public static SplitList<double> ParseDoubleList(string target)
{
SplitList<string> list = ParseStringList(MZTabConstants.BAR, target);
SplitList<double> valueList = new SplitList<double>(MZTabConstants.BAR);
foreach (string listItem in list){
double value = ParseDouble(listItem);
if (value.Equals(double.MinValue)){
valueList.Clear();
break;
}
valueList.Add(value);
}
return valueList;
}
public static SplitList<SpectraRef> ParseSpectraRefList(Metadata metadata, string target)
{
SplitList<string> list = ParseStringList(MZTabConstants.BAR, target);
SplitList<SpectraRef> refList = new SplitList<SpectraRef>(MZTabConstants.BAR);
Regex regex = new Regex("ms_run\\[(\\d+)\\]:(.*)");
foreach (string item in list){
if (regex.IsMatch(item.Trim())){
int ms_file_id = int.Parse(regex.Match(item.Trim()).Groups[1].Value);
string reference = regex.Match(item.Trim()).Groups[2].Value;
MsRun msRun = metadata.MsRunMap[ms_file_id];
SpectraRef sref = msRun == null ? null : new SpectraRef(msRun, reference);
if (sref == null){
refList.Clear();
break;
}
refList.Add(sref);
}
}
return refList;
}
/**
* A publication on this unit. PubMed ids must be prefixed by “pubmed:”,
* DOIs by “doi:”. Multiple identifiers MUST be separated by “|”.
*/
public static SplitList<PublicationItem> ParsePublicationItems(string target)
{
SplitList<string> list = ParseStringList(MZTabConstants.BAR, target);
SplitList<PublicationItem> itemList = new SplitList<PublicationItem>(MZTabConstants.BAR);
foreach (string pubList in list){
var pub = ParseString(pubList);
if (pub == null){
itemList.Clear();
break;
}
string[] items = pub.Split(new[]{"" + MZTabConstants.COLON}, StringSplitOptions.None);
PublicationType type;
if (items.Length != 2 || (type = PublicationItem.FindType(items[0].Trim())) == null){
itemList.Clear();
break;
}
string accession = items[1].Trim();
PublicationItem item = new PublicationItem(type, accession);
itemList.Add(item);
}
return itemList;
}
/**
* A list of '|' separated parameters
*/
public static SplitList<Param> ParseParamList(string target)
{
SplitList<string> list = ParseStringList(MZTabConstants.BAR, target);
SplitList<Param> paramList = new SplitList<Param>(MZTabConstants.BAR);
foreach (string item in list){
Param param = ParseParam(item);
if (param == null){
paramList.Clear();
return paramList;
}
paramList.Add(param);
}
return paramList;
}
public static SplitList<Modification> ParseModificationList(Section section, string target)
{
target = ParseString(target);
if (target == null){
return null;
}
SplitList<Modification> modList = new SplitList<Modification>(MZTabConstants.COMMA);
if (target.Equals("0")){
modList.Add(Modification.CreateNoModification(section));
return modList;
}
target = translateCommaToTab(target);
SplitList<string> list = ParseStringList(MZTabConstants.COMMA, target);
foreach (string item in list){
Modification mod = ParseModification(section, item.Trim());
if (mod == null){
modList.Clear();
break;
}
modList.Add(mod);
}
return modList;
}
/**
* A '|' delimited list of GO accessions
*/
public static SplitList<string> ParseGoTermList(string target)
{
SplitList<string> list = ParseStringList(MZTabConstants.COMMA, target);
SplitList<string> goList = new SplitList<string>(MZTabConstants.COMMA);
foreach (string listitem in list){
var item = ParseString(listitem);
if (item.StartsWith("GO:")){
goList.Add(item);
}
else{
goList.Clear();
break;
}
}
return goList;
}
