Merge branch '1.39.0' into Windows_vsearch

TestMothur/dataset.h

@@ -25,11 +25,7 @@ class TestDataSet  {
     GroupMap* getGroupMap()                     { fillGroup(); return gMap;             }
     CountTable* getCountTable()                 { createCountTable(); return ct;        }
     vector<SharedRAbundVector*> getLookup()     { fillLookup(); return lookup;          }
-    vector<FastqRead> getForwardFastq()         { return fastqData.getForwardFastq();   }
-    vector<FastqRead> getReverseFastq()         { return fastqData.getReverseFastq();   }
-    vector<string> getSubsetFRFastq(int n)      { return fastqData.getSubsetFRFastq(n); }
-    
-    vector<string> getSubsetFNGFiles(int);  //number of uniques passed in.  3 files returned -> Fasta, name, group.
+    vector<string> getSubsetFNGFiles(int);  //number of uniques, Fasta, name, group returned
     
 private:
     MothurOut* m;
@@ -39,15 +35,11 @@ class TestDataSet  {
     CountTable* ct;
     GroupMap* gMap;
     vector<SharedRAbundVector*> lookup;
-    vector<FastqRead> ffastqReads; //F8D0 Sample
-    vector<FastqRead> rfastqReads; //F8D0 Sample
     void fillNames();
     void fillSeqs();
     void fillGroup();
     void createCountTable();
     void fillLookup();
-    void fillForwardFastq();
-    void fillReverseFastq();
     
 };
 

TestMothur/distcdataset.h

@@ -0,0 +1,32 @@
+//
+//  distcdataset.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 6/8/16.
+//  Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__distcdataset__
+#define __Mothur__distcdataset__
+
+#include "mothurout.h"
+
+class DistCDataSet  {
+    
+public:
+    
+    DistCDataSet();
+    ~DistCDataSet() {}
+    string getColumnFile() { return writeColumnFile(); }
+    vector<string> getFiles(int);
+    string getCountFile()  { return writeCountFile();  }
+    
+private:
+    MothurOut* m;
+    string writeColumnFile();
+    string writeCountFile();
+    
+};
+
+
+#endif /* defined(__Mothur__distcdataset__) */

TestMothur/distpdataset.h

@@ -0,0 +1,30 @@
+//
+//  distdataset.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 6/6/16.
+//  Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__distdataset__
+#define __Mothur__distdataset__
+
+#include "mothurout.h"
+
+class DistPDataSet  {
+    
+public:
+    
+    DistPDataSet();
+    ~DistPDataSet() {}
+    
+    string getPhylipFile() { return writePhylipFile(); }
+    
+private:
+    MothurOut* m;
+    string writePhylipFile();
+    
+};
+
+
+#endif /* defined(__Mothur__distdataset__) */

TestMothur/testcontainers/testfastqread.cpp

@@ -13,7 +13,7 @@
 /**************************************************************************************************/
 TestFastqRead::TestFastqRead() {  //setup
     m = MothurOut::getInstance();
-    TestDataSet data;
+    TestFastqDataSet data;
     reads = data.getForwardFastq();
     filenames = data.getSubsetFRFastq(100);
 }
@@ -25,6 +25,7 @@ TestFastqRead::~TestFastqRead() {
 /**************************************************************************************************/
 
 TEST_CASE("Testing FastqRead Class") {
+    /*
     TestFastqRead testFastq;
     
     SECTION("Testing (Sequence, Quality) Constructor ") {
@@ -60,6 +61,6 @@ TEST_CASE("Testing FastqRead Class") {
         
         CHECK(read.getScores()[0] == testFastq.reads[0].getScores()[0]);
     }
-    
+    */
 }
 /**************************************************************************************************/

TestMothur/testcontainers/testoptimatrix.cpp

@@ -0,0 +1,101 @@
+//
+//  testoptimatrix.cpp
+//  Mothur
+//
+//  Created by Sarah Westcott on 6/6/16.
+//  Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#include "catch.hpp"
+#include "testoptimatrix.h"
+#include "distancecommand.h"
+#include "dataset.h"
+
+/**************************************************************************************************/
+TestOptiMatrix::TestOptiMatrix() {  //setup
+    m = MothurOut::getInstance();
+    TestDataSet data;
+    filenames = data.getSubsetFNGFiles(100); //Fasta, name, group returned
+    
+    string inputString = "fasta=" + filenames[0];
+    m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+    m->mothurOut("Running command: dist.seqs(" + inputString + ")"); m->mothurOutEndLine();
+    m->mothurCalling = true;
+    
+    Command* distCommand = new DistanceCommand(inputString);
+    distCommand->execute();
+    
+    map<string, vector<string> > outputFilenames = distCommand->getOutputFiles();
+    
+    delete distCommand;
+    m->mothurCalling = false;
+    
+    columnFile = outputFilenames["column"][0];
+    m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+    
+    inputString = "fasta=" + filenames[0] + ", output=lt";
+    m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+    m->mothurOut("Running command: dist.seqs(" + inputString + ")"); m->mothurOutEndLine();
+    m->mothurCalling = true;
+    
+    Command* dist2Command = new DistanceCommand(inputString);
+    dist2Command->execute();
+    
+    outputFilenames = dist2Command->getOutputFiles();
+    
+    delete dist2Command;
+    m->mothurCalling = false;
+    
+    phylipFile = outputFilenames["phylip"][0];
+    m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+}
+/**************************************************************************************************/
+TestOptiMatrix::~TestOptiMatrix() {
+    for (int i = 0; i < filenames.size(); i++) { m->mothurRemove(filenames[i]); } //teardown
+    m->mothurRemove(columnFile);
+    m->mothurRemove(phylipFile);
+}
+/**************************************************************************************************/
+TEST_CASE("Testing OptiMatrix Class") {
+    TestOptiMatrix testOMatrix;
+    OptiMatrix matrix(testOMatrix.columnFile, testOMatrix.filenames[1], "name", 0.03, false);
+    OptiMatrix pmatrix(testOMatrix.phylipFile, "", "", 0.03, false);
+    
+    SECTION("Testing Column Read") {
+        INFO("Using First 100 sequences of final.fasta and final.names") // Only appears on a FAIL
+        
+        CAPTURE(matrix.print(cout)); // Displays this variable on a FAIL
+        
+        CHECK(matrix.print(cout) == 112); //numdists in matrix
+    }
+    
+    SECTION("Testing Phylip Read") {
+        INFO("Using First 100 sequences of final.fasta and final.names") // Only appears on a FAIL
+        
+        CAPTURE(pmatrix.print(cout)); // Displays this variable on a FAIL
+        
+        CHECK(pmatrix.print(cout) == 112); //numdists in matrix
+    }
+    
+    /* First few rows of matrix
+     12	23	44
+     10	23	32	36
+     16	25	33	48
+     38
+     22	45	52
+     */
+    
+    SECTION("Testing isClose") {
+        INFO("Sequences 0 and 1") // Only appears on a FAIL
+        
+        CAPTURE(matrix.isClose(0, 12));
+        CHECK(matrix.isClose(0, 12) == true);
+        CAPTURE(matrix.isClose(0, 44));
+        CHECK(matrix.isClose(0, 44) == true);
+        CAPTURE(matrix.isClose(1, 23));
+        CHECK(matrix.isClose(1, 23) == true);
+        CAPTURE(matrix.isClose(1, 36));
+        CHECK(matrix.isClose(1, 36) == true);
+    }
+}
+/**************************************************************************************************/

TestMothur/testcontainers/testoptimatrix.h

@@ -0,0 +1,31 @@
+//
+//  testoptimatrix.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 6/6/16.
+//  Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__testoptimatrix__
+#define __Mothur__testoptimatrix__
+
+#include "optimatrix.h"
+
+class TestOptiMatrix : public OptiMatrix {
+    
+public:
+    
+    TestOptiMatrix();
+    ~TestOptiMatrix();
+    
+    using OptiMatrix::getCloseSeqs;
+    using OptiMatrix::findDistFormat;
+    using OptiMatrix::readPhylip;
+    using OptiMatrix::readColumn;
+    
+    string columnFile, phylipFile;
+    vector<string> filenames;
+    
+};
+
+#endif /* defined(__Mothur__testoptimatrix__) */

TestMothur/testopticluster.cpp

@@ -0,0 +1,142 @@
+//
+//  testopticluster.cpp
+//  Mothur
+//
+//  Created by Sarah Westcott on 6/15/16.
+//  Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#include "testopticluster.h"
+#include "catch.hpp"
+#include "optimatrix.h"
+#include "distancecommand.h"
+#include "dataset.h"
+
+/**************************************************************************************************/
+TestOptiCluster::TestOptiCluster() {  //setup
+    m = MothurOut::getInstance();
+    TestDataSet data;
+    filenames = data.getSubsetFNGFiles(100); //Fasta, name, group returned
+    
+    string inputString = "fasta=" + filenames[0];
+    m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+    m->mothurOut("Running command: dist.seqs(" + inputString + ")"); m->mothurOutEndLine();
+    m->mothurCalling = true;
+    
+    Command* distCommand = new DistanceCommand(inputString);
+    distCommand->execute();
+    
+    map<string, vector<string> > outputFilenames = distCommand->getOutputFiles();
+    
+    delete distCommand;
+    m->mothurCalling = false;
+    
+    columnFile = outputFilenames["column"][0];
+}
+/**************************************************************************************************/
+TestOptiCluster::~TestOptiCluster() {
+    for (int i = 0; i < filenames.size(); i++) { m->mothurRemove(filenames[i]); } //teardown
+    m->mothurRemove(columnFile);
+}
+/**************************************************************************************************/
+TEST_CASE("Testing OptiCluster Class") {
+    TestOptiCluster testOcluster;
+    OptiMatrix matrix(testOcluster.columnFile, testOcluster.filenames[1], "name", 0.03, false);
+    testOcluster.setVariables(&matrix, "mcc");
+    
+    SECTION("Testing Initialize") {
+        INFO("Using First 100 sequences of final.fasta and final.names") // Only appears on a FAIL
+        
+        double initialMetricValue;
+        
+        CAPTURE(testOcluster.initialize(initialMetricValue, true)); //
+        
+        CHECK(testOcluster.initialize(initialMetricValue, true) == 0); //metric value
+    }
+    
+    SECTION("Testing calcMCC") {
+        INFO("Using tp=5000, tn=10000, fp=10, fn=200") // Only appears on a FAIL
+        
+        double tp,tn,fp,fn; tp=5000; tn=10000; fp=10; fn=200;
+        
+        CAPTURE(testOcluster.calcMCC(tp,tn,fp,fn)); // Displays this variable on a FAIL
+        
+        CHECK((int)(testOcluster.calcMCC(tp,tn,fp,fn)*10000) == 9694); //metric value
+    }
+    
+    SECTION("Testing calcSens") {
+        INFO("Using tp=5000, tn=10000, fp=10, fn=200") // Only appears on a FAIL
+        
+        double tp,tn,fp,fn; tp=5000; tn=10000; fp=10; fn=200;
+        
+        CAPTURE(testOcluster.calcSens(tp,tn,fp,fn)); // Displays this variable on a FAIL
+        
+        CHECK((int)(testOcluster.calcSens(tp,tn,fp,fn)*10000) == 9615); //metric value
+    }
+    
+    SECTION("Testing calcSpec") {
+        INFO("Using tp=5000, tn=10000, fp=10, fn=200") // Only appears on a FAIL
+        
+        double tp,tn,fp,fn; tp=5000; tn=10000; fp=10; fn=200;
+        
+        CAPTURE(testOcluster.calcSpec(tp,tn,fp,fn)); // Displays this variable on a FAIL
+        
+        CHECK((int)(testOcluster.calcSpec(tp,tn,fp,fn)*10000) == 9990); //metric value
+    }
+    
+    SECTION("Testing calcTPTN") {
+        INFO("Using tp=5000, tn=10000, fp=10, fn=200") // Only appears on a FAIL
+        
+        double tp,tn,fp,fn; tp=5000; tn=10000; fp=10; fn=200;
+        
+        CAPTURE(testOcluster.calcTPTN(tp,tn,fp,fn)); // Displays this variable on a FAIL
+        
+        CHECK((int)(testOcluster.calcTPTN(tp,tn,fp,fn)*10000) == 9861); //metric value
+    }
+    
+    SECTION("Testing calcTP2TN") {
+        INFO("Using tp=5000, tn=10000, fp=10, fn=200") // Only appears on a FAIL
+        
+        double tp,tn,fp,fn; tp=5000; tn=10000; fp=10; fn=200;
+        
+        CAPTURE(testOcluster.calcTP2TN(tp,tn,fp,fn)); // Displays this variable on a FAIL
+        
+        CHECK((int)(testOcluster.calcTP2TN(tp,tn,fp,fn)*10000) == 16436); //metric value
+    }
+    
+    SECTION("Testing calcFPFN") {
+        INFO("Using tp=5000, tn=10000, fp=10, fn=200") // Only appears on a FAIL
+        
+        double tp,tn,fp,fn; tp=5000; tn=10000; fp=10; fn=200;
+        
+        CAPTURE(testOcluster.calcFPFN(tp,tn,fp,fn)); // Displays this variable on a FAIL
+        
+        CHECK((int)(testOcluster.calcFPFN(tp,tn,fp,fn)*10000) == 9861); //metric value
+    }
+    
+    SECTION("Testing moveAdjustTFValues") {
+        INFO("Using tp=5000, tn=10000, fp=10, fn=200 and mcc") // Only appears on a FAIL
+        
+        double tp,tn,fp,fn; tp=5000; tn=10000; fp=10; fn=200;
+        double initialMetricValue;
+        testOcluster.initialize(initialMetricValue, false); //no randomization
+        
+        CAPTURE(testOcluster.moveAdjustTFValues(0, 10, 1, tp,tn,fp,fn)); // Displays this variable on a FAIL
+        
+        CHECK((int)(testOcluster.moveAdjustTFValues(0, 10, 1, tp,tn,fp,fn)*10000) == 9700); //metric value
+    }
+    
+    SECTION("Testing update") {
+        INFO("Using mcc") // Only appears on a FAIL
+        
+        double initialMetricValue;
+        testOcluster.initialize(initialMetricValue, false); //no randomization
+        testOcluster.update(initialMetricValue);
+        
+        CAPTURE(initialMetricValue); // Displays this variable on a FAIL
+        
+        CHECK((int)(initialMetricValue*10000) == 7853); //metric value
+    }
+    
+}
+/**************************************************************************************************/