ngsrich: NGSrich_0.5.5/src/datastructures/GenomeLine.java comparison

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--1:000000000000
+:89ad0a9cca52
+package datastructures;
+import java.util.Scanner;
+public class GenomeLine implements Line {
+	boolean misformat = false;
+	String seqName, chrom, gene;
+	int start, end;
+	//fw.write(field(1)+"\t"+field(3)+"\t"
+	//		+field(5)+"\t"+field(6)+"\t"+field(13)+"\r\n");
+	public GenomeLine(String line){
+		Scanner s = new Scanner(line);
+		if(line.startsWith("#")) misformat = true;
+		else
+		try{
+			seqName = s.next();s.next();
+			chrom = s.next();s.next();
+			start = s.nextInt();
+			end = s.nextInt();s.next();s.next();s.next();s.next();s.next();s.next();
+			gene = s.next();}
+		catch(Exception e){
+			misformat = true;
+		}
+	}
+	public boolean valid(){
+		return misformat == false;
+	}
+	public String chrom() {
+		return chrom;
+	}
+	public int end() {
+		return end;
+	}
+	public int start() {
+		return start;
+	}
+	public String gene(){
+		return gene;
+	}
+	public String seqName(){
+		return seqName;
+	}
+	public String toString(){
+		return seqName + "\t" + chrom + "\t" + start + "\t" + end + "\t" + gene;
+	}
+}

Mercurial > repos > pfrommolt > ngsrich