private PertSource buildFromXML(String elemName, Attributes attrs) throws IOException { String id = AttributeExtractor.extractAttribute(elemName, attrs, "pertSrc", "id", true); String src = AttributeExtractor.extractAttribute(elemName, attrs, "pertSrc", "src", true); String type = AttributeExtractor.extractAttribute(elemName, attrs, "pertSrc", "type", true); type = CharacterEntityMapper.unmapEntities(type, false); String proxyKey = AttributeExtractor.extractAttribute(elemName, attrs, "pertSrc", "proxy", false); String proxySign = AttributeExtractor.extractAttribute(elemName, attrs, "pertSrc", "proxySign", false); if ((proxySign == null) && (proxyKey != null)) { throw new IOException(); } String notes = AttributeExtractor.extractAttribute(elemName, attrs, "pertSrc", "notes", false); PertSource nps = new PertSource(id, src, type, proxyKey, proxySign); if (notes != null) { nps.setNotes(Splitter.stringBreak(notes, ",", 0, false)); } return (nps); }
/** * ************************************************************************* * * 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; }
/** * ************************************************************************* * * Handle the * attributes for the keyword * */ public static ExpressionEntry buildFromXML(BTState appState, String elemName, Attributes attrs) throws IOException { if (!elemName.equals("data")) { return (null); } String region = null; String time = null; String expr = null; String confidence = null; String startStrategy = null; String endStrategy = null; String variable = null; String srcStr = null; String stratSrcStr = null; if (attrs != null) { int count = attrs.getLength(); for (int i = 0; i < count; i++) { String key = attrs.getQName(i); if (key == null) { continue; } String val = attrs.getValue(i); if (key.equals("region")) { region = CharacterEntityMapper.unmapEntities(val, false); } else if (key.equals("time")) { time = val; } else if (key.equals("expr")) { expr = val; } else if (key.equals("confidence")) { confidence = val; } else if (key.equals("starttype")) { startStrategy = val; } else if (key.equals("endtype")) { endStrategy = val; } else if (key.equals("value")) { variable = val; } else if (key.equals("source")) { srcStr = val; } else if (key.equals("stratSource")) { stratSrcStr = val; } } } if ((region == null) || (time == null) || (expr == null)) { throw new IOException(); } return (new ExpressionEntry( appState, region, time, expr, srcStr, confidence, stratSrcStr, startStrategy, endStrategy, variable)); }