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));
}
