X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=clustercommand.cpp;h=6043d39be8d559010e156111f41a856b716cda40;hb=c921bbf0623d5200f69b5d83b3c70ea533c69412;hp=30c45e167ad6a398b23727293577f92362f5d6c7;hpb=47faf5463d44570ad66148384763db1c8238b563;p=mothur.git

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 30c45e1..6043d39 100644
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -9,6 +9,56 @@
 
 #include "clustercommand.h"
 
+//**********************************************************************************************************************
+vector<string> ClusterCommand::getValidParameters(){	
+	try {
+		string AlignArray[] =  {"cutoff","precision","method","showabund","timing","hard","outputdir","inputdir"};
+		vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ClusterCommand", "getValidParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+ClusterCommand::ClusterCommand(){	
+	try {
+		abort = true;
+		//initialize outputTypes
+		vector<string> tempOutNames;
+		outputTypes["list"] = tempOutNames;
+		outputTypes["rabund"] = tempOutNames;
+		outputTypes["sabund"] = tempOutNames;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ClusterCommand", "ClusterCommand");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> ClusterCommand::getRequiredParameters(){	
+	try {
+		vector<string> myArray; 
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ClusterCommand", "getRequiredParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+vector<string> ClusterCommand::getRequiredFiles(){	
+	try {
+		string Array[] =  {"phylip","column","or"};
+		vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ClusterCommand", "getRequiredFiles");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 //This function checks to make sure the cluster command has no errors and then clusters based on the method chosen.
 ClusterCommand::ClusterCommand(string option)  {
@@ -37,6 +87,12 @@ ClusterCommand::ClusterCommand(string option)  {
 				}
 			}
 			
+			//initialize outputTypes
+			vector<string> tempOutNames;
+			outputTypes["list"] = tempOutNames;
+			outputTypes["rabund"] = tempOutNames;
+			outputTypes["sabund"] = tempOutNames;
+		
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	outputDir = "";		}
 			
@@ -57,7 +113,7 @@ ClusterCommand::ClusterCommand(string option)  {
 			convert(temp, precision); 
 			
 			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "F"; }
-			hard = isTrue(temp);
+			hard = m->isTrue(temp);
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);
 			if (temp == "not found") { temp = "10"; }
@@ -67,8 +123,8 @@ ClusterCommand::ClusterCommand(string option)  {
 			method = validParameter.validFile(parameters, "method", false);
 			if (method == "not found") { method = "furthest"; }
 			
-			if ((method == "furthest") || (method == "nearest") || (method == "average")) { }
-			else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest or average."); m->mothurOutEndLine(); abort = true; }
+			if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted")) { }
+			else { m->mothurOut("Not a valid clustering method.  Valid clustering algorithms are furthest, nearest, average, and weighted."); m->mothurOutEndLine(); abort = true; }
 
 			showabund = validParameter.validFile(parameters, "showabund", false);
 			if (showabund == "not found") { showabund = "T"; }
@@ -91,18 +147,19 @@ ClusterCommand::ClusterCommand(string option)  {
 				if (method == "furthest")	{	cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method); }
 				else if(method == "nearest"){	cluster = new SingleLinkage(rabund, list, matrix, cutoff, method); }
 				else if(method == "average"){	cluster = new AverageLinkage(rabund, list, matrix, cutoff, method);	}
+				else if(method == "weighted"){	cluster = new WeightedLinkage(rabund, list, matrix, cutoff, method);	}
 				tag = cluster->getTag();
 				
-				if (outputDir == "") { outputDir += hasPath(globaldata->inputFileName); }
-				fileroot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
+				if (outputDir == "") { outputDir += m->hasPath(globaldata->inputFileName); }
+				fileroot = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
 			
-				openOutputFile(fileroot+ tag + ".sabund",	sabundFile);
-				openOutputFile(fileroot+ tag + ".rabund",	rabundFile);
-				openOutputFile(fileroot+ tag + ".list",		listFile);
+				m->openOutputFile(fileroot+ tag + ".sabund",	sabundFile);
+				m->openOutputFile(fileroot+ tag + ".rabund",	rabundFile);
+				m->openOutputFile(fileroot+ tag + ".list",		listFile);
 				
-				outputNames.push_back(fileroot+ tag + ".sabund");
-				outputNames.push_back(fileroot+ tag + ".rabund");
-				outputNames.push_back(fileroot+ tag + ".list");
+				outputNames.push_back(fileroot+ tag + ".sabund"); outputTypes["sabund"].push_back(fileroot+ tag + ".sabund");
+				outputNames.push_back(fileroot+ tag + ".rabund"); outputTypes["rabund"].push_back(fileroot+ tag + ".rabund");
+				outputNames.push_back(fileroot+ tag + ".list"); outputTypes["list"].push_back(fileroot+ tag + ".list");
 			}
 		}
 	}
@@ -164,13 +221,13 @@ int ClusterCommand::execute(){
 				if (globaldata->getFormat() == "phylip") { globaldata->setPhylipFile(""); }
 				else if (globaldata->getFormat() == "column") { globaldata->setColumnFile(""); }
 				sabundFile.close();rabundFile.close();listFile.close();
-				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	}
+				for (int i = 0; i < outputNames.size(); i++) {	remove(outputNames[i].c_str()); 	} outputTypes.clear();
 				return 0;
 			}
 		
-			if (print_start && isTrue(timing)) {
+			if (print_start && m->isTrue(timing)) {
 				m->mothurOut("Clustering (" + tag + ") dist " + toString(matrix->getSmallDist()) + "/" 
-					+ toString(roundDist(matrix->getSmallDist(), precision)) 
+					+ toString(m->roundDist(matrix->getSmallDist(), precision)) 
 					+ "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
 				cout.flush();
 				print_start = false;
@@ -183,9 +240,9 @@ int ClusterCommand::execute(){
 			float dist = matrix->getSmallDist();
 			float rndDist;
 			if (hard) {
-				rndDist = ceilDist(dist, precision); 
+				rndDist = m->ceilDist(dist, precision); 
 			}else{
-				rndDist = roundDist(dist, precision); 
+				rndDist = m->roundDist(dist, precision); 
 			}
 
 			if(previousDist <= 0.0000 && dist != previousDist){
@@ -201,7 +258,7 @@ int ClusterCommand::execute(){
 			oldList = *list;
 		}
 
-		if (print_start && isTrue(timing)) {
+		if (print_start && m->isTrue(timing)) {
 			m->mothurOut("Clustering (" + tag + ") for distance " + toString(previousDist) + "/" + toString(rndPreviousDist) 
 					 + "\t(precision: " + toString(precision) + ", Nodes: " + toString(matrix->getNNodes()) + ")");
 			cout.flush();
@@ -231,7 +288,12 @@ int ClusterCommand::execute(){
 		rabundFile.close();
 		listFile.close();
 	
-		if (saveCutoff != cutoff) { m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();  }
+		if (saveCutoff != cutoff) { 
+			if (hard)	{  saveCutoff = m->ceilDist(saveCutoff, precision);	}
+			else		{	saveCutoff = m->roundDist(saveCutoff, precision);  }
+
+			m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine(); 
+		}
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -239,7 +301,7 @@ int ClusterCommand::execute(){
 		m->mothurOutEndLine();
 
 		
-		//if (isTrue(timing)) {
+		//if (m->isTrue(timing)) {
 			m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster"); m->mothurOutEndLine();
 		//}
 		
@@ -256,7 +318,7 @@ int ClusterCommand::execute(){
 
 void ClusterCommand::printData(string label){
 	try {
-		if (isTrue(timing)) {
+		if (m->isTrue(timing)) {
 			m->mothurOut("\tTime: " + toString(time(NULL) - start) + "\tsecs for " + toString(oldRAbund.getNumBins()) 
 		     + "\tclusters. Updates: " + toString(loops)); m->mothurOutEndLine();
 		}
@@ -265,7 +327,7 @@ void ClusterCommand::printData(string label){
 		start = time(NULL);
 
 		oldRAbund.setLabel(label);
-		if (isTrue(showabund)) {
+		if (m->isTrue(showabund)) {
 			oldRAbund.getSAbundVector().print(cout);
 		}
 		oldRAbund.print(rabundFile);