Adds hard change to mgcluster and sens.spec

source/commands/mgclustercommand.cpp

@@ -20,7 +20,6 @@ vector<string> MGClusterCommand::setParameters(){
 		CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "","",false,false,true); parameters.push_back(pcutoff);
 		CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
 		CommandParameter pmethod("method", "Multiple", "furthest-nearest-average", "average", "", "", "","",false,false); parameters.push_back(pmethod);
-		CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
 		CommandParameter pmin("min", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmin);
 		CommandParameter pmerge("merge", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmerge);
         CommandParameter padjust("adjust", "String", "", "F", "", "", "","",false,false); parameters.push_back(padjust);
@@ -42,7 +41,7 @@ vector<string> MGClusterCommand::setParameters(){
 string MGClusterCommand::getHelpString(){	
 	try {
 		string helpString = "";
-		helpString += "The mgcluster command parameter options are blast, name, cutoff, precision, hard,  method, merge, min, length, penalty and adjust. The blast parameter is required.\n";
+		helpString += "The mgcluster command parameter options are blast, name, cutoff, precision,  method, merge, min, length, penalty and adjust. The blast parameter is required.\n";
 		helpString += "The mgcluster command reads a blast and name file and clusters the sequences into OPF units similar to the OTUs.\n";
 		helpString += "This command outputs a .list, .rabund and .sabund file that can be used with mothur other commands to estimate richness.\n";
 		helpString += "The cutoff parameter is used to specify the maximum distance you would like to cluster to. The default is 0.70.\n";
@@ -211,9 +210,6 @@ MGClusterCommand::MGClusterCommand(string option) {
 			temp = validParameter.validFile(parameters, "merge", false);			if (temp == "not found") { temp = "true"; }
 			merge = m->isTrue(temp);
 			
-			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
-			hard = m->isTrue(temp);
-            
             temp = validParameter.validFile(parameters, "adjust", false);				if (temp == "not found") { if (cutoffSet) { temp = "F"; }else { temp="T"; } }
             if (m->isNumeric1(temp))    { m->mothurConvert(temp, adjust);   }
             else if (m->isTrue(temp))   { adjust = 1.0;                     }
@@ -342,12 +338,8 @@ int MGClusterCommand::execute(){
             }
             
             float dist = distMatrix->getSmallDist();
-            float rndDist;
-            if (hard) {
-                rndDist = m->ceilDist(dist, precision);
-            }else{
-                rndDist = m->roundDist(dist, precision);
-            }
+            float rndDist = m->ceilDist(dist, precision);
+            
             
             if(previousDist <= 0.0000 && dist != previousDist){
                 oldList.setLabel("unique");

source/commands/mgclustercommand.h

@@ -56,7 +56,7 @@ class MGClusterCommand : public Command {
 	double cutoff;
 	float penalty, adjust;
 	int precision, length, precisionLength;
-	bool abort, minWanted, hclusterWanted, merge, hard, cutoffSet;
+	bool abort, minWanted, hclusterWanted, merge, cutoffSet;
 	
 	void printData(ListVector*, map<string, int>&);
 	ListVector* mergeOPFs(map<string, int>, float);

source/commands/sensspeccommand.cpp

@@ -20,7 +20,6 @@ vector<string> SensSpecCommand::setParameters(){
 		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
 		CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "","",false,false); parameters.push_back(pcutoff);
 		CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
-		CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
 		CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
         CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
 		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
@@ -223,13 +222,6 @@ SensSpecCommand::SensSpecCommand(string option)  {
 				outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it
 			}
 
-			//check for optional parameter and set defaults
-			// ...at some point should added some additional type checking...
-			temp = validParameter.validFile(parameters, "hard", false);
-			if (temp == "not found"){	hard = 1;	}
-			else if(!m->isTrue(temp))	{	hard = 0;	}
-			else if(m->isTrue(temp))	{	hard = 1;	}
-
 			temp = validParameter.validFile(parameters, "cutoff", false);		if (temp == "not found") { temp = "-1.00"; }
 			m->mothurConvert(temp, cutoff);
 
@@ -310,7 +302,7 @@ int SensSpecCommand::process(map<string, int>& seqMap, ListVector*& list, bool&
 			if(label != "unique"){
 				origCutoff = label;
 				convert(label, cutoff);
-				if(!hard){	cutoff += (0.49 / double(precision));	}
+                origCutoff = toString(m->ceilDist(cutoff, precision));
 			}
 			else{
 				origCutoff = "unique";
@@ -459,9 +451,8 @@ int SensSpecCommand::processListFile(){
 
 		string origCutoff = "";
 		bool getCutoff = 0;
-		if(cutoff == -1.00)	{	getCutoff = 1;															}
-		else if( !hard )	{	origCutoff = toString(cutoff);	cutoff += (0.49 / double(precision));	}
-		else 				{	origCutoff = toString(cutoff);	}
+		if(cutoff == -1.00)	{	getCutoff = 1;                                          }
+		else 				{	origCutoff = toString(m->ceilDist(cutoff, precision));	}
 
 		map<string, int> seqMap;
 

source/commands/sensspeccommand.h

@@ -49,7 +49,6 @@ class SensSpecCommand : public Command {
 
 	long int truePositives, falsePositives, trueNegatives, falseNegatives;
 	bool abort, allLines, square;
-	bool hard;
 	double cutoff;
 	int precision;