<commit_before>package xtandem;

import java.util.ArrayList;

/**
 * This class contains all the parsed data from a xtandem file peptide
 * 
 * @author <NAME>
 */
public class Peptide {

	/**
	 * This variable contains the peptide id (as an index).
	 */
	private String iPeptideID;
	/**
	 * Contains the start position of the peptide == beginning of the protein's peptide sequence
	 */
	private int iStart = 0;
	/**
	 * Contains the end position of the peptide == end ot the protein's peptide sequence
	 */
	private int iEnd = 0;
	/**
	 * This String contains the peptide sequence
	 */
	private String iSequence = null;
	/**
	 * This String contains the original FASTA file path
	 */
	private String iFastaFilePath = null;
	/**
	 * This String contains the domain identifier (spectrum#).(i#).(domain#)
	 */
	private String iDomainID = null;
	/**
	 * Contains the domain start position == first residue of the domain
	 */
	private int iDomainStart = 0;
	/**
	 * Contains the domain end position == last residue of the domain
	 */
	private int iDomainEnd = 0;
	/**
	 * This double holds the expectation value for the peptide identification
	 */
	private double iDomainExpect = 0;
	/**
	 * This double holds the calculated peptide mass + a proton
	 */
	private double domainMh = 0;
	/**
	 * This double holds the spectrum mh minus the calculated mh
	 */
	private double domainDeltaMh = 0;
	/**
	 * This double hold Tandem's score for the identification
	 */
	private double domainHyperScore = 0;
	/**
	 * This double holds the next score of the domain
	 */
	private double domainNextScore = 0;
	/**
	 * This list contains all the differnt sorts of ions.
	 */
	private ArrayList<Ion> iIons = null;
	/**
	 * This String holds the upstream flanking sequence
	 */
	private String upFlankSequence = null;
	/**
	 * This String holds the downstream flanking sequence
	 */
	private String downFlankSequence = null;
	/**
	 * This String presents the sequence of the domain
	 */
	private String domainSequence = null;
    /**
     * Contains the total of missed cleavages
     */
    private int missedCleavages = 0;
    /**
     * Contains the protein to the peptide.
     */
    private Protein iProtein = null;

    /**
     * The Peptide constructor gets the peptide id the start + end position and the sequences as string.
     */
    public Peptide(String aPeptideID,int aStart, int aEnd, String aSequence){
    	iPeptideID = aPeptideID;
    	iStart = aStart;
    	iEnd = aEnd;
    	iSequence = aSequence;
    }

    /**
     * This method gets the start position of the peptide
     *
     * @return int iStart
     */
	public int getStart() {
		return iStart;
	}

	/**
     * This method sets the start position of the peptide
     *
     * @param aStart
     */<commit_msg>- deleted protein variable<commit_after>package xtandem;

import java.util.ArrayList;

/**
 * This class contains all the parsed data from a xtandem file peptide
 * 
 * @author <NAME>
 */
public class Peptide {

	/**
	 * This variable contains the peptide id (as an index).
	 */
	private String iPeptideID;
	/**
	 * Contains the start position of the peptide == beginning of the protein's peptide sequence
	 */
	private int iStart = 0;
	/**
	 * Contains the end position of the peptide == end ot the protein's peptide sequence
	 */
	private int iEnd = 0;
	/**
	 * This String contains the peptide sequence
	 */
	private String iSequence = null;
	/**
	 * This String contains the original FASTA file path
	 */
	private String iFastaFilePath = null;
	/**
	 * This String contains the domain identifier (spectrum#).(i#).(domain#)
	 */
	private String iDomainID = null;
	/**
	 * Contains the domain start position == first residue of the domain
	 */
	private int iDomainStart = 0;
	/**
	 * Contains the domain end position == last residue of the domain
	 */
	private int iDomainEnd = 0;
	/**
	 * This double holds the expectation value for the peptide identification
	 */
	private double iDomainExpect = 0;
	/**
	 * This double holds the calculated peptide mass + a proton
	 */
	private double domainMh = 0;
	/**
	 * This double holds the spectrum mh minus the calculated mh
	 */
	private double domainDeltaMh = 0;
	/**
	 * This double hold Tandem's score for the identification
	 */
	private double domainHyperScore = 0;
	/**
	 * This double holds the next score of the domain
	 */
	private double domainNextScore = 0;
	/**
	 * This list contains all the differnt sorts of ions.
	 */
	private ArrayList<Ion> iIons = null;
	/**
	 * This String holds the upstream flanking sequence
	 */
	private String upFlankSequence = null;
	/**
	 * This String holds the downstream flanking sequence
	 */
	private String downFlankSequence = null;
	/**
	 * This String presents the sequence of the domain
	 */
	private String domainSequence = null;
    /**
     * Contains the total of missed cleavages
     */
    private int missedCleavages = 0;


    /**
     * The Peptide constructor gets the peptide id the start + end position and the sequences as string.
     */
    public Peptide(String aPeptideID,int aStart, int aEnd, String aSequence){
    	iPeptideID = aPeptideID;
    	iStart = aStart;
    	iEnd = aEnd;
    	iSequence = aSequence;
    }

    /**
     * This method gets the start position of the peptide
     *
     * @return int iStart
     */
	public int getStart() {
		return iStart;
	}

	/**
     * This method sets the start position of the peptide
     *
     * @param aStart
     */
{'fraction_non_alphanumeric': 0.08872593950504125, 'fraction_numerical': 0.0036663611365719525, 'mean_word_length': 2.861288039631989, 'pattern_counts': {'":': 0, '<': 7, '<?xml version=': 0, '>': 7, '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': '4299604', 'n_tokens_mistral': 1703, 'n_tokens_neox': 1492, 'n_words': 635}