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Merge branch '1.39.0' into Opticluster

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2 parents 9ca9b2a + 06c3d20 commit 25c446ca24620a909d781f08d3b2c1979724ae1c @mothur-westcott mothur-westcott committed on GitHub Jan 5, 2017
Unified Split
Showing with 1,887 additions and 1,043 deletions.
  1. +29 −14 Mothur.xcodeproj/project.pbxproj
  2. +0 −1 TestMothur/main.cpp
  3. +129 −0 TestMothur/testclassifier/testphylotree.cpp
  4. +32 −0 TestMothur/testclassifier/testphylotree.hpp
  5. +2 −2 TestMothur/testtrimoligos.hpp
  6. +12 −0 source/calculators/filters.h
  7. +0 −1 source/classifier/classify.cpp
  8. +17 −21 source/classifier/phylosummary.cpp
  9. +8 −5 source/classifier/phylotree.cpp
  10. +5 −0 source/classifier/phylotree.h
  11. +26 −15 source/classifier/taxonomyequalizer.cpp
  12. +2 −2 source/commands/catchallcommand.cpp
  13. +4 −2 source/commands/chimeraperseuscommand.cpp
  14. +4 −2 source/commands/chimeraslayercommand.cpp
  15. +7 −6 source/commands/chimerauchimecommand.cpp
  16. +7 −6 source/commands/chimeravsearchcommand.cpp
  17. +3 −3 source/commands/classifyotucommand.cpp
  18. +3 −2 source/commands/classifyseqscommand.cpp
  19. +5 −5 source/commands/clustercommand.cpp
  20. +4 −4 source/commands/clustersplitcommand.cpp
  21. +54 −45 source/commands/createdatabasecommand.cpp
  22. +1 −1 source/commands/getcommandinfocommand.cpp
  23. +2 −4 source/commands/getgroupscommand.cpp
  24. +4 −6 source/commands/getlineagecommand.cpp
  25. +2 −1 source/commands/getotulabelscommand.cpp
  26. +3 −5 source/commands/getseqscommand.cpp
  27. +2 −5 source/commands/listseqscommand.cpp
  28. +6 −2 source/commands/makebiomcommand.cpp
  29. +127 −23 source/commands/makecontigscommand.cpp
  30. +626 −166 source/commands/makecontigscommand.h
  31. +90 −7 source/commands/makefilecommand.cpp
  32. +2 −0 source/commands/makefilecommand.h
  33. +25 −10 source/commands/mergetaxsummarycommand.cpp
  34. +0 −1 source/commands/mgclustercommand.cpp
  35. +3 −4 source/commands/pcrseqscommand.cpp
  36. +1 −29 source/commands/phylotypecommand.cpp
  37. +0 −2 source/commands/phylotypecommand.h
  38. +103 −67 source/commands/preclustercommand.cpp
  39. +56 −28 source/commands/preclustercommand.h
  40. +2 −4 source/commands/removegroupscommand.cpp
  41. +4 −5 source/commands/removelineagecommand.cpp
  42. +2 −1 source/commands/removeotulabelscommand.cpp
  43. +3 −5 source/commands/removeseqscommand.cpp
  44. +3 −2 source/commands/screenseqscommand.cpp
  45. +5 −3 source/commands/sensspeccommand.cpp
  46. +30 −9 source/commands/setdircommand.cpp
  47. +1 −1 source/commands/setdircommand.h
  48. +1 −10 source/commands/sffinfocommand.cpp
  49. +8 −8 source/commands/sffmultiplecommand.cpp
  50. +16 −16 source/commands/shhhercommand.cpp
  51. +2 −1 source/commands/shhhseqscommand.cpp
  52. +4 −4 source/commands/sortseqscommand.cpp
  53. +3 −0 source/commands/sparcccommand.cpp
  54. +2 −2 source/commands/splitgroupscommand.cpp
  55. +5 −1 source/commands/sracommand.cpp
  56. +1 −1 source/commands/sracommand.h
  57. +2 −2 source/commands/subsamplecommand.cpp
  58. +56 −57 source/commands/summarytaxcommand.cpp
  59. +1 −0 source/commands/summarytaxcommand.h
  60. +1 −2 source/datastructures/blastalign.cpp
  61. +9 −9 source/datastructures/blastdb.cpp
  62. +104 −59 source/datastructures/sequencecountparser.cpp
  63. +6 −4 source/datastructures/sequencecountparser.h
  64. +0 −54 source/datastructures/sequencedb.cpp
  65. +0 −2 source/datastructures/sequencedb.h
  66. +68 −200 source/datastructures/sequenceparser.cpp
  67. +2 −2 source/datastructures/sequenceparser.h
  68. +13 −5 source/engine.cpp
  69. +88 −64 source/mothurout.cpp
  70. +8 −4 source/mothurout.h
  71. +20 −4 source/optionparser.cpp
  72. +6 −0 source/trimoligos.h
  73. +5 −5 source/validparameter.cpp
View
43 Mothur.xcodeproj/project.pbxproj
@@ -407,6 +407,7 @@
48E418561D08893A004C36AB /* (null) in Sources */ = {isa = PBXBuildFile; };
48E981CF189C38FB0042BE9D /* (null) in Sources */ = {isa = PBXBuildFile; };
48EDB76C1D1320DD00F76E93 /* chimeravsearchcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48EDB76A1D1320DD00F76E93 /* chimeravsearchcommand.cpp */; };
+ 48F06CCD1D74BEC4004A45DD /* testphylotree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48F06CCB1D74BEC4004A45DD /* testphylotree.cpp */; };
48F98E4D1A9CFD670005E81B /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48F98E4C1A9CFD670005E81B /* completelinkage.cpp */; };
7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */; };
835FE03D19F00640005AA754 /* classifysvmsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7B2181FE17AD777B00286E6A /* classifysvmsharedcommand.cpp */; };
@@ -783,12 +784,12 @@
};
8DD76FAF0486AB0100D96B5E /* CopyFiles */ = {
isa = PBXCopyFilesBuildPhase;
- buildActionMask = 8;
- dstPath = Users/SarahsWork/desktop/debug;
+ buildActionMask = 12;
+ dstPath = "";
dstSubfolderSpec = 16;
files = (
);
- runOnlyForDeploymentPostprocessing = 1;
+ runOnlyForDeploymentPostprocessing = 0;
};
/* End PBXCopyFilesBuildPhase section */
@@ -871,6 +872,8 @@
48DB37B21B3B27E000C372A4 /* makefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = makefilecommand.h; path = source/commands/makefilecommand.h; sourceTree = SOURCE_ROOT; };
48EDB76A1D1320DD00F76E93 /* chimeravsearchcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = chimeravsearchcommand.cpp; path = source/commands/chimeravsearchcommand.cpp; sourceTree = SOURCE_ROOT; };
48EDB76B1D1320DD00F76E93 /* chimeravsearchcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = chimeravsearchcommand.h; path = source/commands/chimeravsearchcommand.h; sourceTree = SOURCE_ROOT; };
+ 48F06CCB1D74BEC4004A45DD /* testphylotree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = testphylotree.cpp; path = testclassifier/testphylotree.cpp; sourceTree = "<group>"; };
+ 48F06CCC1D74BEC4004A45DD /* testphylotree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; name = testphylotree.hpp; path = testclassifier/testphylotree.hpp; sourceTree = "<group>"; };
48F98E4C1A9CFD670005E81B /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = completelinkage.cpp; path = source/completelinkage.cpp; sourceTree = SOURCE_ROOT; };
7B2181FE17AD777B00286E6A /* classifysvmsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = classifysvmsharedcommand.cpp; path = source/commands/classifysvmsharedcommand.cpp; sourceTree = SOURCE_ROOT; };
7B2181FF17AD777B00286E6A /* classifysvmsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = classifysvmsharedcommand.h; path = source/commands/classifysvmsharedcommand.h; sourceTree = SOURCE_ROOT; };
@@ -1738,6 +1741,7 @@
children = (
481FB5201AC0A6B60076CFF3 /* catch.hpp */,
481FB51B1AC0A63E0076CFF3 /* main.cpp */,
+ 48F06CCA1D74BC6F004A45DD /* testclassifier */,
48D6E9691CA4262A008DF76B /* dataset.cpp */,
48D6E96A1CA4262A008DF76B /* dataset.h */,
48910D4F1D58E26C00F60EDB /* distcdataset.h */,
@@ -1791,6 +1795,15 @@
name = testcontainers;
sourceTree = "<group>";
};
+ 48F06CCA1D74BC6F004A45DD /* testclassifier */ = {
+ isa = PBXGroup;
+ children = (
+ 48F06CCB1D74BEC4004A45DD /* testphylotree.cpp */,
+ 48F06CCC1D74BEC4004A45DD /* testphylotree.hpp */,
+ );
+ name = testclassifier;
+ sourceTree = "<group>";
+ };
7B17437A17AF6F02004C161B /* svm */ = {
isa = PBXGroup;
children = (
@@ -2567,7 +2580,7 @@
08FB7793FE84155DC02AAC07 /* Project object */ = {
isa = PBXProject;
attributes = {
- LastUpgradeCheck = 0620;
+ LastUpgradeCheck = 0730;
ORGANIZATIONNAME = "Schloss Lab";
TargetAttributes = {
481FB5181AC0A63E0076CFF3 = {
@@ -2830,6 +2843,7 @@
481FB5351AC1B5D90076CFF3 /* fasta.cpp in Sources */,
481FB6321AC1B7EA0076CFF3 /* groupmap.cpp in Sources */,
481FB5FF1AC1B7970076CFF3 /* removeseqscommand.cpp in Sources */,
+ 48F06CCD1D74BEC4004A45DD /* testphylotree.cpp in Sources */,
481FB6771AC1B88F0076CFF3 /* readcluster.cpp in Sources */,
481FB5831AC1B6FF0076CFF3 /* ccode.cpp in Sources */,
481FB5681AC1B6B20076CFF3 /* sharedochiai.cpp in Sources */,
@@ -3368,10 +3382,10 @@
"DYLIB_CURRENT_VERSION[sdk=*]" = "";
GCC_DYNAMIC_NO_PIC = NO;
GCC_MODEL_TUNING = G5;
- GCC_OPTIMIZATION_LEVEL = 0;
+ GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.37.1\\\"\"",
- "RELEASE_DATE=\"\\\"04/11/2016\\\"\"",
+ "VERSION=\"\\\"1.38.1\\\"\"",
+ "RELEASE_DATE=\"\\\"09/26/2016\\\"\"",
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
);
GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
@@ -3403,10 +3417,10 @@
DEPLOYMENT_LOCATION = YES;
DSTROOT = TARGET_BUILD_DIR;
GCC_MODEL_TUNING = G5;
- GCC_OPTIMIZATION_LEVEL = 0;
+ GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.37.1\\\"\"",
- "RELEASE_DATE=\"\\\"04/11/2016\\\"\"",
+ "VERSION=\"\\\"1.38.1\\\"\"",
+ "RELEASE_DATE=\"\\\"09/26/2016\\\"\"",
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
);
GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
@@ -3433,11 +3447,12 @@
CLANG_CXX_LIBRARY = "libstdc++";
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;
GCC_ENABLE_SSE42_EXTENSIONS = NO;
- GCC_OPTIMIZATION_LEVEL = 0;
+ GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
"VERSION=\"\\\"1.36.0\\\"\"",
@@ -3487,10 +3502,10 @@
GCC_C_LANGUAGE_STANDARD = c11;
GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
GCC_MODEL_TUNING = "";
- GCC_OPTIMIZATION_LEVEL = 0;
+ GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.37.6\\\"\"",
- "RELEASE_DATE=\"\\\"06/20/2016\\\"\"",
+ "VERSION=\"\\\"1.38.1\\\"\"",
+ "RELEASE_DATE=\"\\\"09/26/2016\\\"\"",
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
);
GCC_VERSION = "";
View
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
*/
//***********************************************************//
View
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;");
+ }
+
+}
+/**************************************************************************************************/
View
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 */
View
4 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);
};
View
12 source/calculators/filters.h
@@ -62,6 +62,18 @@ class Filters {
}
}
+
+ void doVerticalAllBases() {
+
+ for(int i=0;i<alignmentLength;i++){
+ if(gap[i] == numSeqs) { filter[i] = '0'; }
+ else if(a[i] == numSeqs) { filter[i] = '0'; }
+ else if(t[i] == numSeqs) { filter[i] = '0'; }
+ else if(c[i] == numSeqs) { filter[i] = '0'; }
+ else if(g[i] == numSeqs) { filter[i] = '0'; }
+ }
+
+ }
void doTrump(Sequence seq) {
View
1 source/classifier/classify.cpp
@@ -101,7 +101,6 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
m->mothurOut("DONE."); m->mothurOutEndLine();
m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();
-
readTaxonomy(taxFile);
//sanity check
Oops, something went wrong.

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