added count file to get.groups and remove.groups. added shortcut parameter to classif...

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 43a021ee7d94e9d0638a4cbf2154717f8d9d3e89..bab774012f20283e12b43606349b5b519721f0b7 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -34,6 +34,7 @@ vector<string> ClassifySeqsCommand::setParameters(){
                CommandParameter pprobs("probs", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pprobs);
                CommandParameter piters("iters", "Number", "", "100", "", "", "",false,true); parameters.push_back(piters);
                CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
+        CommandParameter pshortcuts("shortcuts", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pshortcuts);
                CommandParameter pnumwanted("numwanted", "Number", "", "10", "", "", "",false,true); parameters.push_back(pnumwanted);
                CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
                CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
@@ -557,6 +558,9 @@ ClassifySeqsCommand::ClassifySeqsCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "probs", false);            if (temp == "not found"){       temp = "true";                  }
                        probs = m->isTrue(temp);
+            
+            temp = validParameter.validFile(parameters, "shortcuts", false);   if (temp == "not found"){       temp = "true";                  }
+                       writeShortcuts = m->isTrue(temp);
                        
                        //temp = validParameter.validFile(parameters, "flip", false);                   if (temp == "not found"){       temp = "T";                             }
                        //flip = m->isTrue(temp); 
@@ -601,12 +605,12 @@ int ClassifySeqsCommand::execute(){
        try {
                if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
         
-               if(method == "bayesian"){       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip);             }
+               if(method == "bayesian"){       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip, writeShortcuts);             }
                else if(method == "knn"){       classify = new Knn(taxonomyFileName, templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, numWanted, rand());                               }
                else {
                        m->mothurOut(search + " is not a valid method option. I will run the command using bayesian.");
                        m->mothurOutEndLine();
-                       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip);     
+                       classify = new Bayesian(taxonomyFileName, templateFileName, search, kmerSize, cutoff, iters, rand(), flip, writeShortcuts);     
                }
                
                if (m->control_pressed) { delete classify; return 0; }
@@ -1004,7 +1008,7 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
                        string extension = "";
                        if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
                        
-                       classifyData* tempclass = new classifyData((accnos + extension), probs, method, templateFileName, taxonomyFileName, (taxFileName + extension), (tempTaxFile + extension), filename, search, kmerSize, iters, numWanted, m, lines[i]->start, lines[i]->end, match, misMatch, gapOpen, gapExtend, cutoff, i, flip);
+                       classifyData* tempclass = new classifyData((accnos + extension), probs, method, templateFileName, taxonomyFileName, (taxFileName + extension), (tempTaxFile + extension), filename, search, kmerSize, iters, numWanted, m, lines[i]->start, lines[i]->end, match, misMatch, gapOpen, gapExtend, cutoff, i, flip, writeShortcuts);
                        pDataArray.push_back(tempclass);
                        
                        //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.