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Merge pull request #299 from mothur/1.39.0 

1.39.0
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2 parents 8f163fa + 2db8466 commit cfb593dbe4c8ed207b9c7591e0cbd3349068fd18 @mothur-westcott mothur-westcott committed on GitHub Jan 19, 2017
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Showing with 53,737 additions and 2,721 deletions.
  1. +85 −26 Mothur.xcodeproj/project.pbxproj
  2. +1 −9 TestMothur/dataset.h
  3. +46,955 −0 TestMothur/distcdataset.cpp
  4. +32 −0 TestMothur/distcdataset.h
  5. +2,578 −0 TestMothur/distpdataset.cpp
  6. +30 −0 TestMothur/distpdataset.h
  7. +0 −1 TestMothur/main.cpp
  8. +129 −0 TestMothur/testclassifier/testphylotree.cpp
  9. +32 −0 TestMothur/testclassifier/testphylotree.hpp
  10. +3 −2 TestMothur/testcontainers/testfastqread.cpp
  11. +101 −0 TestMothur/testcontainers/testoptimatrix.cpp
  12. +31 −0 TestMothur/testcontainers/testoptimatrix.h
  13. +142 −0 TestMothur/testopticluster.cpp
  14. +36 −0 TestMothur/testopticluster.h
  15. +2 −2 TestMothur/testtrimoligos.hpp
  16. +3 −3 TestMothur/testvsearchfileparser.cpp
  17. +0 −1 TestMothur/testvsearchfileparser.h
  18. +12 −0 source/calculators/filters.h
  19. +0 −1 source/classifier/classify.cpp
  20. +17 −21 source/classifier/phylosummary.cpp
  21. +8 −5 source/classifier/phylotree.cpp
  22. +5 −0 source/classifier/phylotree.h
  23. +26 −15 source/classifier/taxonomyequalizer.cpp
  24. +2 −2 source/cluster.cpp
  25. +4 −6 source/cluster.hpp
  26. +2 −2 source/commands/catchallcommand.cpp
  27. +4 −2 source/commands/chimeraperseuscommand.cpp
  28. +4 −3 source/commands/chimeraperseuscommand.h
  29. +4 −2 source/commands/chimeraslayercommand.cpp
  30. +16 −16 source/commands/chimerauchimecommand.cpp
  31. +8 −6 source/commands/chimerauchimecommand.h
  32. +65 −285 source/commands/chimeravsearchcommand.cpp
  33. +0 −3 source/commands/chimeravsearchcommand.h
  34. +3 −3 source/commands/classifyotucommand.cpp
  35. +3 −2 source/commands/classifyseqscommand.cpp
  36. +209 −32 source/commands/clustercommand.cpp
  37. +10 −5 source/commands/clustercommand.h
  38. +236 −65 source/commands/clustersplitcommand.cpp
  39. +11 −6 source/commands/clustersplitcommand.h
  40. +54 −45 source/commands/createdatabasecommand.cpp
  41. +1 −1 source/commands/distancecommand.cpp
  42. +1 −1 source/commands/getcommandinfocommand.cpp
  43. +2 −4 source/commands/getgroupscommand.cpp
  44. +4 −6 source/commands/getlineagecommand.cpp
  45. +2 −1 source/commands/getotulabelscommand.cpp
  46. +0 −432 source/commands/getotuscommand.cpp
  47. +0 −55 source/commands/getotuscommand.h
  48. +3 −5 source/commands/getseqscommand.cpp
  49. +2 −5 source/commands/listseqscommand.cpp
  50. +6 −2 source/commands/makebiomcommand.cpp
  51. +127 −23 source/commands/makecontigscommand.cpp
  52. +626 −166 source/commands/makecontigscommand.h
  53. +90 −7 source/commands/makefilecommand.cpp
  54. +1 −1 source/commands/makefilecommand.h
  55. +25 −10 source/commands/mergetaxsummarycommand.cpp
  56. +4 −16 source/commands/mgclustercommand.cpp
  57. +1 −1 source/commands/mgclustercommand.h
  58. +3 −4 source/commands/pcrseqscommand.cpp
  59. +1 −29 source/commands/phylotypecommand.cpp
  60. +0 −2 source/commands/phylotypecommand.h
  61. +103 −67 source/commands/preclustercommand.cpp
  62. +56 −28 source/commands/preclustercommand.h
  63. +2 −4 source/commands/removegroupscommand.cpp
  64. +4 −5 source/commands/removelineagecommand.cpp
  65. +2 −1 source/commands/removeotulabelscommand.cpp
  66. +0 −439 source/commands/removeotuscommand.cpp
  67. +0 −52 source/commands/removeotuscommand.h
  68. +3 −5 source/commands/removeseqscommand.cpp
  69. +21 −24 source/commands/screenseqscommand.cpp
  70. +1 −1 source/commands/screenseqscommand.h
  71. +26 −32 source/commands/sensspeccommand.cpp
  72. +1 −2 source/commands/sensspeccommand.h
  73. +30 −9 source/commands/setdircommand.cpp
  74. +1 −1 source/commands/setdircommand.h
  75. +2 −10 source/commands/sffinfocommand.cpp
  76. +8 −8 source/commands/sffmultiplecommand.cpp
  77. +4 −2 source/commands/sharedcommand.cpp
  78. +16 −16 source/commands/shhhercommand.cpp
  79. +2 −1 source/commands/shhhseqscommand.cpp
  80. +2 −1 source/commands/shhhseqscommand.h
  81. +4 −4 source/commands/sortseqscommand.cpp
  82. +3 −0 source/commands/sparcccommand.cpp
  83. +4 −3 source/commands/splitgroupscommand.cpp
  84. +5 −1 source/commands/sracommand.cpp
  85. +1 −1 source/commands/sracommand.h
  86. +2 −2 source/commands/subsamplecommand.cpp
  87. +56 −57 source/commands/summarytaxcommand.cpp
  88. +1 −0 source/commands/summarytaxcommand.h
  89. +1 −2 source/datastructures/blastalign.cpp
  90. +9 −9 source/datastructures/blastdb.cpp
  91. +1 −1 source/datastructures/counttable.h
  92. +445 −0 source/datastructures/optimatrix.cpp
  93. +60 −0 source/datastructures/optimatrix.h
  94. +108 −61 source/datastructures/sequencecountparser.cpp
  95. +7 −5 source/datastructures/sequencecountparser.h
  96. +0 −54 source/datastructures/sequencedb.cpp
  97. +0 −2 source/datastructures/sequencedb.h
  98. +73 −202 source/datastructures/sequenceparser.cpp
  99. +3 −3 source/datastructures/sequenceparser.h
  100. +13 −5 source/engine.cpp
  101. +1 −1 source/linearalgebra.cpp
  102. +0 −171 source/makefile
  103. +4 −3 source/mothur.cpp
  104. +134 −65 source/mothurout.cpp
  105. +10 −4 source/mothurout.h
  106. +632 −0 source/opticluster.cpp
  107. +66 −0 source/opticluster.h
  108. +20 −4 source/optionparser.cpp
  109. +12 −1 source/read/splitmatrix.cpp
  110. +3 −1 source/read/splitmatrix.h
  111. +0 −1 source/singlelinkage.cpp
  112. +6 −0 source/trimoligos.h
  113. +5 −5 source/validparameter.cpp
  114. +2 −3 source/vsearchfileparser.cpp
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111 Mothur.xcodeproj/project.pbxproj

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10 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();
};
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46,955 TestMothur/distcdataset.cpp

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32 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__) */
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2,578 TestMothur/distpdataset.cpp

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30 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__) */
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1 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
*/
//***********************************************************//
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129 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;");
+ }
+
+}
+/**************************************************************************************************/
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32 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 */
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5 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]);
}
-
+ */
}
/**************************************************************************************************/
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101 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);
+ }
+}
+/**************************************************************************************************/
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