changed hard parameter in cluster commands

[mothur.git] / mgclustercommand.cpp

diff --git a/mgclustercommand.cpp b/mgclustercommand.cpp
index 6d5acb2386ad0ccd836ee41d2d8f5b24c5e4048e..023f2142deb8584ad3794170b95e1b1d12889529 100644 (file)
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -20,7 +20,7 @@ MGClusterCommand::MGClusterCommand(string option) {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"blast", "method", "name", "cutoff", "precision", "length", "min", "penalty", "hcluster","merge","outputdir","inputdir"};
+                       string Array[] =  {"blast", "method", "name", "hard", "cutoff", "precision", "length", "min", "penalty", "hcluster","merge","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -104,6 +104,9 @@ MGClusterCommand::MGClusterCommand(string option) {
                        
                        temp = validParameter.validFile(parameters, "hcluster", false);                 if (temp == "not found") { temp = "false"; }
                        hclusterWanted = isTrue(temp); 
+                       
+                       temp = validParameter.validFile(parameters, "hard", false);                     if (temp == "not found") { temp = "F"; }
+                       hard = isTrue(temp);
                }
 
        }
@@ -214,7 +217,13 @@ int MGClusterCommand::execute(){
                                }
                                
                                float dist = distMatrix->getSmallDist();
-                               float rndDist = roundDist(dist, precision);
+                               float rndDist;
+                               if (hard) {
+                                       rndDist = ceilDist(dist, precision); 
+                               }else{
+                                       rndDist = roundDist(dist, precision); 
+                               }
+
                                
                                if(previousDist <= 0.0000 && dist != previousDist){
                                        oldList.setLabel("unique");
@@ -329,7 +338,12 @@ int MGClusterCommand::execute(){
                                                        return 0; 
                                                }
        
-                                               float rndDist = roundDist(seqs[i].dist, precision);
+                                               float rndDist;
+                                               if (hard) {
+                                                       rndDist = ceilDist(seqs[i].dist, precision); 
+                                               }else{
+                                                       rndDist = roundDist(seqs[i].dist, precision); 
+                                               }
                                                                                                
                                                if((previousDist <= 0.0000) && (seqs[i].dist != previousDist)){
                                                        oldList.setLabel("unique");
@@ -538,12 +552,12 @@ ListVector* MGClusterCommand::mergeOPFs(map<string, int> binInfo, float dist){
 void MGClusterCommand::sortHclusterFiles(string unsortedDist, string unsortedOverlap) {
        try {
                //sort distFile
-               string sortedDistFile = sortFile(unsortedDist);
+               string sortedDistFile = sortFile(unsortedDist, outputDir);
                remove(unsortedDist.c_str());  //delete unsorted file
                distFile = sortedDistFile;
                
                //sort overlap file
-               string sortedOverlapFile = sortFile(unsortedOverlap);
+               string sortedOverlapFile = sortFile(unsortedOverlap, outputDir);
                remove(unsortedOverlap.c_str());  //delete unsorted file
                overlapFile = sortedOverlapFile;
        }