changing command name classify.shared to classifyrf.shared

[mothur.git] / clustercommand.cpp

diff --git a/clustercommand.cpp b/clustercommand.cpp
index 93e29fd6e4daad8f09c6d373ba3b57e00ea55b52..94129654e1d2b11275e82d3a5da0382b1448efa9 100644 (file)
--- a/clustercommand.cpp
+++ b/clustercommand.cpp
@@ -29,6 +29,7 @@ vector<string> ClusterCommand::setParameters(){
                CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
                CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+        //CommandParameter padjust("adjust", "String", "", "F", "", "", "","",false,false); parameters.push_back(padjust);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
@@ -45,7 +46,8 @@ string ClusterCommand::getHelpString(){
        try {
                string helpString = "";
                helpString += "The cluster command parameter options are phylip, column, name, count, method, cuttoff, hard, precision, sim, showabund and timing. Phylip or column and name are required, unless you have a valid current file.\n";
-               helpString += "The cluster command should be in the following format: \n";
+               //helpString += "The adjust parameter is used to handle missing distances.  If you set a cutoff, adjust=f by default.  If not, adjust=t by default. Adjust=f, means ignore missing distances and adjust cutoff as needed with the average neighbor method.  Adjust=t, will treat missing distances as 1.0. You can also set the value the missing distances should be set to, adjust=0.5 would give missing distances a value of 0.5.\n";
+        helpString += "The cluster command should be in the following format: \n";
                helpString += "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
                helpString += "The acceptable cluster methods are furthest, nearest, average and weighted.  If no method is provided then average is assumed.\n";       
                return helpString;
@@ -229,10 +231,18 @@ ClusterCommand::ClusterCommand(string option)  {
                        temp = validParameter.validFile(parameters, "sim", false);                              if (temp == "not found") { temp = "F"; }
                        sim = m->isTrue(temp); 
                        
+            //bool cutoffSet = false;
                        temp = validParameter.validFile(parameters, "cutoff", false);
                        if (temp == "not found") { temp = "10"; }
+            //else { cutoffSet = true; }
                        m->mothurConvert(temp, cutoff); 
-                       cutoff += (5 / (precision * 10.0));  
+                       cutoff += (5 / (precision * 10.0));
+            
+            //temp = validParameter.validFile(parameters, "adjust", false);                            if (temp == "not found") { temp = "F"; }
+            //if (m->isNumeric1(temp))    { m->mothurConvert(temp, adjust);   }
+            //else if (m->isTrue(temp))   { adjust = 1.0;                     }
+            //else                        { adjust = -1.0;                    }
+            adjust=-1.0;
                        
                        method = validParameter.validFile(parameters, "method", false);
                        if (method == "not found") { method = "average"; }
@@ -305,7 +315,7 @@ int ClusterCommand::execute(){
             read->read(nameMap);
                }else if (countfile != "") {
             ct = new CountTable();
-            ct->readTable(countfile);
+            ct->readTable(countfile, false);
             read->read(ct);
         }else { read->read(nameMap); }
                
@@ -325,10 +335,10 @@ int ClusterCommand::execute(){
                }
                
                //create cluster
-               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);    }
+               if (method == "furthest")       {       cluster = new CompleteLinkage(rabund, list, matrix, cutoff, method, adjust); }
+               else if(method == "nearest"){   cluster = new SingleLinkage(rabund, list, matrix, cutoff, method, adjust); }
+               else if(method == "average"){   cluster = new AverageLinkage(rabund, list, matrix, cutoff, method, adjust);     }
+               else if(method == "weighted"){  cluster = new WeightedLinkage(rabund, list, matrix, cutoff, method, adjust);    }
                tag = cluster->getTag();
                
                if (outputDir == "") { outputDir += m->hasPath(distfile); }
@@ -336,10 +346,10 @@ int ClusterCommand::execute(){
                
         map<string, string> variables; 
         variables["[filename]"] = fileroot;
-        if (countfile != "") { variables["[tag2]"] = "unique_list"; }
         variables["[clustertag]"] = tag;
         string sabundFileName = getOutputFileName("sabund", variables);
         string rabundFileName = getOutputFileName("rabund", variables);
+        if (countfile != "") { variables["[tag2]"] = "unique_list"; }
         string listFileName = getOutputFileName("list", variables);
         
         if (countfile == "") {