X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=unifracweightedcommand.cpp;h=b2fd628b42218a38db6b61366ba7374b4ea4603a;hb=5694c92fbf646fe01abc87bde2af59e14a9a56b6;hp=2646ede2643feef23477167cb9d627c884cd884c;hpb=257eaa172451ede9d63a0715f6cdb7336a52996b;p=mothur.git

diff --git a/unifracweightedcommand.cpp b/unifracweightedcommand.cpp
index 2646ede..b2fd628 100644
--- a/unifracweightedcommand.cpp
+++ b/unifracweightedcommand.cpp
@@ -24,11 +24,13 @@ vector<string> UnifracWeightedCommand::getValidParameters(){
 //**********************************************************************************************************************
 UnifracWeightedCommand::UnifracWeightedCommand(){	
 	try {
+		abort = true;
 		//initialize outputTypes
 		vector<string> tempOutNames;
 		outputTypes["weighted"] = tempOutNames;
 		outputTypes["wsummary"] = tempOutNames;
 		outputTypes["phylip"] = tempOutNames;
+		outputTypes["column"] = tempOutNames;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "UnifracWeightedCommand", "UnifracWeightedCommand");
@@ -89,6 +91,7 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
 			outputTypes["weighted"] = tempOutNames;
 			outputTypes["wsummary"] = tempOutNames;
 			outputTypes["phylip"] = tempOutNames;
+			outputTypes["column"] = tempOutNames;
 			
 			if (globaldata->gTree.size() == 0) {//no trees were read
 				m->mothurOut("You must execute the read.tree command, before you may execute the unifrac.weighted command."); m->mothurOutEndLine(); abort = true;  }
@@ -111,9 +114,13 @@ UnifracWeightedCommand::UnifracWeightedCommand(string option) {
 			itersString = validParameter.validFile(parameters, "iters", false);			if (itersString == "not found") { itersString = "1000"; }
 			convert(itersString, iters); 
 			
-			string temp = validParameter.validFile(parameters, "distance", false);			if (temp == "not found") { temp = "false"; }
-			phylip = m->isTrue(temp);
-		
+			string temp = validParameter.validFile(parameters, "distance", false);			
+			if (temp == "not found") { phylip = false; outputForm = ""; }
+			else{
+				if ((temp == "lt") || (temp == "column") || (temp == "square")) {  phylip = true;  outputForm = temp; }
+				else { m->mothurOut("Options for distance are: lt, square, or column. Using lt."); m->mothurOutEndLine(); phylip = true; outputForm = "lt"; }
+			}
+			
 			temp = validParameter.validFile(parameters, "random", false);					if (temp == "not found") { temp = "F"; }
 			random = m->isTrue(temp);
 			
@@ -325,7 +332,6 @@ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > na
 	try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 		int process = 1;
-		int num = 0;
 		vector<int> processIDS;
 		
 		EstOutput results;
@@ -348,7 +354,11 @@ int UnifracWeightedCommand::createProcesses(Tree* t, vector< vector<string> > na
 				out.close();
 				
 				exit(0);
-			}else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+			}else { 
+				m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine(); 
+				for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+				exit(0);
+			}
 		}
 		
 		driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, scores);
@@ -492,15 +502,23 @@ void UnifracWeightedCommand::createPhylipFile() {
 		//for each tree
 		for (int i = 0; i < T.size(); i++) { 
 		
-			string phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted.dist";
-			outputNames.push_back(phylipFileName);
-			outputTypes["phylip"].push_back(phylipFileName);
+			string phylipFileName;
+			if ((outputForm == "lt") || (outputForm == "square")) {
+				phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted.phylip.dist";
+				outputNames.push_back(phylipFileName); outputTypes["phylip"].push_back(phylipFileName); 
+			}else { //column
+				phylipFileName = outputDir + m->getSimpleName(globaldata->getTreeFile())  + toString(i+1) + ".weighted.column.dist";
+				outputNames.push_back(phylipFileName); outputTypes["column"].push_back(phylipFileName); 
+			}
+			
 			ofstream out;
 			m->openOutputFile(phylipFileName, out);
 			
-			//output numSeqs
-			out << globaldata->Groups.size() << endl;
-			
+			if ((outputForm == "lt") || (outputForm == "square")) {
+				//output numSeqs
+				out << globaldata->Groups.size() << endl;
+			}
+
 			//make matrix with scores in it
 			vector< vector<float> > dists;	dists.resize(globaldata->Groups.size());
 			for (int i = 0; i < globaldata->Groups.size(); i++) {
@@ -523,11 +541,30 @@ void UnifracWeightedCommand::createPhylipFile() {
 				if (name.length() < 10) { //pad with spaces to make compatible
 					while (name.length() < 10) {  name += " ";  }
 				}
-				out << name << '\t';
 				
-				//output distances
-				for (int l = 0; l < r; l++) {	out  << dists[r][l] << '\t';  }
-				out << endl;
+				if (outputForm == "lt") {
+					out << name << '\t';
+					
+					//output distances
+					for (int l = 0; l < r; l++) {	out  << dists[r][l] << '\t';  }
+					out << endl;
+				}else if (outputForm == "square") {
+					out << name << '\t';
+					
+					//output distances
+					for (int l = 0; l < globaldata->Groups.size(); l++) {	out  << dists[r][l] << '\t';  }
+					out << endl;
+				}else{
+					//output distances
+					for (int l = 0; l < r; l++) {	
+						string otherName = globaldata->Groups[l];
+						if (otherName.length() < 10) { //pad with spaces to make compatible
+							while (otherName.length() < 10) {  otherName += " ";  }
+						}
+						
+						out  << name << '\t' << otherName << dists[r][l] << endl;  
+					}
+				}
 			}
 			out.close();
 		}