<commit_before>package edu.psu.compbio.seqcode.projects.akshay.chexmix.analysis;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.*;

import edu.psu.compbio.seqcode.projects.akshay.chexmix.datasets.*;


public class BuildSeed {
	
	public Map<BLpair,CustomReturn> allpairs = new HashMap<BLpair, CustomReturn>();
	public Map<BindingLocation,Integer> removed = new HashMap<BindingLocation,Integer>();
	public Map<BindingLocation,Double> pccpairwise = new HashMap<BindingLocation,Double>();
	public double cutoff;
	public int smoothsize;
	public BuildSeed(List<BindingLocation> topBlList, int range, int smoothsize, double cutoff) {
		this.cutoff = cutoff;
		this.smoothsize = smoothsize;
		for(int i=0; i<topBlList.size()-1; i++){
			for(int j=i+1; j< topBlList.size(); j++ ){
				if(i != j){
					BLpair pair = new BLpair(topBlList.get(i),topBlList.get(j));
					CustomReturn pccmax = topBlList.get(i).scanTwoBLs(topBlList.get(j), range, smoothsize);
					allpairs.put(pair, pccmax);
				}
			}
		}
	}
	
	public BindingLocation getCenter(){
		for (BLpair pair: allpairs.keySet()){
			if(!removed.containsKey(pair.BL1) && !removed.containsKey(pair.BL2)){
				if(pccpairwise.containsKey(pair.BL1)){
					pccpairwise.put(pair.BL1, pccpairwise.get(pair.BL1) + allpairs.get(pair).pcc);
				}
				else{
					pccpairwise.put(pair.BL1, allpairs.get(pair).pcc);
				}<commit_msg>still debugging<commit_after>package edu.psu.compbio.seqcode.projects.akshay.chexmix.analysis;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.util.*;

import edu.psu.compbio.seqcode.projects.akshay.chexmix.datasets.*;


public class BuildSeed {
	
	public Map<BLpair,CustomReturn> allpairs = new HashMap<BLpair, CustomReturn>();
	public Map<BindingLocation,Integer> removed = new HashMap<BindingLocation,Integer>();
	public Map<BindingLocation,Double> pccpairwise = new HashMap<BindingLocation,Double>();
	public double cutoff;
	public int smoothsize;
	public BuildSeed(List<BindingLocation> topBlList, int range, int smoothsize, double cutoff) {
		this.cutoff = cutoff;
		this.smoothsize = smoothsize;
		for(int i=0; i<topBlList.size()-1; i++){
			for(int j=i+1; j< topBlList.size(); j++ ){
				if(i != j){
					//debugging line
					System.out.println(i+"to"+j);
					BLpair pair = new BLpair(topBlList.get(i),topBlList.get(j));
					CustomReturn pccmax = topBlList.get(i).scanTwoBLs(topBlList.get(j), range, smoothsize);
					allpairs.put(pair, pccmax);
				}
			}
		}
	}
	
	public BindingLocation getCenter(){
		for (BLpair pair: allpairs.keySet()){
			if(!removed.containsKey(pair.BL1) && !removed.containsKey(pair.BL2)){
				if(pccpairwise.containsKey(pair.BL1)){
					pccpairwise.put(pair.BL1, pccpairwise.get(pair.BL1) + allpairs.get(pair).pcc);
				}
				else{
					pccpairwise.put(pair.BL1, allpairs.get(pair).pcc);
				}
{'fraction_non_alphanumeric': 0.14489311163895488, 'fraction_numerical': 0.006107906345436036, 'mean_word_length': 4.791748526522594, 'pattern_counts': {'":': 0, '<': 21, '<?xml version=': 0, '>': 17, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5713548', 'n_tokens_mistral': 1180, 'n_tokens_neox': 1054, 'n_words': 184}