Adds testing units for phylotree

#265

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; };
@@ -2550,7 +2548,7 @@
 		08FB7793FE84155DC02AAC07 /* Project object */ = {
 			isa = PBXProject;
 			attributes = {
-				LastUpgradeCheck = 0620;
+				LastUpgradeCheck = 0730;
 				ORGANIZATIONNAME = "Schloss Lab";
 				TargetAttributes = {
 					481FB5181AC0A63E0076CFF3 = {
@@ -2866,11 +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 */,
@@ -3409,6 +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;
@@ -3535,7 +3532,7 @@
 				MTL_ENABLE_DEBUG_INFO = YES;
 				ONLY_ACTIVE_ARCH = YES;
 				PRODUCT_NAME = "$(TARGET_NAME)";
-				SDKROOT = macosx10.9;
+				SDKROOT = macosx;
 			};
 			name = Debug;
 		};
@@ -3572,7 +3569,7 @@
 				MTL_ENABLE_DEBUG_INFO = NO;
 				ONLY_ACTIVE_ARCH = YES;
 				PRODUCT_NAME = "$(TARGET_NAME)";
-				SDKROOT = macosx10.9;
+				SDKROOT = macosx;
 			};
 			name = Release;
 		};

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
  
  */
 //***********************************************************//

TestMothur/testclassifier/testphylotree.cpp

@@ -6,46 +6,123 @@
 //  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;
-    PhyloTree phylo;
+    
+    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(vsearchParser.getVsearchFile()); // Displays this variable on a FAIL
-        
-        CHECK(vsearchParser.getVsearchFile() == "tempSeqs.txt.sorted.fasta.temp");
-        
-        ifstream in;
-        testVParser.m->openInputFile(vsearchParser.getVsearchFile(), in);
-        
-        while (!in.eof()) {
-            Sequence seq(in); testVParser.m->gobble(in);
-            
-            vector<string> pieces;
-            string name = seq.getName();
-            
-            testVParser.m->splitAtChar(name, pieces, '=');
-            string abundString = pieces[1].substr(0, pieces[1].length()-1);
-            int abund = 0;
-            testVParser.m->mothurConvert(abundString, abund);
-            int totalSeqs = testVParser.ct->getNumSeqs(testVParser.removeAbundances(name));
-            
-            CHECK(abund == totalSeqs);
-        }
-        in.close();
-        testVParser.m->mothurRemove("tempSeqs.txt.sorted.fasta.temp");
+        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;");
     }
     
 }

TestMothur/testclassifier/testphylotree.hpp

@@ -9,6 +9,8 @@
 #ifndef testphylotree_hpp
 #define testphylotree_hpp
 
+#include "phylotree.h"
+
 class TestPhyloTree : public PhyloTree {
     
     
@@ -19,6 +21,8 @@ class TestPhyloTree : public PhyloTree {
     
     MothurOut* m;
     
+    PhyloTree phylo;
+    
     //using PhyloTree::
     //using PhyloTree::  
     

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);
     
 };
 

source/classifier/phylotree.cpp

@@ -233,7 +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");

source/trimoligos.h

@@ -17,6 +17,12 @@
 
 
 class TrimOligos {
+    
+#ifdef UNIT_TEST
+    friend class TestTrimOligos;
+    TrimOligos() {};
+    //add set variables function when completeing unit tests for this class
+#endif
 	
 	public:
         TrimOligos(int,int,int, map<string, int>, map<string, int>, vector<string>); //pdiffs, bdiffs, primers, barcodes, revPrimers