int hStartOffset = link.getHSideTarget().getBegin(); int hEndOffset = link.getHSideTarget().getEnd();
int hStartOffset = link.getHSideTarget().getBegin(); int hEndOffset = link.getHSideTarget().getEnd();
link.getHSideTarget().getCoveredText().replaceAll(" ", "_|_");
int hStartOffset = link.getHSideTarget().getBegin(); int hEndOffset = link.getHSideTarget().getEnd();
int hBegin = l.getHSideTarget().getBegin()+TextSize; int tEnd = l.getTSideTarget().getEnd(); int hEnd = l.getHSideTarget().getEnd()+TextSize; String tText = l.getTSideTarget().getCoveredText(); String hText = l.getHSideTarget().getCoveredText();
int hStartOffset = link.getHSideTarget().getBegin(); int hEndOffset = link.getHSideTarget().getEnd();
/** * Generates summary two-liner for the given link. used in summarizeAlignmentLinks() * * @param l * @return */ private static String summaryOutputSingleLink(Link l, int index) { // Link [n], info:[linker_version_info], strength: [strength num], direction: [direction] // \t Tside: { [Annotations] } // \t Hside: { [Annotations] } String line1 = "Link " + index + ", info: " + l.getAlignerID() + "_" + l.getAlignerVersion() + "_" + l.getLinkInfo() + ", strength: " + l.getStrength() + ", direction: " + l.getDirectionString() + "\n"; String line2 = " Tside: { " + summaryOutputLinkTarget(l.getTSideTarget()) + " }"; String line3 = " Hside: { " + summaryOutputLinkTarget(l.getHSideTarget()) + " }\n"; return (line1 + line2 + line3); }