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comparison KinaMine-Galaxy-7-7/src/kinamine/Peptide.java @ 0:67635b462045 draft

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author jfb
date Tue, 20 Feb 2018 14:31:15 -0500
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1 /**
2 *****************************************************************************
3 * <p>
4 * Copyright (c) Regents of the University of Minnesota. All Rights Reserved.
5 * <p>
6 * Author: Kevin Murray University of Minnesota - (murra668@umn.edu)
7 * <p>
8 *****************************************************************************
9 */
10 package kinamine;
11
12 import java.util.ArrayList;
13 import java.util.Arrays;
14 import java.util.List;
15
16 /**
17 * Peptide object representing the relevant information from the submitted
18 * peptide report. Stores the values necessary for writing a report formatted
19 * for existing Excel sheets.
20 *
21 * @version 1.0
22 * @author murra668
23 */
24 public class Peptide {
25
26 /** Sequence of peptide. */
27 String seq;
28
29 /** Accession of Protein associated with this peptide. */
30 List<String> id;
31
32 /** Full Accessions. */
33 String ref;
34
35 /** Motif of phospho-tyrosine. */
36 ArrayList<String> motif;
37
38 /** Index of phospho-tyrosine in the peptide sequence. */
39 ArrayList<Integer> tyrIndex;
40
41 /** Index of phospho-tyrosine in protein sequence. */
42 ArrayList<Integer> tyrProtIndex;
43
44 /** Length of peptide sequence. */
45 int length;
46
47 /**
48 * Constructs a Peptide object from the parsed peptide info from a line in
49 * the peptide report.
50 *
51 * @param pepInfo tab-separated line of peptide info
52 * @param ids
53 */
54 public Peptide(String[] pepInfo, List ids) {
55
56 /** Store sequence */
57 this.seq = pepInfo[8];
58
59 /** Store sequence length. */
60 this.length = pepInfo[8].length();
61
62 /** Initialize empty motif array. */
63 this.motif = new ArrayList<>();
64
65 /** Extract peptide references. */
66 this.id = ids;
67 this.ref = pepInfo[3];
68
69 /** Store the index of phospho-tyrosine of the peptide and protein. */
70 this.tyrIndex = getIndex(pepInfo[9]);
71 this.tyrProtIndex = getIndex(pepInfo[10]);
72 }
73
74 /**
75 * Gets the index of the phospho-tyrosine in the peptide and corresponding
76 * protein, as indicated by the modification column of the peptide report.
77 * There may be more than one phospho-tyr within a peptide.
78 * <p>
79 * Location formatted as Phospho(Y)@index.
80 *
81 * @param mods string of mod locations
82 * @return ArrayList of integers.
83 */
84 private ArrayList<Integer> getIndex(String mods) {
85
86 /** Modifications are separated by ';'. */
87 List<String> psm = Arrays.asList(mods.split(";"));
88
89 /** Initialize new index array. */
90 ArrayList<Integer> index = new ArrayList<>();
91
92 /** Check all modifications. */
93 for (int i = 0; i < psm.size(); i++) {
94
95 /** Check if phospho-tyr. */
96 if (psm.get(i).contains("Phospho(Y)")) {
97
98 /** Trim for correct indexing. */
99 String mod = psm.get(i).trim();
100
101 /** Add to index array */
102 index.add(Integer.valueOf(mod.substring(11)));
103 }
104 }
105
106 return index;
107
108 }
109 }