X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=phylotree.cpp;h=2e3136e1f42e1a93d15fcab921b2e612f55f3997;hb=e9a30aafc8985389dd99301ca6f2898f52c4d214;hp=8a7c712b0f255db20da492fd95bc15d3116ce151;hpb=159fd324dfecacb6617669246d85c787ae67f630;p=mothur.git

diff --git a/phylotree.cpp b/phylotree.cpp
index 8a7c712..2e3136e 100644
--- a/phylotree.cpp
+++ b/phylotree.cpp
@@ -233,6 +233,48 @@ string PhyloTree::getNextTaxon(string& heirarchy, string seqname){
 		exit(1);
 	}
 }
+/**************************************************************************************************/
+
+vector<string> PhyloTree::getSeqs(string seqTaxonomy){
+	try {
+        string taxCopy = seqTaxonomy;
+        vector<string> names;
+        map<string, int>::iterator childPointer;
+		
+		int currentNode = 0;
+
+        m->removeConfidences(seqTaxonomy);
+        
+        string taxon;
+        while(seqTaxonomy != ""){
+			
+			if (m->control_pressed) { return names; }
+			
+			taxon = getNextTaxon(seqTaxonomy, "");
+            
+            if (m->debug) { m->mothurOut(taxon +'\n'); }
+			
+			if (taxon == "") {  m->mothurOut(taxCopy + " has an error in the taxonomy.  This may be due to a ;;"); m->mothurOutEndLine(); break;  }
+			
+			childPointer = tree[currentNode].children.find(taxon);
+			
+			if(childPointer != tree[currentNode].children.end()){	//if the node already exists, move on
+				currentNode = childPointer->second;
+			}
+			else{											//otherwise, error this taxonomy is not in tree
+				m->mothurOut("[ERROR]: " + taxCopy + " is not in taxonomy tree, please correct."); m->mothurOutEndLine(); m->control_pressed = true; return names;
+			}
+            
+			if (seqTaxonomy == "") {   names = tree[currentNode].accessions;	}
+		}
+        
+        return names;
+    }
+	catch(exception& e) {
+		m->errorOut(e, "PhyloTree", "getSeqs");
+		exit(1);
+	}
+}
 
 /**************************************************************************************************/
 
@@ -259,6 +301,8 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
 			//somehow the parent is getting one too many accnos
 			//use print to reassign the taxa id
 			taxon = getNextTaxon(seqTaxonomy, seqName);
+            
+            if (m->debug) { m->mothurOut(seqName +'\t' + taxon +'\n'); }
 			
 			if (taxon == "") {  m->mothurOut(seqName + " has an error in the taxonomy.  This may be due to a ;;"); m->mothurOutEndLine(); if (currentNode != 0) {  uniqueTaxonomies.insert(currentNode); } break;  }
 			
@@ -341,6 +385,9 @@ void PhyloTree::assignHeirarchyIDs(int index){
 		int counter = 1;
 		
 		for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
+            
+            if (m->debug) { m->mothurOut(toString(index) +'\t' + tree[it->second].name +'\n'); }
+                
 			tree[it->second].heirarchyID = tree[index].heirarchyID + '.' + toString(counter);
 			counter++;
 			tree[it->second].level = tree[index].level + 1;
@@ -399,6 +446,8 @@ void PhyloTree::binUnclassified(string file){
 			}
 		}
 		
+        if (m->debug) { m->mothurOut("maxLevel = " + toString(maxLevel) +'\n'); }
+        
 		int copyNodes = copy.size();
 	
 		//go through the seqs and if a sequence finest taxon is not the same level as the most finely defined taxon then classify it as unclassified where necessary
@@ -409,11 +458,14 @@ void PhyloTree::binUnclassified(string file){
 			
 			int level = copy[itLeaf->second].level;
 			int currentNode = itLeaf->second;
+            
+            if (m->debug) { m->mothurOut(copy[currentNode].name +'\n'); }
 			
 			//this sequence is unclassified at some levels
 			while(level < maxLevel){
 		
 				level++;
+                if (m->debug) { m->mothurOut("level = " + toString(level) +'\n'); }
 			
 				string taxon = "unclassified";