/* The MIT License (MIT) Copyright (c) 2016 Pierre Lindenbaum Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ package com.github.lindenb.jvarkit.util.bio.bed; import java.util.Arrays; import htsjdk.samtools.util.Interval; import htsjdk.tribble.Feature; public class BedLine implements Feature { private final String tokens[]; public BedLine(final String tokens[]) { this.tokens=tokens; } @Override @Deprecated public final String getChr() { return getContig(); } @Override public String getContig() { return tokens[0]; } @Override public int getStart() { return Integer.parseInt(tokens[1]) + 1; /* +1 because the Feature uses a +1 position */ } @Override public int getEnd() { return (tokens.length<3 ?getStart(): Integer.parseInt(tokens[2])); } /** shortcut to <code>new Interval(getContig(), getStart(), getEnd())</code> */ public Interval toInterval() { return new Interval(getContig(), getStart(), getEnd()); } public String get(final int index) { return (index<tokens.length?tokens[index]:null); } public String join(final CharSequence delimiter) { return String.join(delimiter, this.tokens); } public String join() { return join("\t"); } public int getColumnCount() { return tokens.length; } public static boolean isBedHeader(final String line) { return line.startsWith("#") || line.startsWith("track") || line.startsWith("browser"); } @Override public int hashCode() { return Arrays.hashCode(this.tokens); } @Override public boolean equals(Object obj) { if(obj==this) return true; if(obj==null || !(obj instanceof BedLine)) return false; return Arrays.equals(this.tokens, BedLine.class.cast(obj).tokens); } @Override public String toString() { return this.join(); } }