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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.BufferedReader;
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13 import java.io.FileNotFoundException;
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14 import java.io.FileReader;
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15 import java.io.IOException;
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16 import java.util.ArrayList;
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17
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18 /**
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19 * Driver class for KinaMine. Processes arguments collected from GUI.
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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 KinaMineDriver {
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25
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26 /**
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27 * Main run method for KinaMine. Processes arguments and stores file
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28 * contents for compiling a run.
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29 *
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30 * @param args
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31 * @param debug
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32 * @return
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33 */
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34 public static boolean run(String[] args, boolean debug) {
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35
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36 /** Process aruments. */
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37 String pepPath = args[0];
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38 String fastaPath = args[1];
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39 String outPath = args[2];
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40 double fdrScore = Double.valueOf(args[3]);
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41 String outGroup = "output";
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42
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43 /** Read peptide report. */
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44 ArrayList<String> peptides = retTabFile(pepPath);
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45 peptides.remove(0);
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46
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47 ArrayList<String> proteins = new ArrayList<>();
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48
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49 /** Read fasta database */
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50 if (fastaPath.contains("fasta")){
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51 proteins = retFastaFile(fastaPath);
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52 } else {
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53 proteins = retTabFile(fastaPath);
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54 }
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55
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56
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57 /** Create new run. */
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58 Run run = new Run(peptides, proteins, fdrScore);
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59
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60 /** Write run reports. */
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61 Reporter.writeReports(run, outPath, outGroup);
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62
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63 return true;
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64 }
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65
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66 /**
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67 * Reads tabular files.
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68 *
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69 * @param path
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70 * @return Arraylist of lines.
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71 */
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72 public static ArrayList<String> retTabFile(String path) {
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73
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74 /** Initialize lines */
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75 ArrayList<String> lines = new ArrayList<>();
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76
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77 try {
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78
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79 /** Configure reader. */
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80 FileReader fr = new FileReader(path);
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81 BufferedReader br = new BufferedReader(fr);
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82
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83 /** Initialize first line, headers - discard */
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84 String line = br.readLine();
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85
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86 /**
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87 * Read each line in the configuration file and add each line to an
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88 * array (to be returned)
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89 */
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90 while (line != null) {
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91
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92 /** If line is all tabs, end of file */
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93 if (line.startsWith("\t")) {
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94 break;
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95 }
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96
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97 /** Add line to list. */
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98 lines.add(line);
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99 line = br.readLine();
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100 }
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101
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102 /** Close the file */
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103 br.close();
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104
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105 } catch (FileNotFoundException filenotfoundexxption) {
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106 System.out.println(path + ", does not exist");
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107 } catch (IOException ioexception) {
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108 ioexception.printStackTrace();
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109 }
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110
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111 return lines;
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112 }
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113
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114 public static ArrayList<String> retFastaFile(String path) {
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115
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116 /** Initialize lines */
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117 ArrayList<String> lines = new ArrayList<>();
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118
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119 try {
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120
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121 /** Configure reader. */
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122 FileReader fr = new FileReader(path);
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123 BufferedReader br = new BufferedReader(fr);
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124
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125 String line = br.readLine();
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126 String prot = "";
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127
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128 while (line != null) {
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129
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130 if (line.startsWith(">")){
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131 String[] temp = line.split(" ");
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132 prot = temp[0].trim() + "\t \t";
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133 } else {
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134 prot += line.trim();
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135 lines.add(prot);
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136 }
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137
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138 line = br.readLine();
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139 }
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140
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141 br.close();
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142
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143 } catch (FileNotFoundException filenotfoundexxption) {
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144 System.out.println(path + ", does not exist");
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145 } catch (IOException ioexception) {
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146 ioexception.printStackTrace();
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147 }
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148
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149 return lines;
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150 }
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151
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152 }
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