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1 package datastructures;
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2
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3 import java.util.Scanner;
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4
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5 public class GenomeLine implements Line {
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6
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7 boolean misformat = false;
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8 String seqName, chrom, gene;
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9 int start, end;
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10
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11 //fw.write(field(1)+"\t"+field(3)+"\t"
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12 // +field(5)+"\t"+field(6)+"\t"+field(13)+"\r\n");
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13
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14 public GenomeLine(String line){
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15 Scanner s = new Scanner(line);
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16 if(line.startsWith("#")) misformat = true;
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17 else
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18 try{
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19 seqName = s.next();s.next();
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20 chrom = s.next();s.next();
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21 start = s.nextInt();
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22 end = s.nextInt();s.next();s.next();s.next();s.next();s.next();s.next();
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23 gene = s.next();}
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24 catch(Exception e){
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25 misformat = true;
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26 }
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27 }
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28
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29 public boolean valid(){
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30 return misformat == false;
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31 }
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32
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33 public String chrom() {
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34 return chrom;
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35 }
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36
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37 public int end() {
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38 return end;
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39 }
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40
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41 public int start() {
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42 return start;
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43 }
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44
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45 public String gene(){
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46 return gene;
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47 }
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48
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49 public String seqName(){
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50 return seqName;
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51 }
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52
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53 public String toString(){
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54 return seqName + "\t" + chrom + "\t" + start + "\t" + end + "\t" + gene;
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55 }
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56
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57 }
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