/**
* Parses the given mztab string and sets the various properties accordingly. Properties that are
* already set and not defined in the passed string are not altered. The only exception to this
* rule is the unit id: once the unit id was set unmarshalling properties assigned to a different
* unit causes a parsing exception to be thrown.
*
* @param mzTabString
* @throws MzTabParsingException Thrown on any parsing error.
*/
public void unmarshall(String mzTabString) throws MzTabParsingException {
// parse the string line by line
String[] lines = mzTabString.split("\r?\n");
for (String line : lines) {
// ignore empty and non-metadata lines
if (line.trim().length() < 1 || !"MTD".equals(line.substring(0, 3))) {
continue;
}
// parse the line
Matcher matcher = MZTAB_LINE_PATTERN.matcher(line);
// throw a parsing exception if the line couldn't be parsed
if (!matcher.find()) {
throw new MzTabParsingException("Invalid meta-data line encountered: <" + line + ">");
}
// get the various fields
String theUnitId = matcher.group(2).trim();
String subId = matcher.group(3);
String field = matcher.group(4);
String value = matcher.group(5);
TableObject.checkUnitId(theUnitId);
if (subId != null) {
subId = subId.trim();
}
if (field != null) {
field = field.trim();
}
if (value != null) {
value = value.trim();
}
// check that the unitId didn't change - if it wasn't set yet, set it
if (this.unitId == null) {
this.unitId = theUnitId;
} else if (!this.unitId.equals(theUnitId)) {
throw new MzTabParsingException(
"Metadata line passed to Unit object (id = "
+ this.unitId
+ ") with a different UNIT_ID ("
+ theUnitId
+ ")");
}
// parse the field
parseField(subId, field, value);
}
}
public void setUnitId(String unitId) throws MzTabParsingException {
TableObject.checkUnitId(unitId);
this.unitId = unitId;
}
