package network;

import java.io.BufferedReader;

import java.io.BufferedWriter;

import java.io.File;

import java.io.FileReader;

import java.io.FileWriter;

import java.io.IOException;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.Collections;

import java.util.Comparator;

import java.util.HashMap;

import java.util.HashSet;

import java.util.LinkedHashMap;

import java.util.LinkedList;

import java.util.List;

import java.util.Map;

import java.util.Set;

import GraphAlgorithm.ComSearch;

import util.CollectionsEx;

import util.DCNOMIMUMLSIDmap;

/**

 * Provides methods for creating a bipartite network and write it to a network file

 * @author zhengc

 *

 */

public class CommGeneticsLoader {

    public static HashSet<String> entry_set = new HashSet<String>();

    public static HashSet<String> disease_set = new HashSet<String>();

    public static HashSet<String> gene_set = new HashSet<String>();

    public static HashSet<String> DMN_set = new HashSet<String>();

    public static HashSet<String> DCN_set = new HashSet<String>();

    public static List<String> entry_list = new ArrayList<String>();

    public static List<String> disease_list = new ArrayList<String>();

    public static List<String> gene_list = new ArrayList<String>();

    public static List<String> DMN_list = new ArrayList<String>();

    public static List<String> DCN_list = new ArrayList<String>();

    public static int num_gene = 0;

    public static int num_dmn;

    public static int num_dcn;

    public static int num_disease;

    public static Map<Integer, Integer> dis_gene = new HashMap<Integer, Integer>();

    public static Map<String, Integer> entry_index = new HashMap<String, Integer>();

    public static Map<Integer, String> index_entry = new HashMap<Integer, String>();

    public static Map<String, String> idnamemap = new HashMap<String, String>();

    public static Map<String, String> nameidmap = new HashMap<String, String>();

    public static Map<String, String> OMIMidnamemap = new HashMap<String, String>();

    public static Map<String, String> OMIMnameidmap = new HashMap<String, String>();

    public static HashSet<String> soc_set = new HashSet<String>();

    public static Map<String, String> umlssocmap = new HashMap<String, String>();

    public static Map<String, Integer> soc_idx = new HashMap<String, Integer>();

    public static Map<Integer, String> idx_soc = new HashMap<Integer,String>();

    public static final double P = 0.85;

    /**

     * Read DCN net and get DCN disease list

     * @param filename DCN net file

     * @throws IOException

     */

    public static void readCommNet(String filename) throws IOException{

        // get all unique disease set

        BufferedReader br = new BufferedReader(new FileReader(new File(filename)));

        String line = br.readLine();

        while ((line = br.readLine()) != null) {

            String disease = line.split("\\|")[0];

            DCN_set.add(disease);

        }

        br.close();

        DCN_list = util.CollectionsEx.setToList(DCN_set);

        num_dcn = DCN_set.size();

        System.out.println("number of DCN: " + num_dcn);

    }

    /**

     * Write a map from DCN disease UMLS to disease name

     * @param imput map file from disease UMLS to name 

     * @param output a file to be written

     * @throws IOException

     */

    public static void writeDCNIdName(String imput, String output) throws IOException {

        Map<String, String> idnamemap = new HashMap<String, String>();

        BufferedReader br = new BufferedReader(new FileReader(new File(imput)));

        String line = br.readLine();

        while ((line = br.readLine()) != null) {

            String disease_id = line.split("\\|")[0];

            String disease_name = line.split("\\|")[1];

            if(!idnamemap.keySet().contains(disease_id)) {

                idnamemap.put(disease_id, disease_name);

            } 

        }

        br.close();

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

        Set<String> ids = idnamemap.keySet();

        List<String> id_list = util.CollectionsEx.setToList(ids);

        Collections.sort(id_list);

        for(String id : id_list) {

            String name = idnamemap.get(id).replace("-- ", "");

            bw.write(id + "|" + name + "\n");

        }

        bw.close();

    }

    /**

     * Reads DMN to get DMN disease list

     * @param filename DMN net file

     * @throws IOException

     */

    public static void readDMN(String filename) throws IOException{

        // get all unique disease set

        BufferedReader br = new BufferedReader(new FileReader(new File(filename)));

        String line = br.readLine();

        while ((line = br.readLine()) != null) {

            String disease1 = line.split("\\|")[0];

            DMN_set.add(disease1);

            String disease2 = line.split("\\|")[1];

            DMN_set.add(disease2);

        }

        br.close();

        DMN_list = util.CollectionsEx.setToList(DMN_set);

        num_dmn = DMN_set.size();

        System.out.println("number of DMN: " + num_dmn);

    }

    /**

     * Reads PPI to get gene list

     * @param filename

     * @throws IOException

     */

    public static void readPPI(String filename) throws IOException{

        BufferedReader br = new BufferedReader(new FileReader(new File(filename)));

        String line = null;

        while ((line=br.readLine()) != null) {

            String gene = line.split("\\|")[0];

//          System.out.println(2);

            gene_set.add(gene);

        }

        br.close();

        gene_list = util.CollectionsEx.setToList(gene_set);

        num_gene = gene_set.size();

        System.out.println("number of gene: " + num_gene);

    }

    /**

     * Reads UMLS-SOC map file to get UMLS-SOC map

     * @param filename

     * @throws IOException

     */

    public static void readUMLSSOC(String filename) throws IOException{

        BufferedReader br = new BufferedReader(new FileReader(new File(filename)));

        String line = null;

        while ((line=br.readLine()) != null) {

            String[] parts = line.split("\\$");

            String umls = parts[0];

            String soc = parts[8];

            soc_set.add(soc);

            umlssocmap.put(umls, soc);

        }

        br.close();

        int m = 0;

        for (String soc : soc_set) {

            soc_idx.put(soc, m);

            idx_soc.put(m, soc);

            m++;

        }

    }

    /**

     * Creates entry index for all nodes

     * @param entry_list

     */

    public static void createIndex(List<String> entry_list) {

        int m = 0;

        for (String e : entry_list) {

            if (!entry_index.containsKey(e)) {

                entry_index.put(e, m);

                index_entry.put(m, e);

                m++;

            }

        }

        System.out.println("Total nodes: " + entry_index.size());

        System.out.println("--------");

    }

    /**

     * Build a bipartite graph including DCN and PPI, additional DCN-OMIM disease mapping also included

     * @param commnetfile DCN file

     * @param ppifile PPI file

     * @param disgenefile disease genetics file from OMIM

     * @param dcn_omim mapping from DCN disease to OMIM disease

     * @return a bipartite graph

     * @throws IOException

     */

    public static DisGraph createCommGeneticsGraph(String commnetfile, 

            String ppifile, String disgenefile, Map<String, List<String>> dcn_omim) throws IOException {

        readCommNet(commnetfile);

        readPPI(ppifile);

        disease_set.addAll(DCN_set);

        disease_list = util.CollectionsEx.setToList(disease_set);

        entry_list.addAll(disease_list);

        entry_list.addAll(gene_list);

        createIndex(entry_list);

        num_disease = disease_list.size();

        int n = entry_index.size();

        DisGraph cgg = new DisGraph(n);

        // construct DCN net from network file

        // Note: there are two type of network files, attention should be paid that one file contains 

        // additional abbreviation of SOC. Consequently, the second entry should be in column 6 instead 5

        BufferedReader br1 = new BufferedReader(new FileReader(new File(commnetfile)));

        String line1 = null;

        while ((line1 = br1.readLine()) != null) {

            String [] s = line1.split("\\|");

//          System.out.println(s[0]);

            //  System.out.println(s[0]);

            if (entry_index.containsKey(s[0]) && entry_index.containsKey(s[5])) {

                int entry1 = entry_index.get(s[0]);

                int entry2 = entry_index.get(s[5]);

//              double score = Integer.parseInt(s[2]);

                cgg.addEdge(entry1, entry2);

            }

        }

        br1.close();

        // Check if diagonal entry is 1

//      for (int j=0; j<disease_list.size(); j++) {

//          System.out.println(cgg.getNet().get(j, j));

//      }

        BufferedReader br2 = new BufferedReader(new FileReader(new File(ppifile)));

        String line2 = null;

        while ((line2 = br2.readLine()) != null) {

            String [] s = line2.split("\\|");

//          System.out.println(s[0]);

            if (entry_index.containsKey(s[0]) && entry_index.containsKey(s[1])) {

                int entry1 = entry_index.get(s[0]);

                int entry2 = entry_index.get(s[1]);

//              System.out.println(s[0] +"  " + entry1);

//              System.out.println(s[1] +"  " + entry2);

//              double score = Integer.parseInt(s[2]);

                cgg.addEdge(entry1, entry2);

            }

        }

        br2.close();

        // Check if diagonal entry is 1

//      for (int j=disease_list.size(); j<entry_list.size(); j++) {

//          System.out.println(cgg.getNet().get(j, j));

//      }

        BufferedReader br3 = new BufferedReader(new FileReader(new File(disgenefile)));

        String line3 = null;

        Set<String> mappedset = new HashSet<>();

        while ((line3 = br3.readLine()) != null) {

            String [] s = line3.split("\\|");

//          System.out.println(s[0]);

            String disid = s[0];

            String gene = s[1];

            if (entry_index.containsKey(disid) && entry_index.containsKey(gene)) {

                mappedset.add(disid);

                int entry1 = entry_index.get(disid);

                int entry2 = entry_index.get(gene);

//                  System.out.println(s[0] +"  " + entry1);

//                  System.out.println(s[1] +"  " + entry2);

//                  double score = Integer.parseInt(s[2]);

                cgg.addEdge(entry1, entry2);

            }

            // add additional dcn_omim map

            for (String id : dcn_omim.keySet()) {

                List<String> omim_ids = dcn_omim.get(id);

                if (!entry_index.containsKey(disid) && omim_ids.contains(disid)) {

                    disid = id; // update id

                    if (entry_index.containsKey(disid) && entry_index.containsKey(gene)) {

                        int entry1 = entry_index.get(disid);

                        int entry2 = entry_index.get(gene);

                        cgg.addEdge(entry1, entry2);

                    }

                }

            }

        }

        br3.close();

        // Check if diagonal entry is 1

//      for (int j=disease_list.size(); j<entry_list.size(); j++) {

//          System.out.println(cgg.getNet().get(j, j));

//      }

        System.out.println("Total mapped disease: " + mappedset.size());

//      for (int i=0; i<n; i++) {

//          cgg.addEdge(i, i);

//      }

        return cgg;

    }

    /**

     * Build a bipartite graph including DCN, DMN and PPI

     * @param commnetfile DCN file

     * @param dmnfile DMN file

     * @param ppifile PPI file

     * @param disgenefile disease genetics file from OMIM

     * @return a bipartite graph

     * @throws IOException

     */

    public static DisGraph createCommGeneticsGraph(String commnetfile, String dmnfile, 

            String ppifile, String disgenefile) throws IOException {

        readCommNet(commnetfile);

        readDMN(dmnfile);

        readPPI(ppifile);

        disease_set.addAll(DCN_set);

        disease_set.addAll(DMN_set);

        disease_list = util.CollectionsEx.setToList(disease_set);

        entry_list.addAll(disease_list);

        entry_list.addAll(gene_list);

        createIndex(entry_list);

        num_disease = disease_list.size();

        int n = entry_index.size();

        DisGraph cgg = new DisGraph(n); 

//      System.out.println(n);

        BufferedReader br1 = new BufferedReader(new FileReader(new File(commnetfile)));

        String line1 = null;

        while ((line1 = br1.readLine()) != null) {

            String [] s = line1.split("\\|");

//          System.out.println(s[0]);

            //  System.out.println(s[0]);

            if (entry_index.containsKey(s[0]) && entry_index.containsKey(s[4])) {

                int entry1 = entry_index.get(s[0]);

                int entry2 = entry_index.get(s[4]);

//              double score = Integer.parseInt(s[2]);

                cgg.addEdge(entry2, entry1);

            }

        }

        br1.close();

        BufferedReader br2 = new BufferedReader(new FileReader(new File(dmnfile)));

        String line2 = null;

        while ((line2 = br2.readLine()) != null) {

            String [] s = line2.split("\\|");

//          System.out.println(s[0]);

            //  System.out.println(s[0]);

            if (entry_index.containsKey(s[0]) && entry_index.containsKey(s[1])) {

                int entry1 = entry_index.get(s[0]);

                int entry2 = entry_index.get(s[1]);

//              double score = Integer.parseInt(s[2]);

                cgg.addEdge(entry1, entry2);

            }

        }

        br2.close();

        BufferedReader br3 = new BufferedReader(new FileReader(new File(ppifile)));

        String line3 = null;

        while ((line3 = br3.readLine()) != null) {

            String [] s = line3.split("\\|");

//          System.out.println(s[0]);

            if (entry_index.containsKey(s[0]) && entry_index.containsKey(s[1])) {

                int entry1 = entry_index.get(s[0]);

                int entry2 = entry_index.get(s[1]);

//              System.out.println(s[0] +"  " + entry1);

//              System.out.println(s[1] +"  " + entry2);

//              double score = Integer.parseInt(s[2]);

                cgg.addEdge(entry1, entry2);

            }

        }

        br3.close();

        BufferedReader br4 = new BufferedReader(new FileReader(new File(disgenefile)));

        String line4 = null;

        Set<String> mappedset = new HashSet<>();

        while ((line4 = br4.readLine()) != null) {

            String [] s = line4.split("\\|");

//          System.out.println(s[0]);

            String disid = s[0];

            String gene = s[1];

            if (entry_index.containsKey(disid) && entry_index.containsKey(gene)) {

                mappedset.add(disid);

                int entry1 = entry_index.get(disid);

                int entry2 = entry_index.get(s[1]);

//                  System.out.println(s[0] +"  " + entry1);

//                  System.out.println(s[1] +"  " + entry2);

//                  double score = Integer.parseInt(s[2]);

                cgg.addEdge(entry1, entry2);

            }

        }

        br4.close();

        System.out.println("Total mapped disease: " + mappedset.size());

        for (int i=0; i<n; i++) {

            cgg.addEdge(i, i);

        }

        return cgg;

    }

    /**

     * Build a bipartite graph including DCN and PPI, extra mapping and DMN are optional

     * 

     * @param commnetfile DCN file

     * @param dmnfile DMN file

     * @param ppifile PPI file

     * @param disgenefile disease genetics file from OMIM

     * @param dcn_omim mapping from DCN disease to OMIM disease

     * @param dmn a flag to indicate if DMN will be included

     * @param extra a flag to indicate if extra mapping will be included

     * @return a bipartite graph

     * @throws IOException

     */

    public static DisGraph createCommGeneticsGraph(String commnetfile, String dmnfile, 

            String ppifile, String disgenefile, Map<String, List<String>> dcn_omim, Boolean dmn, Boolean extra) throws IOException {

        readCommNet(commnetfile);

        disease_set.addAll(DCN_set);

        if(dmn) {

            readDMN(dmnfile);

            disease_set.addAll(DMN_set);

        }

        disease_list = util.CollectionsEx.setToList(disease_set);

        readPPI(ppifile);

        entry_list.addAll(disease_list);

        entry_list.addAll(gene_list);

        createIndex(entry_list);

        num_disease = disease_list.size();

        int n = entry_index.size();

        DisGraph cgg = new DisGraph(n); 

//      System.out.println(n);

        BufferedReader br1 = new BufferedReader(new FileReader(new File(commnetfile)));

        String line1 = null;

        while ((line1 = br1.readLine()) != null) {

            String [] s = line1.split("\\|");

//          System.out.println(s[0]);

            //  System.out.println(s[0]);

            if (entry_index.containsKey(s[0]) && entry_index.containsKey(s[4])) {

                int entry1 = entry_index.get(s[0]);

                int entry2 = entry_index.get(s[4]);

//              double score = Integer.parseInt(s[2]);

                cgg.addEdge(entry2, entry1);

            }

        }

        br1.close();

        if(dmn) {

            BufferedReader br2 = new BufferedReader(new FileReader(new File(dmnfile)));

            String line2 = null;

            while ((line2 = br2.readLine()) != null) {

                String [] s = line2.split("\\|");

//              System.out.println(s[0]);

                //  System.out.println(s[0]);

                if (entry_index.containsKey(s[0]) && entry_index.containsKey(s[1])) {

                    int entry1 = entry_index.get(s[0]);

                    int entry2 = entry_index.get(s[1]);

//                  double score = Integer.parseInt(s[2]);

                    cgg.addEdge(entry1, entry2);

                }

            }

            br2.close();

        }

        BufferedReader br3 = new BufferedReader(new FileReader(new File(ppifile)));

        String line3 = null;

        while ((line3 = br3.readLine()) != null) {

            String [] s = line3.split("\\|");

//          System.out.println(s[0]);

            if (entry_index.containsKey(s[0]) && entry_index.containsKey(s[1])) {

                int entry1 = entry_index.get(s[0]);

                int entry2 = entry_index.get(s[1]);

//              System.out.println(s[0] +"  " + entry1);

//              System.out.println(s[1] +"  " + entry2);

//              double score = Integer.parseInt(s[2]);

                cgg.addEdge(entry1, entry2);

            }

        }

        br3.close();

        BufferedReader br4 = new BufferedReader(new FileReader(new File(disgenefile)));

        String line4 = null;

        Set<String> mappedset = new HashSet<>();

        while ((line4 = br4.readLine()) != null) {

            String [] s = line4.split("\\|");

//          System.out.println(s[0]);

            String disid = s[0];

            String gene = s[1];

            if (entry_index.containsKey(disid) && entry_index.containsKey(gene)) {

                mappedset.add(disid);

                int entry1 = entry_index.get(disid);

                int entry2 = entry_index.get(gene);

//                  System.out.println(s[0] +"  " + entry1);

//                  System.out.println(s[1] +"  " + entry2);

//                  double score = Integer.parseInt(s[2]);

                cgg.addEdge(entry1, entry2);

            }

            // Additional mapping according to biological meaning

//          if (!entry_index.containsKey(disid) && extra) {

//              for (String id : dcn_omim.keySet()) {

//                  List<String> omim_ids = dcn_omim.get(id);

//                  if (omim_ids.contains(disid)) {

//                      disid = id; // update id

//                      if (entry_index.containsKey(disid) && entry_index.containsKey(gene)) {

//                          int entry1 = entry_index.get(disid);

//                          int entry2 = entry_index.get(gene);

//                          cgg.addEdge(entry1, entry2);

//                      }

//                  }

//          }

            if(extra) {

                for (String id : dcn_omim.keySet()) {

                    List<String> omim_ids = dcn_omim.get(id);

                    if (!entry_index.containsKey(disid) && omim_ids.contains(disid)) {

                        disid = id; // update id

                        if (entry_index.containsKey(disid) && entry_index.containsKey(gene)) {

                            int entry1 = entry_index.get(disid);

                            int entry2 = entry_index.get(gene);

                            cgg.addEdge(entry1, entry2);

                        }

                    }

                }

            }

        }

        br4.close();

        System.out.println("Total mapped disease: " + mappedset.size());

        for (int i=0; i<n; i++) {

            cgg.addEdge(i, i);

        }

        return cgg;

    }

    public static DisGraph createCommGeneticsGraph(DisGraph dg, DisGraph pp, 

            Map<Integer, List<Integer>> dis_genelist) {

        int N1 = dg.getNodes();

        int N2 = pp.getNodes();

        DisGraph cgg = new DisGraph(N1 + N2);

        //add disease comorbidity network

        for (int i=0; i<N1; i++) {

            Set<Integer> neibors = dg.getNeibor(i).getKeys();

            for (int neibor : neibors) {

                cgg.addEdge(i, neibor);

            }

        }

        //add protein-protein interaction network

        for (int i=0; i<N2; i++) {

            Set<Integer> neibors = pp.getNeibor(i).getKeys();

            for (int neibor : neibors) {

                int idx1 = i + N1;

                int idx2 = neibor + N1;

                cgg.addEdge(idx1, idx2);

            }

        }

        //add disease-gene connection

        for (int dis_idx: dis_genelist.keySet()) {

            for (int gene_idx: dis_genelist.get(dis_idx)) {

                cgg.addEdge(dis_idx, gene_idx + N1);

            }

        }

        return cgg;

    }

    /**

     * Creates a UMLS-name mapping

     * @param mapfiles mapping file

     * @throws IOException

     */

    public static void createIdNameMap(List<String> mapfiles) throws IOException {

        for (String mapfile : mapfiles) {

            BufferedReader br = new BufferedReader(new FileReader(mapfile));

            String line = null;

            while((line = br.readLine()) != null){

                String[] parts = line.split("\\|");

                idnamemap.put(parts[0], parts[1].toLowerCase());

                nameidmap.put(parts[1].toLowerCase(), parts[0]);

            }

            br.close();

        }

    }

    /**

     * Create UMLS-name mapping for OMIM

     * @param mapfiles

     * @throws IOException

     */

    public static void createOMIMIdNameMap(List<String> mapfiles) throws IOException {

        for (String mapfile : mapfiles) {

            BufferedReader br = new BufferedReader(new FileReader(mapfile));

            String line = null;

            while((line = br.readLine()) != null){

                String[] parts = line.split("\\|");

                OMIMidnamemap.put(parts[1], parts[0].toLowerCase());

                OMIMnameidmap.put(parts[0].toLowerCase(), parts[1]);

            }

            br.close();

        }

    }

    /**

     * Write the bipartite graph to a file, format is "node1|node2|score"

     * @param cgg the bipartite file

     * @param filename a file to be written

     * @throws IOException

     */

    private static void writeCommGeneticsNet(DisGraph cgg, String filename) throws IOException {

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

        for (int i = 0; i < cgg.getNet().size(); i++) {

            Set<Integer> sv = cgg.getNet().getKey(i);

            for (int k : sv) {

                String d1 = index_entry.get(i);

                String d2 = index_entry.get(k);

                double score = cgg.getNet().get(i, k);

                bw.write(d1 + "|" + d2 + "|" + score + "|" + "\n");

            }

        }

        bw.close();

    }

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

//      #########################################################################

//      ----------------------- Method 1: Build network from files  --------------------

//      #########################################################################

        /*

         * Create additional DCN_OMIM map for give disease

         */

//      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_final/data/OMIM/mapped_OMIM/OMIM_disease_gene_umls_id_diso";

//      

//      String commnetfile = "/Users/zhengc/workspace/FARES_final/analysis/network/DCN/fares_comm_net_lift_final_abbr.txt";;

////        String dmnfile = "/Users/zhengc/workspace/FARES_final/analysis/AD_comorbidity/data/dmn_dm.txt";

//      String ppifile = "/Users/zhengc/workspace/FARES_final/analysis/AD_comorbidity/data/gene_gene_string_cut.txt";

//      String disgenefile = "/Users/zhengc/workspace/FARES_final/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);

//          System.out.println("Total edges: " + cgg.getEdges());

//      } catch (IOException e) {

//          // TODO Auto-generated catch block

//          e.printStackTrace();

//      }

//      

//      

//      

//      /* Write commgenetics file */

//      String netfile = "/Users/zhengc/workspace/FARES_final/analysis/network/DCN_PPI/DCN_PPI_net_lift.txt";

//      writeCommGeneticsNet(cgg, netfile);

//      

//      String disUMLS_name_file = "/Users/zhengc/workspace/FARES_final/analysis/network/DCN_PPI/disUMLS_name_lift.txt";

//      writeDCNIdName(commnetfile, disUMLS_name_file);

//      

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

//      util.DCNOMIMUMLSIDmap.createDCNIdNameMap(dcnmapfile);

//      String diseaseid = util.DCNOMIMUMLSIDmap.dcnnameidmap.get(DCN_dis);

//      System.out.println(diseaseid);

//      int disease_idx = entry_index.get(diseaseid);

//      System.out.println(disease_idx);

//      System.out.println(cgg.getNeibor(disease_idx));

//      

//      Map<String, Double> commDisMap = ComSearch.searchFaers2(diseaseid, cgg);

//      System.out.println("\nNeibor node method......");

//      System.out.println("Number of comorbidities found: " + commDisMap.size() + "\n");

//      for (String dis : commDisMap.keySet()) {

//          System.out.println(dis);

//      }

//      #########################################################################

//      --------------------- Method 2: Build network from  network -------------

//      #########################################################################

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

        String omimmapfile = "/Users/zhengc/workspace/FARES_final/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();

        for (String dis: dcn_omim.keySet()) {

            System.out.println(dcn_omim.get(dis));

        }

        /*

         * Build heterogenous network

         */

        String rulefile = "./data/ID_indications_all_clean_width_umls_id_diso_filtered_sp_lift_1_0.000002_3_processed.txt";

        String commnetfile = "./results/fares_comm_net_lift_final_abbr.txt";;

        String ppifile = "./data/gene_gene_string_cut.txt";

        String disgenefile = "./data/OMIM_disease_gene_umls_id_diso";

        CommLoader.readAssocRules(rulefile);

        DisGraph commnet = CommLoader.createCommNet(rulefile);

        CommLoader.readPPI(ppifile);

        DisGraph ppinet = CommLoader.createPPINet(ppifile);

        Map<Integer, List<Integer>> dis_gene = CommLoader.readDisGene(disgenefile, dcn_omim);

        DisGraph cgg2 = createCommGeneticsGraph(commnet, ppinet, dis_gene);

        System.out.println(cgg2.getEdges());

        System.out.println(cgg2.getNodes());

        String netfile = "./results/DCN_PPI/DCN_PPI_net_lift.txt";

        writeCommGeneticsNet(cgg, netfile);

        String disUMLS_name_file = "./results/disUMLS_name_lift.txt";

        writeDCNIdName(commnetfile, disUMLS_name_file);

    }

}