/** * Create a new span with a single read in it. * * @param start alignment start of the span * @param span alignment span */ public AlignmentSpan(final int start, final int span) { this.setStart(start); this.setSpan(span); this.count = 1; }
/** * Create a new span with a multiple reads in it. * * @param start alignment start of the span * @param span alignment span * @param count number of reads in the span */ public AlignmentSpan(final int start, final int span, final int count) { this.setStart(start); this.setSpan(span); this.count = count; }
/** * Create a new span with a single read in it. * * @param start alignment start of the span * @param span alignment span */ public AlignmentSpan(final int start, final int span) { this.setStart(start); this.setSpan(span); this.count = 1; }
/** * Create a new span with a multiple reads in it. * * @param start alignment start of the span * @param span alignment span * @param count number of reads in the span */ public AlignmentSpan(final int start, final int span, final int count) { this.setStart(start); this.setSpan(span); this.count = count; }
/** * Add multiple reads to the span. * * @param start alignment start * @param span alignment span * @param count number of reads to add */ public void add(final int start, final int span, final int count) { if (this.getStart() > start) { this.setSpan(Math.max(this.getStart() + this.getSpan(), start + span) - start); this.setStart(start); } else if (this.getStart() < start) { this.setSpan(Math.max(this.getStart() + this.getSpan(), start + span) - this.getStart()); } else { this.setSpan(Math.max(this.getSpan(), span)); } this.count += count; }
/** * Add multiple reads to the span. * * @param start alignment start * @param span alignment span * @param count number of reads to add */ public void add(final int start, final int span, final int count) { if (this.getStart() > start) { this.setSpan(Math.max(this.getStart() + this.getSpan(), start + span) - start); this.setStart(start); } else if (this.getStart() < start) { this.setSpan(Math.max(this.getStart() + this.getSpan(), start + span) - this.getStart()); } else { this.setSpan(Math.max(this.getSpan(), span)); } this.count += count; }