/** * ************************************************************************* * * 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; }