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

[mothur.git] / bayesian.cpp

diff --git a/bayesian.cpp b/bayesian.cpp
index 1dc38337aef1bcc3b695ff56e86061cdab58c13d..bccf0ce0dda18501c129b7604546f4e9fc43382b 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -12,13 +12,14 @@
 #include "phylosummary.h"
 #include "referencedb.h"
 /**************************************************************************************************/
-Bayesian::Bayesian(string tfile, string tempFile, string method, int ksize, int cutoff, int i, int tid, bool f) : 
+Bayesian::Bayesian(string tfile, string tempFile, string method, int ksize, int cutoff, int i, int tid, bool f, bool sh) : 
 Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
        try {
                ReferenceDB* rdb = ReferenceDB::getInstance();
                
                threadID = tid;
                flip = f;
+        shortcuts = sh;
                string baseName = tempFile;
                        
                if (baseName == "saved") { baseName = rdb->getSavedReference(); }
@@ -63,7 +64,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
                        }
                        saveIn.close();                 
                }
-               
+FilesGood = false;
                if(probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood){       
                        if (tempFile == "saved") { m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory.");     m->mothurOutEndLine(); }
                        
@@ -113,7 +114,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
                                WordPairDiffArr.resize(numKmers);
                        
                                for (int j = 0; j < wordGenusProb.size(); j++) {        wordGenusProb[j].resize(genusNodes.size());             }
-                    ofstream out;
+                ofstream out;
                                ofstream out2;
                                
                                #ifdef USE_MPI
@@ -124,17 +125,19 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
                                #endif
 
                                
-                               m->openOutputFile(probFileName, out);
+                if (shortcuts) { 
+                    m->openOutputFile(probFileName, out); 
                                
-                               //output mothur version
-                               out << "#" << m->getVersion() << endl;
+                    //output mothur version
+                    out << "#" << m->getVersion() << endl;
                                
-                               out << numKmers << endl;
+                    out << numKmers << endl;
                                
-                               m->openOutputFile(probFileName2, out2);
+                    m->openOutputFile(probFileName2, out2);
                                
-                               //output mothur version
-                               out2 << "#" << m->getVersion() << endl;
+                    //output mothur version
+                    out2 << "#" << m->getVersion() << endl;
+                }
                                
                                #ifdef USE_MPI
                                        }
@@ -151,7 +154,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
                                                if (pid == 0) {  
                                        #endif
 
-                                       out << i << '\t';
+                    if (shortcuts) {  out << i << '\t'; }
                                        
                                        #ifdef USE_MPI
                                                }
@@ -188,7 +191,7 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
                                                                if (pid == 0) {  
                                                        #endif
 
-                                                       out << k << '\t' << wordGenusProb[i][k] << '\t' ; 
+                            if (shortcuts) { out << k << '\t' << wordGenusProb[i][k] << '\t' ; }
                                                        
                                                        #ifdef USE_MPI
                                                                }
@@ -204,8 +207,10 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
                                                if (pid == 0) {  
                                        #endif
                                        
-                                       out << endl;
-                                       out2 << probabilityInTemplate << '\t' << numNotZero << '\t' << log(probabilityInTemplate) << endl;
+                            if (shortcuts) { 
+                                out << endl;
+                                out2 << probabilityInTemplate << '\t' << numNotZero << '\t' << log(probabilityInTemplate) << endl;
+                            }
                                        
                                        #ifdef USE_MPI
                                                }
@@ -218,9 +223,10 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
                                        if (pid == 0) {  
                                #endif
                                
-                               out.close();
-                               out2.close();
-                               
+                        if (shortcuts) { 
+                            out.close();
+                            out2.close();
+                        }
                                #ifdef USE_MPI
                                        }
                                #endif