changed random forest output filename

[mothur.git] / parsimonycommand.h

diff --git a/parsimonycommand.h b/parsimonycommand.h
index db062c6d84a67b72dd1b0b7163f0eae9ca8f0aa5..7f7ad893b74140087248edfd7deb7b8c3441e671 100644 (file)
--- a/parsimonycommand.h
+++ b/parsimonycommand.h
@@ -11,50 +11,64 @@
 
 #include "command.hpp"
 #include "parsimony.h"
-#include "treemap.h"
+#include "counttable.h"
+#include "progress.hpp"
+#include "sharedutilities.h"
+#include "fileoutput.h"
+#include "readtree.h"
 
-using namespace std;
-
-class GlobalData;
 
 class ParsimonyCommand : public Command {
+
+public:
+       ParsimonyCommand(string);       
+       ParsimonyCommand();
+       ~ParsimonyCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "parsimony";                           }
+       string getCommandCategory()             { return "Hypothesis Testing";          }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "Slatkin M, Maddison WP (1989). A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-13. \nSlatkin M, Maddison WP (1990). Detecting isolation by distance using phylogenies of genes. Genetics 126: 249-60. \nMartin AP (2002). Phylogenetic approaches for describing and comparing the diversity of microbial communities. Appl Environ Microbiol 68: 3673-82. \nSchloss PD, Handelsman J (2006). Introducing TreeClimber, a test to compare microbial community structure. Appl Environ Microbiol 72: 2379-84.\nhttp://www.mothur.org/wiki/Parsimony"; }
+       string getDescription()         { return "generic test that describes whether two or more communities have the same structure"; }
+
+       int execute();
+       void help() { m->mothurOut(getHelpString()); }
+       
+private:
+       FileOutput* output;
+       vector<Tree*> T;           //user trees
+       Tree* randT;  //random tree
+       Tree* copyUserTree; 
+       CountTable* ct; 
+       CountTable* savect;
+       vector<string> groupComb; // AB. AC, BC...
+       string sumFile, randomtree, allGroups, outputDir, treefile, groupfile, namefile, countfile;
+       int iters, numGroups, numComp, counter, processors, numUniquesInName;
+       vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
+       vector< vector<float> > userTreeScores; //scores for users trees for each comb.
+       vector< vector<float> > UScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
+       EstOutput userData;                     //pscore info for user tree
+       EstOutput randomData;           //pscore info for random trees
+       map<int, double>  validScores;  //map contains scores from both user and random
+       vector< map<int, double> > rscoreFreq;  //map <pscore, number of random trees with that score.> -vector entry for each combination.
+       vector< map<int, double> > uscoreFreq;  //map <pscore, number of user trees with that score.> -vector entry for each combination.
+       vector< map<int, double> > rCumul;  //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
+       vector< map<int, double> > uCumul;  //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
+       
+       ofstream outSum;
+       bool abort;
+       string groups, itersString;
+       vector<string> Groups, outputNames; //holds groups to be used
+       map<string, string> nameMap;
        
-       public:
-               ParsimonyCommand();     
-               ~ParsimonyCommand() { delete pars; }
-               int execute();  
+       void printParsimonyFile();  
+       int printUSummaryFile();
+       void getUserInput();
+       int readNamesFile();
        
-       private:
-               GlobalData* globaldata;
-               vector<Tree*> T;           //user trees
-               Tree* randT;  //random tree
-               Tree* copyUserTree; 
-               TreeMap* tmap; 
-               TreeMap* savetmap;
-               Parsimony* pars;
-               vector<string> groupComb; // AB. AC, BC...
-               string parsFile, sumFile, randomtree;
-               int iters, numGroups, numComp;
-               vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
-               vector< vector<float> > userTreeScores; //scores for users trees for each comb.
-               vector< vector<float> > UScoreSig;  //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
-               EstOutput userData;                     //pscore info for user tree
-               EstOutput randomData;           //pscore info for random trees
-               vector< map<int, double> > validScores;  //map contains scores from both user and random
-               vector< map<int, double> > rscoreFreq;  //map <pscore, number of random trees with that score.> -vector entry for each combination.
-               vector< map<int, double> > uscoreFreq;  //map <pscore, number of user trees with that score.> -vector entry for each combination.
-               vector< map<int, double> > rCumul;  //map <pscore, cumulative percentage of number of random trees with that score or lower.> -vector entry for each combination.
-               vector< map<int, double> > uCumul;  //map <pscore, cumulative percentage of number of user trees with that score or lower .> -vector entry for each combination.
-               map<int, double>::iterator it;
-               map<int, double>::iterator it2;
-               
-               ofstream out, outSum;
-               
-               void printParsimonyFile();  
-               void printUSummaryFile();
-               void getUserInput();
-               void setGroups();
-               
 };