Fixes taxon_unclassified bug

mothur · ee7be1e0724f2cfe7f3346c83bda6d5e84263bb0 · mothur-westcott committed Sep 14, 2016 · Sep 14, 2016 · ee7be1e
1 parent 32aafff
commit ee7be1e0724f2cfe7f3346c83bda6d5e84263bb0
Unified Split

Showing with 17 additions and 14 deletions.

+11 −11 source/classifier/phylosummary.cpp

+1 −1 source/commands/classifyseqscommand.cpp

+5 −2 source/mothurout.cpp
diff --git a/source/classifier/phylosummary.cpp b/source/classifier/phylosummary.cpp
@@ -177,6 +177,8 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
 		
 		while (seqTaxonomy != "") {
 			
+            level++;
+            
 			if (m->control_pressed) { return 0; }
 			
 			//somehow the parent is getting one too many accnos
@@ -287,12 +289,10 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
 					break;
 				}
 			}
-			
-			level++;
-            
-            if (level > maxLevel) { maxLevel = level; }
-			
         }
+        
+        if (level > maxLevel) { maxLevel = level; }
+        
 		return 0;
 	}
 	catch(exception& e) {
@@ -318,6 +318,8 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, map<string, bool> containsGro
 		
 		while (seqTaxonomy != "") {
 			
+            level++;
+            
 			if (m->control_pressed) { return 0; }
 			
 			//somehow the parent is getting one too many accnos
@@ -343,7 +345,7 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, map<string, bool> containsGro
 					int index = tree.size() - 1;
 					
 					tree[index].parent = currentNode;
-					tree[index].level = (level+1);
+					tree[index].level = level;
 					tree[index].total = 1;
 					tree[currentNode].children[taxon] = index;
 						
@@ -360,12 +362,10 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, map<string, bool> containsGro
 					break;
 				}
 			}
-			
-			level++;
-            
-            if (level > maxLevel) { maxLevel = level; }
-			
 		}
+        
+        if (level > maxLevel) { maxLevel = level; }
+        
 		return 0;
 	}
 	catch(exception& e) {
diff --git a/source/commands/classifyseqscommand.cpp b/source/commands/classifyseqscommand.cpp
@@ -748,7 +748,7 @@ int ClassifySeqsCommand::execute(){
             outTax.close();
             
             m->mothurRemove(newTaxonomyFile);
-            rename(unclass.c_str(), newTaxonomyFile.c_str());
+            m->renameFile(unclass, newTaxonomyFile);
             
             if (m->control_pressed) {  outputTypes.clear(); if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);	} delete classify; return 0; }
             
diff --git a/source/mothurout.cpp b/source/mothurout.cpp
@@ -3434,13 +3434,16 @@ bool MothurOut::mothurConvert(string item, intDist& num){
 string MothurOut::addUnclassifieds(string tax, int maxlevel, bool probs) {
     try{
         string newTax, taxon;
-        int level = 1;
         
+        string savedTax = tax;
         vector<string> taxons; splitAtChar(tax, taxons, ';'); taxons.pop_back();
         vector<int> confidences;
         
+        if (taxons.size() == maxlevel) { return savedTax; }
+        
         int index = 0;
         int confidence = 0;
+        int level = 1;
         for (int i = 0; i < taxons.size(); i++) {
             index = i;
             string thisTax = taxons[i]+";";
@@ -3450,7 +3453,7 @@ string MothurOut::addUnclassifieds(string tax, int maxlevel, bool probs) {
             if (thisTax == "unclassified;"){ index--; break; }
             else{ newTax += taxons[i] + ";";  }
         }
-        level = index+2;
+        level = index+1;
         
         string thisTax = taxons[index]+";";