added save parameter to align.seqs, chimera commands, classify.seqs, and seq.error...

[mothur.git] / bayesian.cpp

diff --git a/bayesian.cpp b/bayesian.cpp
index cf55d5c585ee2c7c2ca6534f7192996f2ef34d02..0b55efd3258fe036ec0d12955786f6d61b798c5c 100644 (file)
--- a/bayesian.cpp
+++ b/bayesian.cpp
@@ -10,15 +10,22 @@
 #include "bayesian.h"
 #include "kmer.hpp"
 #include "phylosummary.h"
-
+#include "referencedb.h"
 /**************************************************************************************************/
 Bayesian::Bayesian(string tfile, string tempFile, string method, int ksize, int cutoff, int i) : 
 Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
        try {
+               ReferenceDB* rdb = ReferenceDB::getInstance();
+               
+               string baseName = tempFile;
+               if (baseName == "saved") { baseName = rdb->getSavedReference(); }
+               
+               string baseTName = tfile;
+               if (baseTName == "saved") { baseTName = rdb->getSavedTaxonomy(); }
                
                /************calculate the probablity that each word will be in a specific taxonomy*************/
-               string tfileroot = tfile.substr(0,tfile.find_last_of(".")+1);
-               string tempfileroot = m->getRootName(m->getSimpleName(tempFile));
+               string tfileroot = baseTName.substr(0,baseTName.find_last_of(".")+1);
+               string tempfileroot = m->getRootName(m->getSimpleName(baseName));
                string phyloTreeName = tfileroot + "tree.train";
                string phyloTreeSumName = tfileroot + "tree.sum";
                string probFileName = tfileroot + tempfileroot + char('0'+ kmerSize) + "mer.prob";
@@ -40,7 +47,23 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                        FilesGood = checkReleaseDate(probFileTest, probFileTest2, phyloTreeTest, probFileTest3);
                }
                
+               //if you want to save, but you dont need to calculate then just read
+               if (rdb->save && probFileTest && probFileTest2 && phyloTreeTest && probFileTest3 && FilesGood) {  
+                       ifstream saveIn;
+                       m->openInputFile(tempFile, saveIn);
+                       
+                       while (!saveIn.eof()) {
+                               Sequence temp(saveIn);
+                               m->gobble(saveIn);
+                               
+                               rdb->referenceSeqs.push_back(temp); 
+                       }
+                       saveIn.close();                 
+               }
+               
                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(); }
+                       
                        m->mothurOut("Reading template taxonomy...     "); cout.flush();
                        
                        phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
@@ -49,10 +72,17 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                        
                        genusNodes = phyloTree->getGenusNodes(); 
                        genusTotals = phyloTree->getGenusTotals();
-               
-                       m->mothurOut("Reading template probabilities...     "); cout.flush();
-                       readProbFile(probFileTest, probFileTest2, probFileName, probFileName2); 
                        
+                       if (tfile == "saved") { 
+                               m->mothurOutEndLine();  m->mothurOut("Using probabilties from " + rdb->getSavedTaxonomy() + " that are saved in memory...    ");        cout.flush();; 
+                               wordGenusProb = rdb->wordGenusProb;
+                       }else {
+                               m->mothurOut("Reading template probabilities...     "); cout.flush();
+                               readProbFile(probFileTest, probFileTest2, probFileName, probFileName2);
+                       }       
+                       
+                       //save probabilities
+                       if (rdb->save) { rdb->wordGenusProb = wordGenusProb; }
                }else{
                
                        //create search database and names vector
@@ -194,6 +224,9 @@ Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i)  {
                                delete phyloTree;
                                
                                phyloTree = new PhyloTree(phyloTreeTest, phyloTreeName);
+                               
+                               //save probabilities
+                               if (rdb->save) { rdb->wordGenusProb = wordGenusProb; }
                        }
                }