X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=hclustercommand.cpp;h=dbc0e1bb9917b0d2cfdebfa83a5a97a17b6eb905;hb=d2cbe389d0e42eccb6bbb888462fe17e22a487a8;hp=6e3ec243addd289a6d44226adeddd6a3fccbb0d2;hpb=3c856e629e20261496b0433c2587f27b2c8ba3f6;p=mothur.git

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index 6e3ec24..dbc0e1b 100644
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -21,7 +21,7 @@ HClusterCommand::HClusterCommand(string option){
 		
 		else {
 			//valid paramters for this command
-			string Array[] =  {"cutoff","precision","method","showabund","timing","phylip","column","name","sorted"};
+			string Array[] =  {"cutoff","precision","method","phylip","column","name","sorted","showabund","timing"};
 			vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
 			
 			OptionParser parser(option);
@@ -53,8 +53,8 @@ HClusterCommand::HClusterCommand(string option){
 			if (namefile == "not open") { abort = true; }	
 			else if (namefile == "not found") { namefile = ""; }
 			
-			if ((phylipfile == "") && (columnfile == "")) { mothurOut("When executing a cluster command you must enter a phylip or a column."); mothurOutEndLine(); abort = true; }
-			else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When executing a cluster command you must enter ONLY ONE of the following: phylip or column."); mothurOutEndLine(); abort = true; }
+			if ((phylipfile == "") && (columnfile == "")) { mothurOut("When executing a hcluster command you must enter a phylip or a column."); mothurOutEndLine(); abort = true; }
+			else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When executing a hcluster command you must enter ONLY ONE of the following: phylip or column."); mothurOutEndLine(); abort = true; }
 		
 			if (columnfile != "") {
 				if (namefile == "") {  cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
@@ -114,11 +114,12 @@ HClusterCommand::HClusterCommand(string option){
 
 void HClusterCommand::help(){
 	try {
-		mothurOut("The cluster command can only be executed after a successful read.dist command.\n");
-		mothurOut("The cluster command parameter options are method, cuttoff, precision, showabund and timing. No parameters are required.\n");
-		mothurOut("The cluster command should be in the following format: \n");
-		mothurOut("cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
-		mothurOut("The acceptable cluster methods are furthest, nearest and average.  If no method is provided then furthest is assumed.\n\n");	
+		mothurOut("The hcluster command parameter options are cutoff, precision, method, phylip, column, name, showabund, timing and sorted. Phylip or column and name are required.\n");
+		mothurOut("The phylip and column parameter allow you to enter your distance file, and sorted indicates whether your column distance file is already sorted. \n");
+		mothurOut("The name parameter allows you to enter your name file and is required if your distance file is in column format. \n");
+		mothurOut("The hcluster command should be in the following format: \n");
+		mothurOut("hcluster(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n");
+		mothurOut("The acceptable hcluster methods is furthest, but we hope to add nearest and average in the future.\n\n");	
 	}
 	catch(exception& e) {
 		errorOut(e, "HClusterCommand", "help");
@@ -160,7 +161,7 @@ int HClusterCommand::execute(){
 	
 		mothurOut("It took " + toString(time(NULL) - estart) + " seconds to sort. "); mothurOutEndLine();
 		estart = time(NULL);
-		
+	
 		//list vector made by read contains all sequence names
 		if(list != NULL){
 			rabund = new RAbundVector(list->getRAbundVector());
@@ -168,8 +169,6 @@ int HClusterCommand::execute(){
 			mothurOut("Error: no list vector!"); mothurOutEndLine(); return 0;
 		}
 		
-		
-		
 		float previousDist = 0.00000;
 		float rndPreviousDist = 0.00000;
 		oldRAbund = *rabund;
@@ -178,7 +177,7 @@ int HClusterCommand::execute(){
 		print_start = true;
 		start = time(NULL);
 		
-//cout << "here" << endl;	
+	
 		ifstream in;
 		openInputFile(distfile, in);
 		string firstName, secondName;
@@ -188,7 +187,7 @@ int HClusterCommand::execute(){
 		bool clusteredSomething;
 		vector<seqDist> seqs; seqs.resize(1); // to start loop
 		exitedBreak = false;  //lets you know if there is a distance stored in next
-		
+	
 		while (seqs.size() != 0){
 		
 			seqs = getSeqs(in);
@@ -206,12 +205,12 @@ int HClusterCommand::execute(){
 					print_start = false;
 				}
 				
-	///cout << "before cluster update" << endl;
+	//cout << "before cluster update" << endl;
 				if (seqs[i].seq1 != seqs[i].seq2) {
 					clusteredSomething = cluster->update(seqs[i].seq1, seqs[i].seq2, seqs[i].dist);
 					
 					float rndDist = roundDist(seqs[i].dist, precision);
-					//cout << "after cluster update clusterSomething = " << clusteredSomething << " rndDist = " << rndDist << " rndPreviousDist = " << rndPreviousDist << endl;			
+		//cout << "after cluster update clusterSomething = " << clusteredSomething << " rndDist = " << rndDist << " rndPreviousDist = " << rndPreviousDist << endl;			
 					
 					
 					if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
@@ -260,6 +259,7 @@ int HClusterCommand::execute(){
 		rabundFile.close();
 		listFile.close();
 		
+		delete cluster;
 		//if (isTrue(timing)) {
 			mothurOut("It took " + toString(time(NULL) - estart) + " seconds to cluster. "); mothurOutEndLine();
 		//}
@@ -325,17 +325,18 @@ vector<seqDist> HClusterCommand::getSeqs(ifstream& filehandle){
 			
 			//save first one
 			if (prevDistance == -1) { prevDistance = distance; }
-			
+	//cout << prevDistance << endl;	
+//if (globaldata->nameMap == NULL) { cout << "null" << endl; }
 			map<string,int>::iterator itA = globaldata->nameMap->find(firstName);
 			map<string,int>::iterator itB = globaldata->nameMap->find(secondName);
 			
 			if(itA == globaldata->nameMap->end()){
-				cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";
+				cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);
 			}
 			if(itB == globaldata->nameMap->end()){
-				cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n";
+				cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);
 			}
-			
+	//cout << "here" << endl;		
 			//using cutoff
 			if (distance > cutoff) { break; }