/**
* ************************************************************************* * * Write the source
* to XML *
*/
public void writeXML(PrintWriter out, Indenter ind) {
ind.indent();
out.print("<pertSrc id=\"");
out.print(id_);
out.print("\" src=\"");
out.print(srcNameKey_);
out.print("\" type=\"");
out.print(typeKey_);
out.print("\"");
if (!proxySign_.equals(NO_PROXY)) {
out.print(" proxy=\"");
out.print(proxyForKey_);
out.print("\"");
out.print(" proxySign=\"");
out.print(proxySign_);
out.print("\"");
}
if (!annotations_.isEmpty()) {
String notesStr = Splitter.tokenJoin(annotations_, ",");
out.print(" notes=\"");
out.print(notesStr);
out.print("\"");
}
out.println("/>");
return;
}
/**
* ************************************************************************* * * Write the
* expression to XML *
*/
public void writeXML(PrintWriter out, Indenter ind) {
ind.indent();
out.print("<data region=\"");
out.print(CharacterEntityMapper.mapEntities(region_, false));
out.print("\" time=\"");
out.print(time_);
out.print("\" expr=\"");
out.print(mapExpression(expr_));
if (source_ != NO_SOURCE_SPECIFIED) {
out.print("\" source=\"");
out.print(mapToSourceTag(source_));
}
if (confidence_ != TimeCourseGene.USE_BASE_CONFIDENCE) {
out.print("\" confidence=\"");
out.print(TimeCourseGene.mapConfidence(confidence_));
}
String invert = mapStrategy(startStrategy_);
if (invert != null) {
out.print("\" starttype=\"");
out.print(invert);
}
invert = mapStrategy(endStrategy_);
if (invert != null) {
out.print("\" endtype=\"");
out.print(invert);
}
if (strategySource_ != NO_SOURCE_SPECIFIED) {
out.print("\" stratSource=\"");
out.print(mapToSourceTag(strategySource_));
}
if (expr_ == VARIABLE) {
out.print("\" value=\"");
out.print(variable_);
}
out.println("\" />");
return;
}