m->openOutputFile(notIncluded, out2);
 		
 		consensusTree = new Tree();
@@ -150,15 +179,22 @@ int ConcensusCommand::execute(){
 			out2 << '\t' << it2->second << endl;
 		}
 		
-		outputFile = filename + ".cons.tre";
+		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();
 		
 		delete consensusTree; 
 		
+		//set first tree file as new current treefile
+		string currentTree = "";
+		itTypes = outputTypes.find("tree");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); }
+		}
+		*/
 		return 0;
 	}
 	catch(exception& e) {