changes while testing

[mothur.git] / lefsecommand.h

diff --git a/lefsecommand.h b/lefsecommand.h
index 095ad48da125fbfe83f30aaff41eb62ec18c610f..cb1bbb6da80f7da1567979dd158fb5861e74a685 100644 (file)
--- a/lefsecommand.h
+++ b/lefsecommand.h
@@ -12,7 +12,7 @@
 #include "command.hpp"
 
 /* 
- Columns = groups, rows are OTUs, class = design??
+ Columns = groups, rows are OTUs, class = design
  
  From http://huttenhower.sph.harvard.edu/galaxy/root?tool_id=lefse_upload
  Input data consist of a collection of m samples (columns) each made up of n numerical features (rows, typically normalized per-sample, red representing high values and green low). These samples are labeled with a class (taking two or more possible values) that represents the main biological hypothesis under investigation; they may also have one or more subclass labels reflecting within-class groupings.
@@ -22,4 +22,58 @@
  Step 3: the resulting subset of vectors is used to build a Linear Discriminant Analysis model from which the relative difference among classes is used to rank the features. The final output thus consists of a list of features that are discriminative with respect to the classes, consistent with the subclass grouping within classes, and ranked according to the effect size with which they differentiate classes.
 */
 
+
+#include "command.hpp"
+#include "inputdata.h"
+#include "designmap.h"
+
+/**************************************************************************************************/
+
+class LefseCommand : public Command {
+public:
+    LefseCommand(string);
+    LefseCommand();
+    ~LefseCommand(){}
+    
+    vector<string> setParameters();
+    string getCommandName()                    { return "lefse";                       }
+    string getCommandCategory()                { return "OTU-Based Approaches";                }
+    
+    string getOutputPattern(string);
+       string getHelpString();
+    string getCitation() { return "Segata, N., J. Izard, L. Waldron, D. Gevers, L. Miropolsky, W. S. Garrett, and C. Huttenhower. 2011. Metagenomic biomarker discovery and explanation. Genome Biol 12:R60, http://www.mothur.org/wiki/Lefse"; }
+    string getDescription()            { return "brief description"; }
+    
+    int execute();
+    void help() { m->mothurOut(getHelpString()); }
+    
+private:
+    bool abort, allLines, wilc, wilcsamename, curv, subject, normMillion;
+    string outputDir, sharedfile, designfile, mclass, subclass, rankTec, multiClassStrat;
+    vector<string> outputNames;
+    set<string> labels;
+    double anovaAlpha, wilcoxonAlpha, fBoots, ldaThreshold;
+    int nlogs, iters, strict, minC;
+    
+    int process(vector<SharedRAbundFloatVector*>&, DesignMap&);
+    int normalize(vector<SharedRAbundFloatVector*>&);
+    map<int, double> runKruskalWallis(vector<SharedRAbundFloatVector*>&, DesignMap&);
+    map<int, double> runWilcoxon(vector<SharedRAbundFloatVector*>&, DesignMap&, map<int, double>, map<string, set<string> >& class2SubClasses, map<string, vector<int> >& subClass2GroupIndex, map<string, string>);
+    bool testOTUWilcoxon(map<string, set<string> >& class2SubClasses, vector<float> abunds, map<string, vector<int> >& subClass2GroupIndex, map<string, string>);
+    map<int, double> testLDA(vector<SharedRAbundFloatVector*>&, map<int, double>, map<string, vector<int> >& class2GroupIndex, map<string, vector<int> >&);
+    bool contastWithinClassesOrFewPerClass(vector< vector<double> >&, vector<int> rands, int minCl, map<string, vector<int> > class2GroupIndex,  map<int, string> indexToClass);
+    vector< vector<double> > lda(vector< vector<double> >& adjustedLookup, vector<int> rand_s, map<int, string>& indexToClass, vector<string>);
+    vector< vector<double> > getMeans(vector<SharedRAbundFloatVector*>& lookup, map<string, vector<int> >& class2GroupIndex);
+    int printResults(vector< vector<double> >, map<int, double>, map<int, double>, string, vector<string>);
+    
+    //for testing
+    bool printToCoutForRTesting(vector< vector<double> >& adjustedLookup, vector<int> rand_s, map<string, vector<int> >& class2GroupIndex, map<int, double> bins, map<string, vector<int> >&, vector<string>);
+    int makeShared(int);
+};
+
+/**************************************************************************************************/
+
+
+
+
 #endif /* defined(__Mothur__lefsecommand__) */