added classify.otu command

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index 5e7e78744e766d778bb9d6ce04fe244735fc81a3..94a60d4db9ff198423a401b74cbb7e78e9c010a5 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -118,8 +118,8 @@ void ClassifyOtuCommand::help(){
                m->mothurOut("The name parameter allows you add a names file with your taxonomy file.\n");
                m->mothurOut("The label parameter allows you to select what distance levels you would like a output files created for, and is separated by dashes.\n");
                m->mothurOut("The default value for label is all labels in your inputfile.\n");
-               m->mothurOut("The cutoff parameter allows you to specify a concensus confidence threshold for your taxonomy.  The default is 51, meaning 51%. Cutoff cannot be below 51.\n");
-               m->mothurOut("The probs parameter shuts off the outputting of the concensus confidence results. The default is true, meaning you want the confidence to be shown.\n");
+               m->mothurOut("The cutoff parameter allows you to specify a consensus confidence threshold for your taxonomy.  The default is 51, meaning 51%. Cutoff cannot be below 51.\n");
+               m->mothurOut("The probs parameter shuts off the outputting of the consensus confidence results. The default is true, meaning you want the confidence to be shown.\n");
                m->mothurOut("The classify.otu command should be in the following format: classify.otu(taxonomy=yourTaxonomyFile, list=yourListFile, name=yourNamesFile, label=yourLabels).\n");
                m->mothurOut("Example classify.otu(taxonomy=abrecovery.silva.full.taxonomy, list=abrecovery.fn.list, label=0.10).\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n");
@@ -293,7 +293,7 @@ int ClassifyOtuCommand::readTaxonomyFile() {
        }
 }
 //**********************************************************************************************************************
-string ClassifyOtuCommand::findConcensusTaxonomy(int bin, ListVector* thisList, int& size) {
+string ClassifyOtuCommand::findConsensusTaxonomy(int bin, ListVector* thisList, int& size) {
        try{
                string conTax = "";
                vector<string> names;
@@ -316,7 +316,7 @@ string ClassifyOtuCommand::findConcensusTaxonomy(int bin, ListVector* thisList,
                        it = taxMap.find(names[i]);
                        
                        if (it == taxMap.end()) { //this name is not in taxonomy file, skip it
-                               m->mothurOut(names[i] + " is not in your taxonomy file.  I will not include it in the concensus."); m->mothurOutEndLine();
+                               m->mothurOut(names[i] + " is not in your taxonomy file.  I will not include it in the consensus."); m->mothurOutEndLine();
                        }else{
                                
                                //if namesfile include the names
@@ -325,7 +325,7 @@ string ClassifyOtuCommand::findConcensusTaxonomy(int bin, ListVector* thisList,
                                        it2 = nameMap.find(names[i]);
                                        
                                        if (it2 == nameMap.end()) { //this name is not in name file, skip it
-                                               m->mothurOut(names[i] + " is not in your name file.  I will not include it in the concensus."); m->mothurOutEndLine();
+                                               m->mothurOut(names[i] + " is not in your name file.  I will not include it in the consensus."); m->mothurOutEndLine();
                                        }else{
                                                
                                                vector<string> nameFileNames;
@@ -371,11 +371,11 @@ string ClassifyOtuCommand::findConcensusTaxonomy(int bin, ListVector* thisList,
                        }
                                
                        //is this taxonomy above cutoff
-                       int concensusConfidence = ceil((bestChildSize / (float) size) * 100);
+                       int consensusConfidence = ceil((bestChildSize / (float) size) * 100);
                        
-                       if (concensusConfidence >= cutoff) { //if yes, add it
+                       if (consensusConfidence >= cutoff) { //if yes, add it
                                if (probs) {
-                                       conTax += bestChild.name + "(" + toString(concensusConfidence) + ");";
+                                       conTax += bestChild.name + "(" + toString(consensusConfidence) + ");";
                                }else{
                                        conTax += bestChild.name + ";";
                                }
@@ -396,7 +396,7 @@ string ClassifyOtuCommand::findConcensusTaxonomy(int bin, ListVector* thisList,
                        
        }
        catch(exception& e) {
-               m->errorOut(e, "ClassifyOtuCommand", "findConcensusTaxonomy");
+               m->errorOut(e, "ClassifyOtuCommand", "findConsensusTaxonomy");
                exit(1);
        }
 }
@@ -417,7 +417,7 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                
                //for each bin in the list vector
                for (int i = 0; i < processList->getNumBins(); i++) {
-                       conTax  = findConcensusTaxonomy(i, processList, size);
+                       conTax  = findConsensusTaxonomy(i, processList, size);
                        
                        if (m->control_pressed) { out.close();  return 0; }