Merge pull request #271 from mothur/TaxSpaces_265

Tax spaces 265
mothur · a23ea7d307cbf3eaea4d05756701966750df9862 · mothur-westcott committed on GitHub Sep 12, 2016 · Sep 12, 2016 · a23ea7d
2 parents bfc09fe + 822ba85
commit a23ea7d307cbf3eaea4d05756701966750df9862
diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
@@ -12,7 +12,6 @@
 		219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */; };
 		480E8DB11CAB12ED00A0D137 /* testfastqread.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 480E8DAF1CAB12ED00A0D137 /* testfastqread.cpp */; };
 		480E8DB21CAB1F5E00A0D137 /* vsearchfileparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 489B55701BCD7F0100FB7DC8 /* vsearchfileparser.cpp */; };
-		480E8DB31CAB1F7900A0D137 /* averagelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 2114A7671C654D7400D3D8D9 /* averagelinkage.cpp */; };
 		481623E21B56A2DB004C60B7 /* pcrseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 481623E11B56A2DB004C60B7 /* pcrseqscommand.cpp */; };
 		481FB51C1AC0A63E0076CFF3 /* main.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 481FB51B1AC0A63E0076CFF3 /* main.cpp */; };
 		481FB5261AC0ADA00076CFF3 /* sequence.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7E9B7DB12D37EC400DA6239 /* sequence.cpp */; };
@@ -373,7 +372,6 @@
 		48705AC619BE32C50075E977 /* mergesfffilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48705ABF19BE32C50075E977 /* mergesfffilecommand.cpp */; };
 		48705AC719BE32C50075E977 /* sharedrjsd.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48705AC119BE32C50075E977 /* sharedrjsd.cpp */; };
 		487C5A871AB88B93002AF48A /* mimarksattributescommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 487C5A851AB88B93002AF48A /* mimarksattributescommand.cpp */; };
-		487D09EB1CB2CEF3007039BF /* vsearchfileparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 489B55701BCD7F0100FB7DC8 /* vsearchfileparser.cpp */; };
 		487D09EC1CB2CEFE007039BF /* averagelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 2114A7671C654D7400D3D8D9 /* averagelinkage.cpp */; };
 		488841611CC515A000C5E972 /* (null) in Sources */ = {isa = PBXBuildFile; };
 		488841621CC515A000C5E972 /* (null) in Sources */ = {isa = PBXBuildFile; };
@@ -401,6 +399,7 @@
 		48DB37B41B3B27E000C372A4 /* makefilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48DB37B11B3B27E000C372A4 /* makefilecommand.cpp */; };
 		48E981CF189C38FB0042BE9D /* (null) in Sources */ = {isa = PBXBuildFile; };
 		48EDB76C1D1320DD00F76E93 /* chimeravsearchcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48EDB76A1D1320DD00F76E93 /* chimeravsearchcommand.cpp */; };
+		48F06CCD1D74BEC4004A45DD /* testphylotree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48F06CCB1D74BEC4004A45DD /* testphylotree.cpp */; };
 		48F98E4D1A9CFD670005E81B /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48F98E4C1A9CFD670005E81B /* completelinkage.cpp */; };
 		7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */; };
 		835FE03D19F00640005AA754 /* classifysvmsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7B2181FE17AD777B00286E6A /* classifysvmsharedcommand.cpp */; };
@@ -853,6 +852,8 @@
 		48DB37B21B3B27E000C372A4 /* makefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = makefilecommand.h; path = source/commands/makefilecommand.h; sourceTree = SOURCE_ROOT; };
 		48EDB76A1D1320DD00F76E93 /* chimeravsearchcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = chimeravsearchcommand.cpp; path = source/commands/chimeravsearchcommand.cpp; sourceTree = SOURCE_ROOT; };
 		48EDB76B1D1320DD00F76E93 /* chimeravsearchcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = chimeravsearchcommand.h; path = source/commands/chimeravsearchcommand.h; sourceTree = SOURCE_ROOT; };
+		48F06CCB1D74BEC4004A45DD /* testphylotree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = testphylotree.cpp; path = testclassifier/testphylotree.cpp; sourceTree = "<group>"; };
+		48F06CCC1D74BEC4004A45DD /* testphylotree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; name = testphylotree.hpp; path = testclassifier/testphylotree.hpp; sourceTree = "<group>"; };
 		48F98E4C1A9CFD670005E81B /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = completelinkage.cpp; path = source/completelinkage.cpp; sourceTree = SOURCE_ROOT; };
 		7B2181FE17AD777B00286E6A /* classifysvmsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = classifysvmsharedcommand.cpp; path = source/commands/classifysvmsharedcommand.cpp; sourceTree = SOURCE_ROOT; };
 		7B2181FF17AD777B00286E6A /* classifysvmsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = classifysvmsharedcommand.h; path = source/commands/classifysvmsharedcommand.h; sourceTree = SOURCE_ROOT; };
@@ -1718,6 +1719,7 @@
 			children = (
 				481FB5201AC0A6B60076CFF3 /* catch.hpp */,
 				481FB51B1AC0A63E0076CFF3 /* main.cpp */,
+				48F06CCA1D74BC6F004A45DD /* testclassifier */,
 				48D6E9691CA4262A008DF76B /* dataset.cpp */,
 				48D6E96A1CA4262A008DF76B /* dataset.h */,
 				4827A4DA1CB3ED2100345170 /* fastqdataset.cpp */,
@@ -1763,6 +1765,15 @@
 			name = testcontainers;
 			sourceTree = "<group>";
 		};
+		48F06CCA1D74BC6F004A45DD /* testclassifier */ = {
+			isa = PBXGroup;
+			children = (
+				48F06CCB1D74BEC4004A45DD /* testphylotree.cpp */,
+				48F06CCC1D74BEC4004A45DD /* testphylotree.hpp */,
+			);
+			name = testclassifier;
+			sourceTree = "<group>";
+		};
 		7B17437A17AF6F02004C161B /* svm */ = {
 			isa = PBXGroup;
 			children = (
@@ -2537,7 +2548,7 @@
 		08FB7793FE84155DC02AAC07 /* Project object */ = {
 			isa = PBXProject;
 			attributes = {
-				LastUpgradeCheck = 0620;
+				LastUpgradeCheck = 0730;
 				ORGANIZATIONNAME = "Schloss Lab";
 				TargetAttributes = {
 					481FB5181AC0A63E0076CFF3 = {
@@ -2796,6 +2807,7 @@
 				481FB5351AC1B5D90076CFF3 /* fasta.cpp in Sources */,
 				481FB6321AC1B7EA0076CFF3 /* groupmap.cpp in Sources */,
 				481FB5FF1AC1B7970076CFF3 /* removeseqscommand.cpp in Sources */,
+				48F06CCD1D74BEC4004A45DD /* testphylotree.cpp in Sources */,
 				481FB6771AC1B88F0076CFF3 /* readcluster.cpp in Sources */,
 				481FB5831AC1B6FF0076CFF3 /* ccode.cpp in Sources */,
 				481FB5681AC1B6B20076CFF3 /* sharedochiai.cpp in Sources */,
@@ -2852,11 +2864,9 @@
 				481FB6731AC1B8820076CFF3 /* seqnoise.cpp in Sources */,
 				481FB5DC1AC1B75C0076CFF3 /* makelookupcommand.cpp in Sources */,
 				481FB53D1AC1B5F80076CFF3 /* bstick.cpp in Sources */,
-				480E8DB31CAB1F7900A0D137 /* averagelinkage.cpp in Sources */,
 				481FB6681AC1B8450076CFF3 /* rarecalc.cpp in Sources */,
 				481FB60B1AC1B7AC0076CFF3 /* sffmultiplecommand.cpp in Sources */,
 				481FB59F1AC1B71B0076CFF3 /* classifyrfsharedcommand.cpp in Sources */,
-				487D09EB1CB2CEF3007039BF /* vsearchfileparser.cpp in Sources */,
 				481FB5F51AC1B77E0076CFF3 /* primerdesigncommand.cpp in Sources */,
 				481FB5B41AC1B7300076CFF3 /* distancecommand.cpp in Sources */,
 				481FB5391AC1B5E90076CFF3 /* ace.cpp in Sources */,
@@ -3395,6 +3405,7 @@
 			buildSettings = {
 				CLANG_WARN_UNREACHABLE_CODE = YES;
 				DEPLOYMENT_LOCATION = NO;
+				ENABLE_TESTABILITY = YES;
 				GCC_C_LANGUAGE_STANDARD = c11;
 				GCC_ENABLE_SSE3_EXTENSIONS = NO;
 				GCC_ENABLE_SSE41_EXTENSIONS = NO;
@@ -3521,7 +3532,7 @@
 				MTL_ENABLE_DEBUG_INFO = YES;
 				ONLY_ACTIVE_ARCH = YES;
 				PRODUCT_NAME = "$(TARGET_NAME)";
-				SDKROOT = macosx10.9;
+				SDKROOT = macosx;
 			};
 			name = Debug;
 		};
@@ -3558,7 +3569,7 @@
 				MTL_ENABLE_DEBUG_INFO = NO;
 				ONLY_ACTIVE_ARCH = YES;
 				PRODUCT_NAME = "$(TARGET_NAME)";
-				SDKROOT = macosx10.9;
+				SDKROOT = macosx;
 			};
 			name = Release;
 		};
diff --git a/TestMothur/main.cpp b/TestMothur/main.cpp
@@ -19,7 +19,6 @@ To compile TestMothur you need to uncomment
  
  //MothurOut* MothurOut::_uniqueInstance; in mothurout.cpp
  
- //ReferenceDB* ReferenceDB::myInstance; in referencedb.cpp
  
  */
 //***********************************************************//
diff --git a/TestMothur/testclassifier/testphylotree.cpp b/TestMothur/testclassifier/testphylotree.cpp
@@ -0,0 +1,129 @@
+//
+//  testphylotree.cpp
+//  Mothur
+//
+//  Created by Sarah Westcott on 8/29/16.
+//  Copyright © 2016 Schloss Lab. All rights reserved.
+//
+
+#include "catch.hpp"
+#include "testphylotree.hpp"
+
+/**************************************************************************************************/
+TestPhyloTree::TestPhyloTree() {  //setup
+    m = MothurOut::getInstance();
+    
+    string tax1WithSpaces = "Bacteria(100);Bacteroidetes 7(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);";
+    string tax2WithSpaces = "Bacteria(100);Bacteroidetes 7(100);Bacteroidia(98);Bacteroidales(98);Bacteroidaceae(98);Bacteroides(98);";
+    string tax3WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Lachnospiraceae(100);Blautia(92);";
+    string tax4WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);";
+    string tax5WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Lachnospiraceae(100);Incertae_Sedis(97);";
+    
+    string tax1WithOutSpaces = "Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);";
+    string tax2WithOutSpaces = "Bacteria(100);Bacteroidetes(100);Bacteroidia(98);Bacteroidales(98);Bacteroidaceae(98);Bacteroides(98);";
+    string tax3WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(92);";
+    string tax4WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);";
+    string tax5WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Incertae_Sedis(97);";
+    
+    phylo.addSeqToTree("seq1", tax1WithSpaces);
+    phylo.addSeqToTree("seq2", tax2WithSpaces);
+    phylo.addSeqToTree("seq3", tax3WithSpaces);
+    phylo.addSeqToTree("seq4", tax4WithSpaces);
+    phylo.addSeqToTree("seq5", tax5WithSpaces);
+    phylo.addSeqToTree("seq6", tax1WithOutSpaces);
+    phylo.addSeqToTree("seq7", tax2WithOutSpaces);
+    phylo.addSeqToTree("seq8", tax3WithOutSpaces);
+    phylo.addSeqToTree("seq9", tax4WithOutSpaces);
+    phylo.addSeqToTree("seq10", tax5WithOutSpaces);
+}
+/**************************************************************************************************/
+TestPhyloTree::~TestPhyloTree() {}
+/**************************************************************************************************/
+
+TEST_CASE("Testing PhyloTree Class") {
+    TestPhyloTree testPTree;
+    
+    string tax1WithSpaces = "Bacteria(100);Bacteroidetes 7(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);";
+    string tax2WithSpaces = "Bacteria(100);Bacteroidetes 7(100);Bacteroidia(98);Bacteroidales(98);Bacteroidaceae(98);Bacteroides(98);";
+    string tax3WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Lachnospiraceae(100);Blautia(92);";
+    string tax4WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);";
+    string tax5WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Lachnospiraceae(100);Incertae_Sedis(97);";
+    
+    string tax1WithOutSpaces = "Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);";
+    string tax2WithOutSpaces = "Bacteria(100);Bacteroidetes(100);Bacteroidia(98);Bacteroidales(98);Bacteroidaceae(98);Bacteroides(98);";
+    string tax3WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(92);";
+    string tax4WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);";
+    string tax5WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Incertae_Sedis(97);";
+    
+    SECTION("Add Sequences to Tree") {
+        INFO("Using taxonomies with and without spaces") // Only appears on a FAIL
+        
+        CAPTURE(testPTree.addSeqToTree("seq1", tax1WithSpaces));
+        CHECK(testPTree.addSeqToTree("seq1", tax1WithSpaces) == 5);
+        
+        CAPTURE(testPTree.addSeqToTree("seq2", tax2WithSpaces));
+        CHECK(testPTree.addSeqToTree("seq2", tax2WithSpaces) == 6);
+        
+        CAPTURE(testPTree.addSeqToTree("seq3", tax3WithSpaces));
+        CHECK(testPTree.addSeqToTree("seq3", tax3WithSpaces) == 6);
+        
+        CAPTURE(testPTree.addSeqToTree("seq4", tax4WithSpaces));
+        CHECK(testPTree.addSeqToTree("seq4", tax4WithSpaces) == 6);
+        
+        CAPTURE(testPTree.addSeqToTree("seq5", tax5WithSpaces));
+        CHECK(testPTree.addSeqToTree("seq5", tax5WithSpaces) == 6);
+        
+        CAPTURE(testPTree.addSeqToTree("seq6", tax1WithOutSpaces));
+        CHECK(testPTree.addSeqToTree("seq6", tax1WithOutSpaces) == 5);
+        
+        CAPTURE(testPTree.addSeqToTree("seq7", tax2WithOutSpaces));
+        CHECK(testPTree.addSeqToTree("seq7", tax2WithOutSpaces) == 6);
+        
+        CAPTURE(testPTree.addSeqToTree("seq8", tax3WithOutSpaces));
+        CHECK(testPTree.addSeqToTree("seq8", tax3WithOutSpaces) == 6);
+        
+        CAPTURE(testPTree.addSeqToTree("seq9", tax4WithOutSpaces));
+        CHECK(testPTree.addSeqToTree("seq9", tax4WithOutSpaces) == 6);
+        
+        CAPTURE(testPTree.addSeqToTree("seq10", tax5WithOutSpaces));
+        CHECK(testPTree.addSeqToTree("seq10", tax5WithOutSpaces) == 6);
+    }
+    
+    SECTION("Get Seqs") {
+        INFO("Using taxonomies with and without spaces") // Only appears on a FAIL
+               
+        CAPTURE(testPTree.phylo.getSeqs("Bacteroidetes 7").size());
+        CHECK((testPTree.phylo.getSeqs("Bacteroidetes 7").size()) == 2);
+        
+        vector<string> Bacteroidetes_7 = testPTree.phylo.getSeqs("Bacteroidetes 7");
+        CHECK(Bacteroidetes_7[0] == "seq1");
+        CHECK(Bacteroidetes_7[1] == "seq2");
+        
+        CAPTURE(testPTree.phylo.getSeqs("Clostridia").size());
+        CHECK((testPTree.phylo.getSeqs("Clostridia").size()) == 3);
+        
+        vector<string> Clostridia = testPTree.phylo.getSeqs("Clostridia");
+        CHECK(Clostridia[0] == "seq8");
+        CHECK(Clostridia[1] == "seq9");
+        CHECK(Clostridia[2] == "seq10");
+    }
+   
+    SECTION("Get Genus Totals") {
+        INFO("Using taxonomies with and without spaces") // Only appears on a FAIL
+        
+        CAPTURE(testPTree.phylo.getGenusTotals().size());
+        CHECK(testPTree.phylo.getGenusTotals().size() == 10);
+    }
+
+    SECTION("Get Full Taxonomy") {
+        INFO("Using taxonomies with and without spaces") // Only appears on a FAIL
+        
+        CAPTURE(testPTree.phylo.getFullTaxonomy("seq1"));
+        CHECK(testPTree.phylo.getFullTaxonomy("seq1") == "Bacteria;Bacteroidetes 7;Bacteroidia;Bacteroidales;S24-7;");
+        
+        CAPTURE(testPTree.phylo.getFullTaxonomy("seq10"));
+        CHECK(testPTree.phylo.getFullTaxonomy("seq1") == "Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Incertae_Sedis;");
+    }
+    
+}
+/**************************************************************************************************/
diff --git a/TestMothur/testclassifier/testphylotree.hpp b/TestMothur/testclassifier/testphylotree.hpp
@@ -0,0 +1,32 @@
+//
+//  testphylotree.hpp
+//  Mothur
+//
+//  Created by Sarah Westcott on 8/29/16.
+//  Copyright © 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef testphylotree_hpp
+#define testphylotree_hpp
+
+#include "phylotree.h"
+
+class TestPhyloTree : public PhyloTree {
+    
+    
+public:
+    
+    TestPhyloTree();
+    ~TestPhyloTree();
+    
+    MothurOut* m;
+    
+    PhyloTree phylo;
+    
+    //using PhyloTree::
+    //using PhyloTree::  
+    
+};
+
+
+#endif /* testphylotree_hpp */
diff --git a/TestMothur/testtrimoligos.hpp b/TestMothur/testtrimoligos.hpp
@@ -29,8 +29,8 @@ class TestTrimOligos : public TrimOligos {
     map<int, oligosPair> pairedPrimers;
     map<int, oligosPair> pairedBarcodes;
     
-    using TrimOligos::compareDNASeq(string, string);
-    using TrimOligos::countDiffs(string, string);
+    //using TrimOligos::compareDNASeq(string, string);
+    //using TrimOligos::countDiffs(string, string);
     
 };
 
diff --git a/source/classifier/classify.cpp b/source/classifier/classify.cpp
@@ -101,7 +101,6 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
         m->mothurOut("DONE."); m->mothurOutEndLine();
         m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();
         
-        
         readTaxonomy(taxFile);
         
         //sanity check
diff --git a/source/classifier/phylosummary.cpp b/source/classifier/phylosummary.cpp
@@ -292,10 +292,7 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
             
             if (level > maxLevel) { maxLevel = level; }
 			
-			if ((seqTaxonomy == "") && (level < maxLevel)) {  //if you think you are done and you are not.
-				for (int k = level; k < maxLevel; k++) {  seqTaxonomy += "unclassified;";   }
-			}
-		}
+        }
 		return 0;
 	}
 	catch(exception& e) {
@@ -368,9 +365,6 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, map<string, bool> containsGro
             
             if (level > maxLevel) { maxLevel = level; }
 			
-			if ((seqTaxonomy == "") && (level < maxLevel)) {  //if you think you are done and you are not.
-				for (int k = level; k < maxLevel; k++) {  seqTaxonomy += "unclassified;";   }
-			}
 		}
 		return 0;
 	}
@@ -755,13 +749,15 @@ void PhyloSummary::readTreeStruct(ifstream& in){
 		//read the tree file
 		for (int i = 0; i < tree.size(); i++) {
 	
-			in >> tree[i].level >> tree[i].name >> num; //num contains the number of children tree[i] has
-			
+			in >> tree[i].level >> num; m->gobble(in); //num contains the number of children tree[i] has
+            tree[i].name = m->getline(in); m->gobble(in);
+            
 			//set children
 			string childName;
 			int childIndex;
 			for (int j = 0; j < num; j++) {
-				in >> childName >> childIndex;
+				in >> childIndex; m->gobble(in);
+                childName = m->getline(in); m->gobble(in);
 				tree[i].children[childName] = childIndex;
 			}
 			
diff --git a/source/classifier/phylotree.cpp b/source/classifier/phylotree.cpp
@@ -46,7 +46,8 @@ PhyloTree::PhyloTree(ifstream& in, string filename){
         in >> maxLevel; m->gobble(in);
         
         for (int i = 0; i < tree.size(); i++) {
-            in >> tree[i].name >> tree[i].level >> tree[i].parent; m->gobble(in);
+            tree[i].name = m->getline(in); m->gobble(in);
+            in >> tree[i].level >> tree[i].parent; m->gobble(in);
         }
         
         //read genus nodes
@@ -232,7 +233,7 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
         //save maxLevel for binning the unclassified seqs
         if (level > maxLevel) { maxLevel = level; }
         
-		return 0;
+		return level;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "PhyloTree", "addSeqToTree");
@@ -454,11 +455,12 @@ void PhyloTree::print(ofstream& out, vector<TaxNode>& copy){
 				
 		for (int i = 0; i < copy.size(); i++) {
 				
-			out << copy[i].level << '\t'<< copy[i].name << '\t' << copy[i].children.size();
+			out << copy[i].level << '\t' << copy[i].children.size() << endl;
+            out << copy[i].name << endl;
 			
 			map<string,int>::iterator it;
 			for(it=copy[i].children.begin();it!=copy[i].children.end();it++){
-				out << '\t' << it->first << '\t' << it->second;
+				out << it->second << '\t' << it->first << endl;
 			}
 			out << endl;
 		}
@@ -485,7 +487,8 @@ void PhyloTree::printTreeNodes(string treefilename) {
         outTree << maxLevel << endl;
         
         for (int i = 0; i < tree.size(); i++) {
-            outTree << tree[i].name << '\t' << tree[i].level << '\t' << tree[i].parent << endl;
+            outTree << tree[i].name << endl;
+            outTree << tree[i].level << '\t' << tree[i].parent << endl;
         }
         
         //print genus nodes
diff --git a/source/classifier/phylotree.h b/source/classifier/phylotree.h
@@ -28,6 +28,11 @@ struct TaxNode {
 /**************************************************************************************************/
 
 class PhyloTree {
+    
+#ifdef UNIT_TEST
+    friend class TestPhyloTree;
+#endif
+
 
 public:
 	PhyloTree();