Mercurial > repos > jfb > kinamine7_7

comparison KinaMine-Galaxy-7-7/src/kinamine/Reporter.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.io.*;
13 import java.util.ArrayList;
14 import java.util.Collection;
15 import java.util.Map.Entry;
16 import java.util.Set;
17 import javafx.util.Pair;
18
19 /**
20 * Reporter class to write reports. Currently writes out in .csv format.
21 *
22 * @version 1.0
23 * @author murra668
24 * new author: blank121@umn.edu as of August 2017
25 */
26 public class Reporter {
27
28 /**
29 * Write reports for run.
30 *
31 * @param run
32 * @param outPath
33 * @param outGroup
34 */
35 static void writeReports(Run run, String outPath, String outGroup) {
36
37 /** Write substrates report. */
38 String outputFileSub = outPath + outGroup + "_Substrates.csv";
39 Reporter.substrates(run, outputFileSub);
40
41 /** Write substrate background frequency report. */
42 String outputFileFreq = outPath + outGroup + "_SubBackFreq.csv";
43 Reporter.frequencies(run, outputFileFreq);
44
45 }
46
47 /**
48 * Writes substrates report from the ids and motifs of each peptide.
49 *
50 * @param run
51 * @param outputFileName
52 */
53 private static void substrates(Run run, String outputFileName) {
54
55 /** Format header */
56 // String header = "Substrates," + "Species," + "Reference," + "-7," + "-6,"
57 // + "-5," + "-4," + "-3," + "-2," + "-1," + "0," + "1,"
58 // + "2," + "3," + "4," + "5," + "6," + "7," + "Phosphite"
59 // + "\n";
60 String header = "Substrates," + "Species," + "Reference," + "-7," + "-6,"
61 + "-5," + "-4," + "-3," + "-2," + "-1," + "0," + "1,"
62 + "2," + "3," + "4," + "5," + "6," + "7,"
63 +" ," +" ,"+ " ,"+ "Phosphite"
64 + "\n";
65
66 /** Initialize details */
67 String detail = null;
68
69 try (FileWriter writer = new FileWriter(outputFileName)) {
70
71 /* Write the column headers */
72 writer.append(header);
73
74 Collection<Motif> motifs = run.motifs.values();
75
76 /** Loop through each motif */
77 for (Motif motif : motifs) {
78
79 /** Format ID and blanks */
80 detail = "," + "," + motif.ref + ",";
81
82 String seq = motif.seq;
83 int index = motif.index;
84 //changing the numbers for index only changed where in the excel doc these motifs
85 //showed up
86 //I should fuck with this and try to reallign it
87 //I should do that now
88 if (index < 8) {
89 for (int i = index; i < 8; i++) {
90 detail += ",";
91 }
92 for (int j = 0; j < seq.length(); j++) {
93 detail += seq.charAt(j) + ",";
94 }
95 if (seq.length() - index < 7) {
96 for (int i = seq.length() - index; i < 7; i++) {
97 detail += ",";
98 }
99 }
100 } else if (seq.length() < 15) {
101 for (int j = 0; j < seq.length(); j++) {
102 detail += seq.charAt(j) + ",";
103 }
104 for (int i = seq.length(); i < 15; i++) {
105 detail += ",";
106 }
107
108 } else {
109 for (int j = 0; j < seq.length(); j++) {
110 detail += seq.charAt(j) + ",";
111 }
112 }
113
114 //
115 // if (index < 5) {
116 // for (int i = index; i < 5; i++) {
117 // detail += ",";
118 // }
119 // for (int j = 0; j < seq.length(); j++) {
120 // detail += seq.charAt(j) + ",";
121 // }
122 // if (seq.length() - index < 4) {
123 // for (int i = seq.length() - index; i < 4; i++) {
124 // detail += ",";
125 // }
126 // }
127 // } else if (seq.length() < 9) {
128 // for (int j = 0; j < seq.length(); j++) {
129 // detail += seq.charAt(j) + ",";
130 // }
131 // for (int i = seq.length(); i < 9; i++) {
132 // detail += ",";
133 // }
134 //
135 // } else {
136 // for (int j = 0; j < seq.length(); j++) {
137 // detail += seq.charAt(j) + ",";
138 // }
139 // }
140 ////////////////////////////////////////////////////////////////////////////////
141 /** Format trailing blanks */
142 detail += "," + "," + "," + seq + ",";
143
144 for (String id : motif.regenSeqs){
145 detail += id + ",";
146 }
147 detail += "\n";
148
149 /** Append each line of the report. */
150 writer.append(detail);
151 }
152
153 writer.flush();
154 writer.close();
155
156 } catch (IOException e) {
157 e.printStackTrace();
158 }
159 }
160
161 /**
162 * Write substrates background frequency report from each protein in the
163 * database.
164 *
165 * @param run
166 * @param outputFileName
167 */
168 private static void frequencies(Run run, String outputFileName) {
169
170 /** Initialize the header */
171 StringBuffer header = new StringBuffer();
172 header.append("Amino Acids,");
173
174 /** Write each protein accession. */
175 Object[] prots = run.database.keySet().toArray();
176 for (Object ref : prots) {
177 header.append(ref).append(",");
178 }
179 header.append("\n");
180
181 try (FileWriter writer = new FileWriter(outputFileName)) {
182
183 /* Write the column headers. */
184 writer.append(header);
185
186 Collection<Protein> proteins = run.database.values();
187
188 /** Write frequency of each amino acid. */
189 for (char acid : AminoAcid.ACIDS) {
190 StringBuffer detail = new StringBuffer();
191 detail.append(acid).append(",");
192 for (Protein protein : proteins) {
193 detail.append(protein.comp.get(acid)).append(",");
194 }
195 detail.append("\n");
196 writer.append(detail);
197 }
198
199 writer.append("Properties\n");
200
201 /** Write the property frequency of each amino acid. */
202 for (String prop : AminoAcid.PROPS) {
203 StringBuffer props = new StringBuffer();
204 props.append(prop).append(",");
205 for (Protein protein : proteins) {
206 props.append(protein.props.get(prop)).append(",");
207 }
208 props.append("\n");
209 writer.append(props);
210 }
211
212 writer.append("\n");
213
214 StringBuffer tyr = new StringBuffer("Number of Y,");
215 StringBuffer phosphTyr = new StringBuffer("Number of pY,");
216 StringBuffer aa = new StringBuffer("Total AAs,");
217
218 /** Write the number of tyrosine, phospho-tyrosine, and length. */
219 for (Protein protein : proteins) {
220 tyr.append(protein.numTyr).append(",");
221 phosphTyr.append(protein.phosphoTyr).append(",");
222 aa.append(protein.seq.length()).append(",");
223 }
224
225 writer.append(tyr + "\n");
226 writer.append(phosphTyr + "\n");
227 writer.append(aa + "\n");
228
229 writer.flush();
230 writer.close();
231
232 } catch (IOException e) {
233 e.printStackTrace();
234 }
235 }
236 }