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Benches classify.rf command

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1 parent 2e89f31 commit 8ca2f06dc9062ace4ee3cb3b0072188336f54465 @mothur-westcott mothur-westcott committed Jul 19, 2016
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36 Mothur.xcodeproj/project.pbxproj
@@ -324,12 +324,10 @@
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@@ -369,11 +367,11 @@
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483C952E188F0CAD0035E7B7 /* (null) in Sources */ = {isa = PBXBuildFile; };
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48705AC719BE32C50075E977 /* sharedrjsd.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48705AC119BE32C50075E977 /* sharedrjsd.cpp */; };
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487D09EB1CB2CEF3007039BF /* vsearchfileparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 489B55701BCD7F0100FB7DC8 /* vsearchfileparser.cpp */; };
487D09EC1CB2CEFE007039BF /* averagelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 2114A7671C654D7400D3D8D9 /* averagelinkage.cpp */; };
@@ -403,7 +401,6 @@
48EDB76C1D1320DD00F76E93 /* chimeravsearchcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48EDB76A1D1320DD00F76E93 /* chimeravsearchcommand.cpp */; };
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835FE03E19F00A4D005AA754 /* svm.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7B21820117AD77BD00286E6A /* svm.cpp */; };
83F25B0C163B031200ABE73D /* forest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 83F25B0A163B031200ABE73D /* forest.cpp */; };
@@ -808,8 +805,9 @@
4827A4DB1CB3ED2100345170 /* fastqdataset.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastqdataset.h; sourceTree = "<group>"; };
4829D9651B8387D0002EEED4 /* testbiominfocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = testbiominfocommand.cpp; sourceTree = "<group>"; };
4829D9661B8387D0002EEED4 /* testbiominfocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = testbiominfocommand.h; sourceTree = "<group>"; };
+ 4846AD881D3810DD00DE9913 /* testtrimoligos.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = testtrimoligos.cpp; sourceTree = "<group>"; };
+ 4846AD891D3810DD00DE9913 /* testtrimoligos.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = testtrimoligos.hpp; sourceTree = "<group>"; };
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48705ABB19BE32C50075E977 /* getmimarkspackagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = getmimarkspackagecommand.cpp; path = source/commands/getmimarkspackagecommand.cpp; sourceTree = SOURCE_ROOT; };
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@@ -818,7 +816,6 @@
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487C5A861AB88B93002AF48A /* mimarksattributescommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = mimarksattributescommand.h; path = source/commands/mimarksattributescommand.h; sourceTree = SOURCE_ROOT; };
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@@ -860,8 +857,6 @@
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83F25B0B163B031200ABE73D /* forest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = forest.h; path = source/randomforest/forest.h; sourceTree = SOURCE_ROOT; };
8DD76FB20486AB0100D96B5E /* mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = mothur; sourceTree = BUILT_PRODUCTS_DIR; };
@@ -1723,6 +1718,8 @@
48D6E96A1CA4262A008DF76B /* dataset.h */,
4827A4DA1CB3ED2100345170 /* fastqdataset.cpp */,
4827A4DB1CB3ED2100345170 /* fastqdataset.h */,
+ 4846AD881D3810DD00DE9913 /* testtrimoligos.cpp */,
+ 4846AD891D3810DD00DE9913 /* testtrimoligos.hpp */,
48D6E9661CA42389008DF76B /* testvsearchfileparser.cpp */,
48D6E9671CA42389008DF76B /* testvsearchfileparser.h */,
481FB5221AC0AA010076CFF3 /* testcontainers */,
@@ -1777,8 +1774,6 @@
children = (
A7386C1B1619CACB00651424 /* abstractdecisiontree.hpp */,
A7386C241619E52200651424 /* abstractdecisiontree.cpp */,
- 48705ABA19BE32C50075E977 /* abstractrandomforest.hpp */,
- 48705AC319BE32C50075E977 /* abstractrandomforest.cpp */,
A7386C1D1619CACB00651424 /* decisiontree.hpp */,
A7386C28161A110700651424 /* decisiontree.cpp */,
A7386C1E1619CACB00651424 /* macros.h */,
@@ -1788,8 +1783,6 @@
A77E193A161B289600DB1A2A /* rftreenode.cpp */,
83F25B0A163B031200ABE73D /* forest.cpp */,
83F25B0B163B031200ABE73D /* forest.h */,
- 834D9D561656D7C400E7FAB9 /* regularizedrandomforest.cpp */,
- 834D9D571656D7C400E7FAB9 /* regularizedrandomforest.h */,
);
name = randomforest;
path = /Users/sarahwestcott/Desktop/mothur;
@@ -2735,6 +2728,7 @@
481FB5E61AC1B77E0076CFF3 /* normalizesharedcommand.cpp in Sources */,
481FB5E71AC1B77E0076CFF3 /* nmdscommand.cpp in Sources */,
481FB52B1AC1B09F0076CFF3 /* setseedcommand.cpp in Sources */,
+ 4846AD8A1D3810DD00DE9913 /* testtrimoligos.cpp in Sources */,
481FB5261AC0ADA00076CFF3 /* sequence.cpp in Sources */,
481FB5C61AC1B74F0076CFF3 /* getrelabundcommand.cpp in Sources */,
481FB6571AC1B8100076CFF3 /* inputdata.cpp in Sources */,
@@ -2755,7 +2749,6 @@
481FB5DD1AC1B77E0076CFF3 /* matrixoutputcommand.cpp in Sources */,
481FB5771AC1B6EA0076CFF3 /* spearman.cpp in Sources */,
481FB6031AC1B7970076CFF3 /* secondarystructurecommand.cpp in Sources */,
- 481FB66F1AC1B8520076CFF3 /* regularizedrandomforest.cpp in Sources */,
481FB5361AC1B5DC0076CFF3 /* getopt_long.cpp in Sources */,
481FB5A41AC1B7300076CFF3 /* clustercommand.cpp in Sources */,
481FB5671AC1B6AD0076CFF3 /* sharedmorisitahorn.cpp in Sources */,
@@ -2800,7 +2793,6 @@
481FB5831AC1B6FF0076CFF3 /* ccode.cpp in Sources */,
481FB5681AC1B6B20076CFF3 /* sharedochiai.cpp in Sources */,
481FB66E1AC1B8520076CFF3 /* forest.cpp in Sources */,
- 481FB66A1AC1B8520076CFF3 /* abstractrandomforest.cpp in Sources */,
481FB56A1AC1B6B80076CFF3 /* sharedsobs.cpp in Sources */,
481FB6671AC1B8450076CFF3 /* randomnumber.cpp in Sources */,
481FB5DB1AC1B75C0076CFF3 /* makelefsecommand.cpp in Sources */,
@@ -3170,7 +3162,6 @@
A7E9B95D12D37EC400DA6239 /* sharedsorclass.cpp in Sources */,
A7E9B95E12D37EC400DA6239 /* sharedsorest.cpp in Sources */,
A7E9B95F12D37EC400DA6239 /* sharedthetan.cpp in Sources */,
- 48705AC819BE32C50075E977 /* abstractrandomforest.cpp in Sources */,
A7E9B96012D37EC400DA6239 /* sharedthetayc.cpp in Sources */,
A7E9B96112D37EC400DA6239 /* sharedutilities.cpp in Sources */,
A7E9B96212D37EC400DA6239 /* shen.cpp in Sources */,
@@ -3287,7 +3278,6 @@
A721AB72161C572A009860A1 /* kmertree.cpp in Sources */,
A721AB77161C573B009860A1 /* taxonomynode.cpp in Sources */,
83F25B0C163B031200ABE73D /* forest.cpp in Sources */,
- 834D9D581656D7C400E7FAB9 /* regularizedrandomforest.cpp in Sources */,
A7496D2E167B531B00CC7D7C /* kruskalwalliscommand.cpp in Sources */,
A79EEF8616971D4A0006DEC1 /* filtersharedcommand.cpp in Sources */,
A74C06E916A9C0A9008390A3 /* primerdesigncommand.cpp in Sources */,
@@ -3334,7 +3324,7 @@
"DYLIB_CURRENT_VERSION[sdk=*]" = "";
GCC_DYNAMIC_NO_PIC = NO;
GCC_MODEL_TUNING = G5;
- GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
"VERSION=\"\\\"1.37.1\\\"\"",
"RELEASE_DATE=\"\\\"04/11/2016\\\"\"",
@@ -3369,7 +3359,7 @@
DEPLOYMENT_LOCATION = YES;
DSTROOT = TARGET_BUILD_DIR;
GCC_MODEL_TUNING = G5;
- GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
"VERSION=\"\\\"1.37.1\\\"\"",
"RELEASE_DATE=\"\\\"04/11/2016\\\"\"",
@@ -3397,17 +3387,17 @@
buildSettings = {
CLANG_WARN_UNREACHABLE_CODE = YES;
DEPLOYMENT_LOCATION = NO;
- GCC_C_LANGUAGE_STANDARD = "compiler-default";
+ GCC_C_LANGUAGE_STANDARD = c11;
GCC_ENABLE_SSE3_EXTENSIONS = NO;
GCC_ENABLE_SSE41_EXTENSIONS = NO;
GCC_ENABLE_SSE42_EXTENSIONS = NO;
- GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
"VERSION=\"\\\"1.36.0\\\"\"",
"RELEASE_DATE=\"\\\"07/23/2015\\\"\"",
);
- GCC_VERSION = "/usr/bin/c++";
+ GCC_VERSION = "";
"GCC_VERSION[arch=*]" = "";
GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
@@ -3444,10 +3434,10 @@
buildSettings = {
CLANG_WARN_UNREACHABLE_CODE = YES;
DEPLOYMENT_LOCATION = NO;
- GCC_C_LANGUAGE_STANDARD = "compiler-default";
+ GCC_C_LANGUAGE_STANDARD = c11;
GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
GCC_MODEL_TUNING = "";
- GCC_OPTIMIZATION_LEVEL = 3;
+ GCC_OPTIMIZATION_LEVEL = 0;
GCC_PREPROCESSOR_DEFINITIONS = (
"VERSION=\"\\\"1.37.6\\\"\"",
"RELEASE_DATE=\"\\\"06/20/2016\\\"\"",
View
43 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
+
+
+}
+/**************************************************************************************************/
View
38 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 */
View
2 source/commandfactory.cpp
@@ -305,7 +305,7 @@ CommandFactory::CommandFactory(){
commands["make.table"] = "make.table";
commands["sff.multiple"] = "sff.multiple";
commands["quit"] = "quit";
- commands["classify.rf"] = "classify.rf";
+ //commands["classify.rf"] = "classify.rf";
commands["classify.svm"] = "classify.svm";
commands["filter.shared"] = "filter.shared";
commands["primer.design"] = "primer.design";
View
14 source/commands/classifyrfsharedcommand.cpp
@@ -403,23 +403,23 @@ void ClassifyRFSharedCommand::processSharedAndDesignData(vector<SharedRAbundVect
}
dataSet[i][j] = treatmentToIntMap[treatmentName];
}
- cout << "here" << endl;
+
RandomForest randomForest(dataSet, numDecisionTrees, treeSplitCriterion, doPruning, pruneAggressiveness, discardHighErrorTrees, highErrorTreeDiscardThreshold, optimumFeatureSubsetSelectionCriteria, featureStandardDeviationThreshold);
- cout << "here" << endl;
+
randomForest.populateDecisionTrees();
- cout << "here" << endl;
+
randomForest.calcForrestErrorRate();
- cout << "here" << endl;
+
randomForest.printConfusionMatrix(intToTreatmentMap);
- cout << "here" << endl;
+
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "RF.";
variables["[distance]"] = lookup[0]->getLabel();
string filename = getOutputFileName("summary", variables);
outputNames.push_back(filename); outputTypes["summary"].push_back(filename);
randomForest.calcForrestVariableImportance(filename);
- cout << "here" << endl;
+
//
map<string, string> variable;
variable["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "misclassifications.";
@@ -428,7 +428,7 @@ void ClassifyRFSharedCommand::processSharedAndDesignData(vector<SharedRAbundVect
outputNames.push_back(mc_filename); outputTypes["summary"].push_back(mc_filename);
randomForest.getMissclassifications(mc_filename, intToTreatmentMap, names);
//
- cout << "here" << endl;
+
m->mothurOutEndLine();
}
catch(exception& e) {
Oops, something went wrong.

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