X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=consensuscommand.cpp;h=9880b8dbf01f72abe4a2a50d9630a2d09d3fd6d0;hb=4f9a6e14a608172f8a97f0297a3b8e6ea267c518;hp=dc278017c906dcfeb9f7967bc99f767df7007011;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git

diff --git a/consensuscommand.cpp b/consensuscommand.cpp
index dc27801..9880b8d 100644
--- a/consensuscommand.cpp
+++ b/consensuscommand.cpp
@@ -9,12 +9,64 @@
 
 #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; calledHelp = true; 
+		vector<string> tempOutNames;
+		outputTypes["tree"] = tempOutNames;
+		outputTypes["nodepairs"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ConcensusCommand", "ConcensusCommand");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 
 ConcensusCommand::ConcensusCommand(string fileroot)  {
 	try {
 		globaldata = GlobalData::getInstance();
-		abort = false;
+		abort = false; calledHelp = false;   
+		
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["tree"] = tempOutNames;
+		outputTypes["nodepairs"] = tempOutNames;
 		
 		filename = fileroot;
 		
@@ -55,18 +107,20 @@ ConcensusCommand::~ConcensusCommand(){}
 int ConcensusCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
 		else {  
 			numNodes = t[0]->getNumNodes();
 			numLeaves = t[0]->getNumLeaves();
 		}
 		
 		//get the possible pairings
-		getSets();		
+		getSets();	
+		
+		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();
 		
@@ -82,8 +136,12 @@ int ConcensusCommand::execute(){
 		
 		buildConcensusTree(treeSet);
 		
+		if (m->control_pressed) { delete consensusTree; return 0; }
+		
 		consensusTree->assembleTree();
 		
+		if (m->control_pressed) { delete consensusTree; return 0; }
+		
 		//output species in order
 		out2 << "Species in Order: " << endl << endl;
 		for (int i = 0; i < treeSet.size(); i++) {  out2 << i+1 << ".  " << treeSet[i] << endl; }
@@ -91,8 +149,13 @@ int ConcensusCommand::execute(){
 		//output sets included
 		out2 << endl << "Sets included in the consensus tree:" << endl << endl;
 		
+		if (m->control_pressed) { delete consensusTree; return 0; }
+		
 		vector<string> temp;
 		for (it2 = nodePairsInTree.begin(); it2 != nodePairsInTree.end(); it2++) {
+		
+			if (m->control_pressed) { delete consensusTree; return 0; }
+			
 			//only output pairs not leaves
 			if (it2->first.size() > 1) { 
 				temp.clear();
@@ -118,6 +181,9 @@ int ConcensusCommand::execute(){
 		//output sets not included
 		out2 << endl << "Sets NOT included in the consensus tree:" << endl << endl;
 		for (it2 = nodePairs.begin(); it2 != nodePairs.end(); it2++) {
+		
+			if (m->control_pressed) { delete consensusTree; return 0; }
+			
 			temp.clear();
 			//initialize temp to all "."
 			temp.resize(treeSet.size(), ".");
@@ -136,10 +202,10 @@ 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();
 		
@@ -159,6 +225,8 @@ int ConcensusCommand::buildConcensusTree(vector<string> nodeSet) {
 		vector<string> leftChildSet;
 		vector<string> rightChildSet;
 		
+		if (m->control_pressed) { return 1; }
+		
 		//if you are at a leaf
 		if (nodeSet.size() == 1) {
 			//return the vector index of the leaf you are at
@@ -186,7 +254,7 @@ int ConcensusCommand::buildConcensusTree(vector<string> nodeSet) {
 }
 
 //**********************************************************************************************************************
-void ConcensusCommand::getSets() {
+int ConcensusCommand::getSets() {
 	try {
 		vector<string> temp;
 		treeSet.clear();
@@ -196,6 +264,9 @@ void ConcensusCommand::getSets() {
 			
 			//for each non-leaf node get descendant info.
 			for (int j = numLeaves; j < numNodes; j++) {
+				
+				if (m->control_pressed) { return 1; }
+				
 				temp.clear();
 				//go through pcounts and pull out descendants
 				for (it = t[i]->tree[j].pcount.begin(); it != t[i]->tree[j].pcount.end(); it++) {
@@ -219,6 +290,8 @@ void ConcensusCommand::getSets() {
 		//you want the leaves in there but with insignifigant sightings value so it is added last
 		//for each leaf node get descendant info.
 		for (int j = 0; j < numLeaves; j++) {
+		
+			if (m->control_pressed) { return 1; }
 			
 			//only need the first one since leaves have no descendants but themselves
 			it = t[0]->tree[j].pcount.begin(); 
@@ -239,16 +312,18 @@ void ConcensusCommand::getSets() {
 		
 		//set initial rating on pairs to sightings + subgroup sightings
 		while (nodePairsCopy.size() != 0) {
+			if (m->control_pressed) { return 1; }
 		
-			vector<string> small = getSmallest(nodePairsCopy);
+			vector<string> smallOne = getSmallest(nodePairsCopy);
 			
-			int subgrouprate = getSubgroupRating(small);
+			int subgrouprate = getSubgroupRating(smallOne);
 		
-			nodePairsInitialRate[small] = nodePairs[small] + subgrouprate;
+			nodePairsInitialRate[smallOne] = nodePairs[smallOne] + subgrouprate;
 			
-			nodePairsCopy.erase(small);
+			nodePairsCopy.erase(smallOne);
 		}
 		
+		return 0;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "ConcensusCommand", "getSets");