Only sort mothur generated files

Bug Fix

.gitignore

@@ -14,6 +14,7 @@ TARGET_BUILD_DIRTARGET_BUILD_DIR
 nbproject/
 mothur
 Mothur.1
+DerivedData/
 
 *.stdout
 

Makefile

@@ -13,9 +13,10 @@ OPTIMIZE ?= yes
 USEREADLINE ?= yes
 USEBOOST ?= yes
 BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""
+BOOST_INCLUDE_DIR="\"Enter_your_boost_include_path_here\""
 MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"4/05/2016\""
-VERSION = "\"1.37.0\""
+RELEASE_DATE = "\"7/20/2016\""
+VERSION = "\"1.38.0\""
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
     CXXFLAGS += -DBIT_VERSION
@@ -44,17 +45,13 @@ ifeq  ($(strip $(USEREADLINE)),yes)
 endif
 
 
-#The boost libraries allow you to read gz files.
+#User specified boost library
 ifeq  ($(strip $(USEBOOST)),yes)
 
-#User specified boost library path
-ifeq  ($(strip $(BOOST_LIBRARY_DIR)),"\"Enter_your_boost_library_path_here\"")
-else
-    LDFLAGS += ${BOOST_LIBRARY_DIR}
-endif
+    LDFLAGS += -L ${BOOST_LIBRARY_DIR}
 
     LIBS += -lboost_iostreams -lz
-    CXXFLAGS += -DUSE_BOOST
+    CXXFLAGS += -DUSE_BOOST -I ${BOOST_INCLUDE_DIR}
 endif
 
 #

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 */

makefile-internal

@@ -1,16 +1,16 @@
 64BIT_VERSION ?= yes
 USEREADLINE ?= yes
 USEBOOST ?= yes
-RELEASE_DATE = "\"4/05/2015\""
-VERSION = "\"1.37.0\""
+RELEASE_DATE = "\"7/20/2016\""
+VERSION = "\"1.38.0\""
 
 # Optimize to level 3:
     CXXFLAGS += -O3
 
 
 ifeq  ($(strip $(64BIT_VERSION)),yes)
     #if you are a mac user use the following line
-    #TARGET_ARCH += -arch x86_64
+    TARGET_ARCH += -arch x86_64
 
     #if you using cygwin to build Windows the following line
     #CXX = x86_64-w64-mingw32-g++
@@ -40,12 +40,12 @@ ifeq  ($(strip $(USEBOOST)),yes)
     BOOST_INCLUDE_DIR="/usr/local/include"
     BOOST_LIBRARY_DIR="/usr/local/lib"
 
-    CXXFLAGS += -DUSE_BOOST
+    CXXFLAGS += -DUSE_BOOST -I ${BOOST_INCLUDE_DIR}
 
     LIBS += ${BOOST_LIBRARY_DIR}/libboost_iostreams.a
 
     #if mac
-    LIBS += ${BOOST_LIBRARY_DIR}/zlib.a
+    LIBS += -lz
 
     #if linux or windows
     #LIBS += ${BOOST_LIBRARY_DIR}/libz.a

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 */