package GraphAlgorithm;

import java.io.BufferedWriter;

import java.io.File;

import java.io.FileWriter;

import java.io.IOException;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import network.CommGeneticsLoader;

import network.DisGraph;

import network.SparseVector;

import util.DCNOMIMUMLSIDmap;

/**

 * Implements leave one out cross validation to test the performance of disease genetics prediction

 * @author zhengc

 *

 */

public class CrossValidation {

    private Map<String, Integer> generank = new HashMap<>();

    /**

     * Initiate and create a cross validation object 

     * @param cgg CommGeneticsGraph

     * @param dis query disease

     * @param genelist omim genes for query disease

     * @throws IOException

     */

    public CrossValidation(DisGraph cgg, String dis, List<String> genelist) throws IOException {

        String dis_id = null;

        if (DCNOMIMUMLSIDmap.dcnnameidmap.containsKey(dis)) {

            dis_id = DCNOMIMUMLSIDmap.dcnnameidmap.get(dis);

        } else {

            System.out.println("No such disease in this network!");

        }

        List<String> dislist = new ArrayList<>();

        dislist.add(dis);

        SparseVector seed = RandomWalk.createSeedVector(dislist);

        int dis_idx = CommGeneticsLoader.entry_index.get(dis_id);

        int count = 1;

        for (String gene : genelist) {

            System.out.println(count + " of " +  genelist.size());

            if (CommGeneticsLoader.entry_index.containsKey(gene)) {

                int gene_idx = CommGeneticsLoader.entry_index.get(gene);

                cgg.removeEdge(dis_idx, gene_idx);

                RandomWalk rw = new RandomWalk(cgg, seed, 0.2);

                Map<String, Integer> result = rw.getRWRank();

                int rank = result.get(gene);

                generank.put(gene, rank);

                count++;

            }

        }

    }

    /**

     * Get disease OMIM gene ranking from leave one out cross validation 

     * @return disease OMIM gene ranking map

     */

    public Map<String, Integer> getCV() {

        return generank;

    }

    /** 

     * Write leave one out cross validation to a file

     * @param cv disease OMIM gene ranking map

     * @param cvfile a file to be written

     * @throws IOException

     */

    public static void saveCV(Map<String, Integer> cv, String cvfile) throws IOException {

        BufferedWriter bw = new BufferedWriter(new FileWriter(new File(cvfile)));

        bw.write("Gene" + ","  + "Rank" + "," + "Percentage" +  "\n");

        for (String gene : cv.keySet()) {

//          System.out.println(sortedgenemap.get(s));

            int rank = cv.get(gene);

            double perc = rank / CommGeneticsLoader.num_gene * 100;

            bw.write(gene + "," + rank + "," + perc + "\n");

        }

        bw.close();

    }

    public static void main(String[] args) throws IOException {

        System.out.println("Building network...");

        String dcnmapfile = "/Users/zhengc/workspace/FARES/data/FARES/map/term_umls_id_diso";

        String omimmapfile = "/Users/zhengc/workspace/FARES/data/OMIM/map/OMIM_umls_id_diso";

        util.DCNOMIMUMLSIDmap.createDCNIdNameMap(dcnmapfile);

        util.DCNOMIMUMLSIDmap.createOMIMIdNameMap(omimmapfile);

        String DCN_dis = "dementia";

        String OMIM_pat = "alzheimer";

        DCNOMIMUMLSIDmap domim = new DCNOMIMUMLSIDmap(DCN_dis, OMIM_pat);

        Map<String, List<String>> dcn_omim = domim.getDCNOMIMUMLSIDmap();

        /*

         * Build the bipartite network

         */

        String commnetfile = "/Users/zhengc/Projects/AD_comorbidity/data/fares_comm_net_conf_ISMB_final_public.txt";

        String dmnfile = "/Users/zhengc/Projects/AD_comorbidity/data/dmn_dm.txt";

        String ppifile = "/Users/zhengc/Projects/AD_comorbidity/data/gene_gene_string_cut.txt";

        String disgenefile = "/Users/zhengc/workspace/FARES/data/OMIM/mapped_OMIM/OMIM_disease_gene_umls_id_diso";

        DisGraph cgg = null;

        try {

//          cgg = CommGeneticsLoader.createCommGeneticsGraph(commnetfile, dmnfile, ppifile, disgenefile, dcn_omim);

            cgg = CommGeneticsLoader.createCommGeneticsGraph(commnetfile, ppifile, disgenefile, dcn_omim);

        } catch (IOException e) {

            // TODO Auto-generated catch block

            e.printStackTrace();

        }

        System.out.println("Done!");

        /*

         * Cross validation

         */

        System.out.println("Starting crossvalidate...");

        String genelistfile = "/Users/zhengc/Projects/AD_comorbidity/data/AD_omim_genes.txt";

        List<String> genelist = util.FileToList.createListFromfile(genelistfile);

        CrossValidation cv = new CrossValidation(cgg, DCN_dis, genelist);

        Map<String, Integer> generank = cv.getCV();

        for (String gene : generank.keySet()) {

            System.out.println(gene + ": " + generank.get(gene));

        }

        String cv_result_file = "/Users/zhengc/Projects/AD_comorbidity/results/evaluation/cv_result.csv";

        saveCV(generank, cv_result_file);

    }

}