X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=classify.cpp;h=36179f471da4ac5d40b563e609feb2f8d3d32e6c;hp=7726b3e00cca9de19971b70656f9581e43e97c8a;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=05c52893c6c2467381fe7e7b769d86b6209af2e1

diff --git a/classify.cpp b/classify.cpp
index 7726b3e..36179f4 100644
--- a/classify.cpp
+++ b/classify.cpp
@@ -23,7 +23,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 		if (tfile == "saved") { tfile = rdb->getSavedTaxonomy(); }
 		
 		taxFile = tfile;
-		readTaxonomy(taxFile);	
+		
 		int numSeqs = 0;
 		
 		if (tempFile == "saved") {
@@ -61,7 +61,8 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 					names.push_back(temp.getName());
 					database->addSequence(temp);	
 				}
-				database->generateDB();
+				if ((method == "kmer") && (!shortcuts)) {;} //don't print
+                else {database->generateDB(); }
 			}else if ((method == "kmer") && (!needToGenerate)) {	
 				ifstream kmerFileTest(kmerDBName.c_str());
 				database->readKmerDB(kmerFileTest);	
@@ -73,11 +74,6 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 			
 			database->setNumSeqs(numSeqs);
 			
-			//sanity check
-			bool okay = phyloTree->ErrorCheck(names);
-			
-			if (!okay) { m->control_pressed = true; }
-			
 			m->mothurOut("It took " + toString(time(NULL) - start) + " to load " + toString(rdb->referenceSeqs.size()) + " sequences and generate the search databases.");m->mothurOutEndLine();  
 			
 		}else {
@@ -200,7 +196,8 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 				}
 				fastaFile.close();
 
-				database->generateDB();
+                if ((method == "kmer") && (!shortcuts)) {;} //don't print
+                else {database->generateDB(); } 
 				
 			}else if ((method == "kmer") && (!needToGenerate)) {	
 				ifstream kmerFileTest(kmerDBName.c_str());
@@ -219,18 +216,19 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 				fastaFile.close();
 			}
 	#endif	
-		
+            	
 			database->setNumSeqs(names.size());
 			
-			//sanity check
-			bool okay = phyloTree->ErrorCheck(names);
-			
-			if (!okay) { m->control_pressed = true; }
-			
 			m->mothurOut("DONE."); m->mothurOutEndLine();
 			m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();
 		}
-
+        
+        readTaxonomy(taxFile);
+        
+        //sanity check
+        bool okay = phyloTree->ErrorCheck(names);
+        
+        if (!okay) { m->control_pressed = true; }
 	}
 	catch(exception& e) {
 		m->errorOut(e, "Classify", "generateDatabaseAndNames");
@@ -238,7 +236,7 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
 	}
 }
 /**************************************************************************************************/
-Classify::Classify() {		m = MothurOut::getInstance();	database = NULL;	flipped=false; }
+Classify::Classify() {		m = MothurOut::getInstance();	database = NULL;	phyloTree=NULL; flipped=false; }
 /**************************************************************************************************/
 
 int Classify::readTaxonomy(string file) {
@@ -260,9 +258,6 @@ int Classify::readTaxonomy(string file) {
 		MPI_File inMPI;
 		MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 		MPI_Comm_size(MPI_COMM_WORLD, &processors);
-
-		//char* inFileName = new char[file.length()];
-		//memcpy(inFileName, file.c_str(), file.length());
 		
 		char inFileName[1024];
 		strcpy(inFileName, file.c_str());
@@ -300,34 +295,31 @@ int Classify::readTaxonomy(string file) {
 			iss >> name; m->gobble(iss);
             iss >> taxInfo;
             if (m->debug) { m->mothurOut("[DEBUG]: name = " + name + " tax = " + taxInfo + "\n"); }
-			taxonomy[name] = taxInfo;
-			phyloTree->addSeqToTree(name, taxInfo);
-		}
+			if (m->inUsersGroups(name, names)) {
+                taxonomy[name] = taxInfo;
+                phyloTree->addSeqToTree(name, taxInfo);
+            }else {
+                m->mothurOut("[WARNING]: " + name + " is in your taxonomy file and not in your reference file, ignoring.\n");
+            }		
+        }
 		
 		MPI_File_close(&inMPI);
 		MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
-#else				
-		ifstream inTax;
-		m->openInputFile(file, inTax);
-	
-		//read template seqs and save
-		while (!inTax.eof()) {
-			inTax >> name; m->gobble(inTax);
-            inTax >> taxInfo;
-            
-            if (m->debug) {  m->mothurOut("[DEBUG]: name = '" + name + "' tax = '" + taxInfo + "'\n");  }
-
-			taxonomy[name] = taxInfo;
-			
-			phyloTree->addSeqToTree(name, taxInfo);
-		
-			m->gobble(inTax);
-		}
-		inTax.close();
-#endif	
+#else	
         
-        
-	
+        taxonomy.clear(); 
+        m->readTax(file, taxonomy);
+        map<string, string> tempTaxonomy;
+        for (map<string, string>::iterator itTax = taxonomy.begin(); itTax != taxonomy.end(); itTax++) {  
+            if (m->inUsersGroups(itTax->first, names)) {
+                phyloTree->addSeqToTree(itTax->first, itTax->second); 
+                tempTaxonomy[itTax->first] = itTax->second;
+            }else {
+                m->mothurOut("[WARNING]: " + itTax->first + " is in your taxonomy file and not in your reference file, ignoring.\n");
+            }
+        }
+        taxonomy = tempTaxonomy;
+#endif	
 		phyloTree->assignHeirarchyIDs(0);
 		
 		phyloTree->setUp(file);
@@ -371,3 +363,37 @@ vector<string> Classify::parseTax(string tax) {
 }
 /**************************************************************************************************/
 
+double Classify::getLogExpSum(vector<double> probabilities, int& maxIndex){
+	try {
+        //	http://jblevins.org/notes/log-sum-exp
+        
+        double maxProb = probabilities[0];
+        maxIndex = 0;
+        
+        int numProbs = (int)probabilities.size();
+        
+        for(int i=1;i<numProbs;i++){
+            if(probabilities[i] >= maxProb){
+                maxProb = probabilities[i];
+                maxIndex = i;
+            }
+        }
+        
+        double probSum = 0.0000;
+        
+        for(int i=0;i<numProbs;i++){
+            probSum += exp(probabilities[i] - maxProb);		
+        }
+        
+        probSum = log(probSum) + maxProb;
+        
+        return probSum;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "Classify", "getLogExpSum");
+		exit(1);
+	}
+}
+
+/**************************************************************************************************/
+