changes while testing

[mothur.git] / classifyseqscommand.h

diff --git a/classifyseqscommand.h b/classifyseqscommand.h
index 6d11d9236778028e326c6f4fdd4925dd6430fd50..59d9ee275800195255961639d77fb6c57d97f417 100644 (file)
--- a/classifyseqscommand.h
+++ b/classifyseqscommand.h
@@ -19,9 +19,11 @@
 #include "phylotree.h"
 #include "phylosummary.h"
 #include "knn.h"
+#include "kmertree.h"
+#include "aligntree.h"
 
 
-//KNN and Bayesian methods modeled from algorithms in
+//KNN and Wang methods modeled from algorithms in
 //Naı¨ve Bayesian Classifier for Rapid Assignment of rRNA Sequences 
 //into the New Bacterial Taxonomy􏰎† 
 //Qiong Wang,1 George M. Garrity,1,2 James M. Tiedje,1,2 and James R. Cole1* 
@@ -41,8 +43,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "classify.seqs";               }
        string getCommandCategory()             { return "Phylotype Analysis";  }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-7. [ for Bayesian classifier ] \nAltschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402. [ for BLAST ] \nDeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-72. [ for kmer ] \nhttp://www.mothur.org/wiki/Classify.seqs"; }
        string getDescription()         { return "classify sequences"; }
        
@@ -160,12 +163,16 @@ static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
                        inFASTA.seekg(pDataArray->start-1); pDataArray->m->gobble(inFASTA); 
                }
                
-               pDataArray->count = pDataArray->end;
-               
                //make classify
                Classify* myclassify;
+        string outputMethodTag = pDataArray->method + ".";
                if(pDataArray->method == "bayesian"){   myclassify = new Bayesian(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->cutoff, pDataArray->iters, pDataArray->threadID, pDataArray->flip, pDataArray->writeShortcuts);             }
                else if(pDataArray->method == "knn"){   myclassify = new Knn(pDataArray->taxonomyFileName, pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->numWanted, pDataArray->threadID);                           }
+        else if(pDataArray->method == "zap"){  
+            outputMethodTag = pDataArray->search + "_" + outputMethodTag;
+            if (pDataArray->search == "kmer") {   myclassify = new KmerTree(pDataArray->templateFileName, pDataArray->taxonomyFileName, pDataArray->kmerSize, pDataArray->cutoff); }
+            else {  myclassify = new AlignTree(pDataArray->templateFileName, pDataArray->taxonomyFileName, pDataArray->cutoff);  }
+        }
                else {
                        pDataArray->m->mothurOut(pDataArray->search + " is not a valid method option. I will run the command using bayesian.");
                        pDataArray->m->mothurOutEndLine();
@@ -174,7 +181,7 @@ static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
                
                if (pDataArray->m->control_pressed) { delete myclassify; return 0; }
                
-               int count = 0;
+               pDataArray->count = 0;
                for(int i = 0; i < pDataArray->end; i++){ //end is the number of sequences to process
                        
                        if (pDataArray->m->control_pressed) { delete myclassify; return 0; }
@@ -200,15 +207,15 @@ static DWORD WINAPI MyClassThreadFunction(LPVOID lpParam){
                                        
                                if (myclassify->getFlipped()) { outAcc << candidateSeq->getName() << endl; }
                                
-                               count++;
+                               pDataArray->count++;
                        }
                        delete candidateSeq;
                        //report progress
-                       if((count) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine();         }
+                       if((pDataArray->count) % 100 == 0){     pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(pDataArray->count)+"\n");       }
                        
                }
                //report progress
-               if((count) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine();         }
+               if((pDataArray->count) % 100 != 0){     pDataArray->m->mothurOutJustToScreen("Processing sequence: " + toString(pDataArray->count)+"\n");               }
                
                delete myclassify;
                inFASTA.close();