/**
* ************************************************************************* * * Show the
* expression key
*/
public static void expressionKeyCSV(BTState appState, PrintWriter out, boolean encodeConfidence) {
ResourceManager rMan = appState.getRMan();
out.println("\"\"");
out.println("\"\"");
out.print("\"");
out.print(rMan.getString("csvTcdExport.keyTitle"));
out.println("\"");
out.print("\"");
out.print(rMan.getString((encodeConfidence) ? "csvTcdExport.var" : "csvTcdExport.varNC"));
out.println("\"");
out.print("\"");
out.print(rMan.getString("csvTcdExport.number"));
out.print("\",\"");
out.print(rMan.getString("csvTcdExport.level"));
if (encodeConfidence) {
out.print("\",\"");
out.print(rMan.getString("csvTcdExport.confidence"));
}
out.println("\"");
out.print("0,\"");
out.print(rMan.getString("csvTcdExport." + mapExpression(NO_DATA)));
if (encodeConfidence) {
out.print("\",\"");
out.print(rMan.getString("csvTcdExport.nA"));
}
out.println("\"");
int topConf =
(encodeConfidence) ? (TimeCourseGene.NUM_CONFIDENCE - 1) : TimeCourseGene.NORMAL_CONFIDENCE;
int confLev = 1;
for (int i = 0; i <= topConf; i++) {
String conf = rMan.getString("csvTcdExportConf." + TimeCourseGene.mapConfidence(i));
int expLev = 0;
for (int j = 0; j < NUM_EXPRESSIONS; j++) {
if ((j != NO_DATA) && (j != VARIABLE)) {
String expr = rMan.getString("csvTcdExport." + mapExpression(j));
int totLev = (expLev++) + confLev;
out.print(totLev);
out.print(",\"");
out.print(expr);
if (encodeConfidence) {
out.print("\",\"");
out.print(conf);
}
out.println("\"");
}
}
confLev += expLev;
}
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;
}
