added kruskal.wallis command. added worked on make.lefse. working of lefse command...

[mothur.git] / designmap.h

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+//
+//  designmap.h
+//  Mothur
+//
+//  Created by SarahsWork on 6/17/13.
+//  Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__designmap__
+#define __Mothur__designmap__
+
+#include "mothurout.h"
+
+/* This class is a representation of the design file.  
+ 
+ group    treatment    sex        age
+ F000142    Early       female    young
+ F000132    Late        male        old
+ F000138    Mid         male        old
+ 
+ 
+ */
+
+class DesignMap {
+public:
+       DesignMap() { m = MothurOut::getInstance(); defaultClass = "not found"; }
+       DesignMap(string); 
+       ~DesignMap() {}
+    
+    int read(string);
+    string get(string, string); //groupName, category returns value. example F000132, sex -> male
+    string get(string); //groupName, returns first categories value. example F000132, -> late
+    vector<string> getValues(string); //categoryName, returns values. example treatment, -> early,late,mid
+       int set(string, map<string, string>); //groupName, map<category, value>
+    int push_back(string, vector<string>); //groupName, vector<value> - assumes you put values in order of getNamesOfCategories
+       vector<string> getNamesOfCategories() {
+               sort(namesOfCategories.begin(), namesOfCategories.end());
+        return namesOfCategories;
+       }
+    int getNumCategories() { return namesOfCategories.size(); }
+       int getNum()  {  return designMap.size();  }
+    int getNumUnique(map<string, vector<string> >); //get number of groups belonging to a category or set of categories, with value or a set of values. Must have all categories and values. Example:
+    //  map<treatment - > early, late>, <sex -> male> would return 1. Only one group is male and from early or late.
+    int getNumShared(map<string, vector<string> >); //get number of groups belonging to a category or set of categories, with value or a set of values. Must have at least one categories and values. Example:
+    //  map<treatment - > early, late>, <sex -> male> would return 3. All three group have are either male or from early or late.
+
+    vector<string> getNames();
+    vector<string> getNames(string, string); //get names group from category and value.
+       vector<string> getNamesUnique(map<string, vector<string> >); //get names of groups belonging to a category or set of categories, with value or a set of values. Must have all categories and values. Example:
+    //  map<treatment - > early, late>, <sex -> male> would return F000132. F000132 is the only group which is male and from early or late.
+    vector<string> getNamesShared(map<string, vector<string> >); //get names of groups belonging to a category or set of categories, with value or a set of values. Must have at least one categories and values. Example:
+    //  map<treatment - > early, late>, <sex -> male> would return F000132, F000142, F000138. All three group have are either male or from early or late.
+
+    int print(ofstream&);
+    int print(ofstream&, vector<string>); //print certain categories
+    
+    string getDefaultClass() { return defaultClass; }
+    
+private:
+    string defaultClass;
+       vector<string> namesOfCategories;
+       MothurOut* m;
+       vector< vector<string> > designMap;
+    vector< map<string, int> > totalCategories;  //for each category, total groups assigned to it.   vector[0] early -> 1, vector[1] male -> 2
+    map<string, int> indexNameMap;
+    map<string, int> indexCategoryMap;
+};
+
+
+#endif /* defined(__Mothur__designmap__) */