<commit_before>package org.broadinstitute.sting.indels;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;

import com.sun.org.apache.bcel.internal.generic.RETURN;

public class MultipleAlignment implements Iterable<Integer>  {
	private static final int IMPOSSIBLE = 1000000000;
	private Map<Integer,Integer> index; 
	private List<String> seqs;
	private List<Integer> ext_ids;
	private List<Integer>  alignment_offsets; // offset of seqs[i] w/respect to seqs[0]
	private int best_mm; // mismatch count
	private int next_mm; // next-best mismatch count
		
	public MultipleAlignment() {
		index = new HashMap<Integer,Integer>();
		seqs = new ArrayList<String>();
		alignment_offsets = new ArrayList<Integer>();
		ext_ids = new ArrayList<Integer>();
	}

	public void clear() {
		seqs.clear();
		index.clear();
		alignment_offsets.clear();
		ext_ids.clear();
	}
	
	/** Adds  single sequence with id set to i. Pile must be empty, or IllegalStateException will be thrown<commit_msg>removed unnecessary import that produced a warning. where did it come from in the first place??<commit_after>package org.broadinstitute.sting.indels;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;


public class MultipleAlignment implements Iterable<Integer>  {
	private static final int IMPOSSIBLE = 1000000000;
	private Map<Integer,Integer> index; 
	private List<String> seqs;
	private List<Integer> ext_ids;
	private List<Integer>  alignment_offsets; // offset of seqs[i] w/respect to seqs[0]
	private int best_mm; // mismatch count
	private int next_mm; // next-best mismatch count
		
	public MultipleAlignment() {
		index = new HashMap<Integer,Integer>();
		seqs = new ArrayList<String>();
		alignment_offsets = new ArrayList<Integer>();
		ext_ids = new ArrayList<Integer>();
	}

	public void clear() {
		seqs.clear();
		index.clear();
		alignment_offsets.clear();
		ext_ids.clear();
	}
	
	/** Adds  single sequence with id set to i. Pile must be empty, or IllegalStateException will be thrown
{'fraction_non_alphanumeric': 0.10657276995305165, 'fraction_numerical': 0.010328638497652582, 'mean_word_length': 4.790760869565218, 'pattern_counts': {'":': 0, '<': 21, '<?xml version=': 0, '>': 21, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 2, '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': '2372609', 'n_tokens_mistral': 697, 'n_tokens_neox': 636, 'n_words': 196}