Merge branch 'v.1.38.0'

TestMothur/dataset.h

@@ -29,7 +29,7 @@ class TestDataSet  {
     vector<FastqRead> getReverseFastq()         { return fastqData.getReverseFastq();   }
     vector<string> getSubsetFRFastq(int n)      { return fastqData.getSubsetFRFastq(n); }
     
-    vector<string> getSubsetFNGFiles(int);  //number of uniques, Fasta, name, group returned
+    vector<string> getSubsetFNGFiles(int);  //number of uniques passed in.  3 files returned -> Fasta, name, group.
     
 private:
     MothurOut* m;

TestMothur/testcommands/testrenamefilecommand.cpp

@@ -0,0 +1,97 @@
+//
+//  testrenamefilecommand.cpp
+//  Mothur
+//
+//  Created by Sarah Westcott on 5/4/16.
+//  Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#include "testrenamefilecommand.h"
+#include "dataset.h"
+#include "catch.hpp"
+
+/**************************************************************************************************/
+TestRenameFileCommand::TestRenameFileCommand() {  //setup
+    m = MothurOut::getInstance();
+    TestDataSet data;
+    filenames = data.getSubsetFNGFiles(100);
+}
+/**************************************************************************************************/
+TestRenameFileCommand::~TestRenameFileCommand() {
+    for (int i = 0; i < filenames.size(); i++) { m->mothurRemove(filenames[i]); } //teardown
+}
+/**************************************************************************************************/
+TEST_CASE("Testing RenameFileCommand Class") {
+    TestRenameFileCommand testRename;
+    
+    SECTION("Testing GetNewName - with prefix") {
+        INFO("Using prefix=greatData") // Only appears on a FAIL
+        
+        testRename.prefix = "greatData";
+        testRename.mothurGenerated = true;
+        
+        CAPTURE(testRename.getNewName(testRename.filenames[0], "fasta")); // Displays this variable on a FAIL
+        
+        CHECK(testRename.getNewName(testRename.filenames[0], "fasta") == "greatData.txt");
+        
+        testRename.filenames[0] = testRename.getNewName(testRename.filenames[0], "fasta"); //for teardown
+    }
+    
+    SECTION("Testing GetNewName - with user name") {
+        INFO("Using prefix=greatData") // Only appears on a FAIL
+        
+        testRename.outputfile = "greatData.fasta";
+        testRename.mothurGenerated = false;
+        
+        CAPTURE(testRename.getNewName(testRename.filenames[0], "fasta")); // Displays this variable on a FAIL
+        
+        CHECK(testRename.getNewName(testRename.filenames[0], "fasta") == "greatData.fasta");
+        
+        testRename.filenames[0] = testRename.getNewName(testRename.filenames[0], "fasta");  //for teardown
+    }
+    
+    
+    SECTION("Testing RenameOrCopy - deleteOld=false") {
+        INFO("Uses mothur rename function to move or system command to copy.") // Only appears on a FAIL
+        
+        testRename.deleteOld = false;
+        
+        testRename.renameOrCopy(testRename.filenames[0], "greatData.new.fasta");
+        
+        ifstream in, in2;
+        int ableToOpen = testRename.m->openInputFile("greatData.new.fasta", in);
+        in.close();
+        
+        CAPTURE(ableToOpen);
+            
+        CHECK(ableToOpen == 0);
+        
+        int ableToOpen2 = testRename.m->openInputFile(testRename.filenames[0], in2);
+        in2.close();
+        
+        CAPTURE(ableToOpen2);
+        
+        CHECK(ableToOpen2 == 0);
+        
+        testRename.m->mothurRemove("greatData.new.fasta");
+    }
+    
+    SECTION("Testing RenameOrCopy - deleteOld=true") {
+        INFO("Uses mothur rename function to move or system command to copy.") // Only appears on a FAIL
+        
+        testRename.deleteOld = true;
+        
+        testRename.renameOrCopy(testRename.filenames[0], "greatData.new.fasta");
+        
+        ifstream in, in2;
+        int ableToOpen = testRename.m->openInputFile("greatData.new.fasta", in);
+        in.close();
+        
+        CAPTURE(ableToOpen);
+        
+        CHECK(ableToOpen == 0);
+        
+        testRename.filenames[0] = testRename.getNewName(testRename.filenames[0], "fasta");  //for teardown
+    }
+}
+/**************************************************************************************************/

TestMothur/testcommands/testrenamefilecommand.h

@@ -0,0 +1,40 @@
+//
+//  testrenamefilecommand.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 5/4/16.
+//  Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__testrenamefilecommand__
+#define __Mothur__testrenamefilecommand__
+
+#include "renamefilecommand.h"
+
+class TestRenameFileCommand : public RenameFileCommand {
+    
+public:
+    
+    TestRenameFileCommand();
+    ~TestRenameFileCommand();
+    
+
+    MothurOut* m;
+    vector<string> filenames;
+    
+    //private functions
+    using RenameFileCommand::getNewName;
+    using RenameFileCommand::renameOrCopy;
+    
+    //private variables
+    using RenameFileCommand::prefix;
+    using RenameFileCommand::mothurGenerated;
+    using RenameFileCommand::outputfile;
+    using RenameFileCommand::deleteOld;
+    
+
+    
+};
+
+
+#endif /* defined(__Mothur__testrenamefilecommand__) */

TestMothur/testtrimoligos.cpp

@@ -0,0 +1,43 @@
+//
+//  testtrimoligos.cpp
+//  Mothur
+//
+//  Created by Sarah Westcott on 7/14/16.
+//  Copyright © 2016 Schloss Lab. All rights reserved.
+//
+
+#include "catch.hpp"
+#include "testtrimoligos.hpp"
+
+/**************************************************************************************************/
+TestTrimOligos::TestTrimOligos() {  //setup
+    m = MothurOut::getInstance();
+    
+    //set up barcodes, primers, pairedBarcodes and pairedPrimers
+    
+    //Set up vector of seqs with barcodes and primers
+    
+    //Set up vector of seqs with pairedbarcodes and pairedprimers
+    
+}
+/**************************************************************************************************/
+TestTrimOligos::~TestTrimOligos() {
+    
+}
+/**************************************************************************************************/
+
+TEST_CASE("Testing TrimOligos Class") {
+    TestTrimOligos testTrim;
+    
+    
+    //Create trimoligos classes with various constructors
+    
+    
+    //run all public strip functions
+    
+    
+    //run private functions
+    
+    
+}
+/**************************************************************************************************/

TestMothur/testtrimoligos.hpp

@@ -0,0 +1,38 @@
+//
+//  testtrimoligos.hpp
+//  Mothur
+//
+//  Created by Sarah Westcott on 7/14/16.
+//  Copyright © 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef testtrimoligos_hpp
+#define testtrimoligos_hpp
+
+#include "trimoligos.h"
+#include "sequence.hpp"
+
+class TestTrimOligos : public TrimOligos {
+    
+    
+public:
+    
+    TestTrimOligos();
+    ~TestTrimOligos();
+    
+    MothurOut* m;
+    vector<Sequence> seqs;
+    vector<Sequence> pairedSeqs;
+    
+    map<string, int> barcodes;
+    map<string, int> primers;
+    map<int, oligosPair> pairedPrimers;
+    map<int, oligosPair> pairedBarcodes;
+    
+    using TrimOligos::compareDNASeq(string, string);
+    using TrimOligos::countDiffs(string, string);
+    
+};
+
+
+#endif /* testtrimoligos_hpp */

source/averagelinkage.cpp

@@ -2,10 +2,7 @@
 #define AVERAGE_H
 
 //test
-#include "mothur.h"
 #include "cluster.hpp"
-#include "rabundvector.hpp"
-#include "sparsedistancematrix.h"
 
 /* This class implements the average UPGMA, average neighbor clustering algorithm */
 

source/chimera/mothurchimera.cpp

@@ -8,7 +8,6 @@
  */
 
 #include "mothurchimera.h"
-#include "referencedb.h"
 
 //***************************************************************************************************************
 //this is a vertical soft filter
@@ -100,53 +99,32 @@ vector<Sequence*> MothurChimera::readSeqs(string file) {
 		int count = 0;
 		length = 0;
 		unaligned = false;
-		ReferenceDB* rdb = ReferenceDB::getInstance();
 		
-		if (file == "saved") {
-			
-			
-			m->mothurOutEndLine();  m->mothurOut("Using sequences from " + rdb->getSavedReference() + " that are saved in memory.");	m->mothurOutEndLine();
-			
-			for (int i = 0; i < rdb->referenceSeqs.size(); i++) {
-				Sequence* temp = new Sequence(rdb->referenceSeqs[i].getName(), rdb->referenceSeqs[i].getAligned());
-				
-				if (count == 0) {  length = temp->getAligned().length();  count++;  } //gets first seqs length
-				else if (length != temp->getAligned().length()) {	unaligned = true;	}
-				
-				if (temp->getName() != "") {  container.push_back(temp);  }
-			}
-			
-			templateFileName = rdb->getSavedReference();
-			
-		}else {
-			
-			m->mothurOut("Reading sequences from " + file + "..."); cout.flush();
-			
-			
-			ifstream in;
-			m->openInputFile(file, in);
-			
-			//read in seqs and store in vector
-			while(!in.eof()){
-				
-				if (m->control_pressed) { return container; }
-				
-				Sequence* current = new Sequence(in);  m->gobble(in);
-				
-				if (count == 0) {  length = current->getAligned().length();  count++;  } //gets first seqs length
-				else if (length != current->getAligned().length()) {   unaligned = true;	}
-							
-				if (current->getName() != "") {  
-					container.push_back(current);  
-					if (rdb->save) { rdb->referenceSeqs.push_back(*current); }
-				}
-			}
-			in.close();
+        
+        m->mothurOut("Reading sequences from " + file + "..."); cout.flush();
+        
+        
+        ifstream in;
+        m->openInputFile(file, in);
+        
+        //read in seqs and store in vector
+        while(!in.eof()){
+            
+            if (m->control_pressed) { return container; }
+            
+            Sequence* current = new Sequence(in);  m->gobble(in);
+            
+            if (count == 0) {  length = current->getAligned().length();  count++;  } //gets first seqs length
+            else if (length != current->getAligned().length()) {   unaligned = true;	}
+            
+            if (current->getName() != "") { container.push_back(current); }
+        }
+        in.close();
+        
+        m->mothurOut("Done."); m->mothurOutEndLine();
+        
+        filterString = (string(container[0]->getAligned().length(), '1'));
 		
-			m->mothurOut("Done."); m->mothurOutEndLine();
-			
-			filterString = (string(container[0]->getAligned().length(), '1'));
-		}
 		
 		return container;
 	}