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