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1 /**
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2 *****************************************************************************
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3 * <p>
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4 * Copyright (c) Regents of the University of Minnesota. All Rights Reserved.
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5 * <p>
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6 * Author: Kevin Murray University of Minnesota - (murra668@umn.edu)
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7 * <p>
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8 *****************************************************************************
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9 */
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10 package kinamine;
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11
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12 import java.util.ArrayList;
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13 import java.util.Arrays;
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14 import java.util.List;
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15
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16 /**
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17 * Peptide object representing the relevant information from the submitted
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18 * peptide report. Stores the values necessary for writing a report formatted
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19 * for existing Excel sheets.
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20 *
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21 * @version 1.0
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22 * @author murra668
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23 */
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24 public class Peptide {
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25
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26 /** Sequence of peptide. */
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27 String seq;
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28
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29 /** Accession of Protein associated with this peptide. */
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30 List<String> id;
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31
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32 /** Full Accessions. */
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33 String ref;
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34
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35 /** Motif of phospho-tyrosine. */
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36 ArrayList<String> motif;
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37
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38 /** Index of phospho-tyrosine in the peptide sequence. */
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39 ArrayList<Integer> tyrIndex;
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40
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41 /** Index of phospho-tyrosine in protein sequence. */
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42 ArrayList<Integer> tyrProtIndex;
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43
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44 /** Length of peptide sequence. */
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45 int length;
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46
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47 /**
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48 * Constructs a Peptide object from the parsed peptide info from a line in
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49 * the peptide report.
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50 *
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51 * @param pepInfo tab-separated line of peptide info
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52 * @param ids
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53 */
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54 public Peptide(String[] pepInfo, List ids) {
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55
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56 /** Store sequence */
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57 this.seq = pepInfo[8];
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58
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59 /** Store sequence length. */
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60 this.length = pepInfo[8].length();
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61
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62 /** Initialize empty motif array. */
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63 this.motif = new ArrayList<>();
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64
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65 /** Extract peptide references. */
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66 this.id = ids;
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67 this.ref = pepInfo[3];
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68
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69 /** Store the index of phospho-tyrosine of the peptide and protein. */
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70 this.tyrIndex = getIndex(pepInfo[9]);
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71 this.tyrProtIndex = getIndex(pepInfo[10]);
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72 }
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73
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74 /**
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75 * Gets the index of the phospho-tyrosine in the peptide and corresponding
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76 * protein, as indicated by the modification column of the peptide report.
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77 * There may be more than one phospho-tyr within a peptide.
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78 * <p>
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79 * Location formatted as Phospho(Y)@index.
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80 *
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81 * @param mods string of mod locations
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82 * @return ArrayList of integers.
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83 */
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84 private ArrayList<Integer> getIndex(String mods) {
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85
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86 /** Modifications are separated by ';'. */
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87 List<String> psm = Arrays.asList(mods.split(";"));
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88
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89 /** Initialize new index array. */
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90 ArrayList<Integer> index = new ArrayList<>();
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91
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92 /** Check all modifications. */
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93 for (int i = 0; i < psm.size(); i++) {
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94
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95 /** Check if phospho-tyr. */
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96 if (psm.get(i).contains("Phospho(Y)")) {
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97
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98 /** Trim for correct indexing. */
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99 String mod = psm.get(i).trim();
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100
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101 /** Add to index array */
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102 index.add(Integer.valueOf(mod.substring(11)));
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103 }
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104 }
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105
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106 return index;
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107
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108 }
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109 }
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