itemsetEnrichment.h

/**************************************************************************
 * Copyright (c) 2005-2011 T. M. Murali                                   *
 * Copyright (c) 2008-2011 Naveed Massjouni                               *
 * Copyright (c) 2004 Greg Grothaus                                       *
 *                                                                        *
 * This file is part of Biorithm.                                         *
 *                                                                        *
 * Biorithm is free software: you can redistribute it and/or modify       *
 * it under the terms of the GNU General Public License as published by   *
 * the Free Software Foundation, either version 3 of the License, or      *
 * (at your option) any later version.                                    *
 *                                                                        *
 * Biorithm is distributed in the hope that it will be useful,            *
 * but WITHOUT ANY WARRANTY; without even the implied warranty of         *
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the          *
 * GNU General Public License for more details.                           *
 *                                                                        *
 * You should have received a copy of the GNU General Public License      *
 * along with Biorithm.  If not, see <http://www.gnu.org/licenses/>.      *
 *                                                                        *
 **************************************************************************/

#include<set>
#include<string>
#include<iostream>
#include<fstream>
#include<algorithm>
#include<vector>
#include<cmath>
#include<utility>

#include "motifDataset.h"
#include "setTemplates.C"
#include "readfile.h"
#include "xmotif.h"
#include "motifDataset.h"
#include "enrichment.h"
#include "GO.h"
#include "stlConversions.cpp"

using namespace std;

#ifndef ITEMENRICHGREG
#define ITEMENRICHGREG

struct itemsetEnrichRecord
{
        string theClass;
        int classID;
        double score;
        int xMotifID;
        string relation;
        string reason;
        string theCategory;
        set<string> annotated;

        bool operator<(const itemsetEnrichRecord& a) const
        {
                //sort by score, then by name of function
                if(score!=a.score)
                        return score<a.score;
                return relation<a.relation;
        }
};
struct itemsetNavRecord
{
        int id;
        string theClass;
        double score;

        bool operator<(const itemsetNavRecord& a) const
        {
                //sort first by class, then score
                if(theClass!=a.theClass)
                        return theClass<a.theClass;
                return score<a.score;
        }
};
struct itemsetGeneRecord
{
        string probename;
        int probeid;
        int green;
        bool operator<(const itemsetGeneRecord& a) const
        {
                if(green!=a.green)
                        return green<a.green;
                return probename<a.probename;
        }
};

class itemsetEnrichment
{
private:
  string web;
  double myAlpha;
  map<string,Enrichment<string,string> > functionClasses;
  // list of itemsets in the classifier. i am losing encapsulation
  // here. why should itemsetEnrichment know about the classifier, but
  // i need this info in the navigation file.
  set<itemsetNavRecord> classifierItemsetList;
  // list of itemsets not in the classifier.
  set<itemsetNavRecord> nonClassifierItemsetList;
  GeneOntology *GO;
  motifDataset *myDataset;

  
  void buildDataFile(int id, const itemset &item, vector<itemsetEnrichRecord> &de);
  void buildDataFile();
  void buildIndexFile();
  void buildNavFile();

public:
  itemsetEnrichment(string annotFile, string gofile,
                    string path,motifDataset *m,double alpha);
  void processItemset(const itemset &in,int id);
};
        
#endif