added sharedRabundFloatVector class to represent the relabund file. modified read...

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 9ed67e04433edecd93262c1824732edbb3cd186c..6df5faad98cd9a0cd1a78644794cecc3eef0df7d 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -57,18 +57,18 @@ 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"; }
                        convert(temp, cutoff); 
-                       if (!hard) {    cutoff += (5 / (precision * 10.0));  }
+                       cutoff += (5 / (precision * 10.0));  
                        
                        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"; }
@@ -91,14 +91,15 @@ 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");
@@ -168,9 +169,9 @@ int ClusterCommand::execute(){
                                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;
@@ -181,7 +182,12 @@ int ClusterCommand::execute(){
                        cluster->update(cutoff);
        
                        float dist = matrix->getSmallDist();
-                       float rndDist = roundDist(dist, precision);
+                       float rndDist;
+                       if (hard) {
+                               rndDist = m->ceilDist(dist, precision); 
+                       }else{
+                               rndDist = m->roundDist(dist, precision); 
+                       }
 
                        if(previousDist <= 0.0000 && dist != previousDist){
                                printData("unique");
@@ -196,7 +202,7 @@ 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();
@@ -226,7 +232,12 @@ 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();
@@ -234,7 +245,7 @@ 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();
                //}
                
@@ -251,7 +262,7 @@ 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();
                }
@@ -260,7 +271,7 @@ 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);