private UnimodModification ConvertToModification(OboTerm term)
{
string code = term.Id;
string name = term.Name;
string?definition = null;
string?diffFormula = null;
double diffMonoMass = 0;
double diffAvMass = 0;
if (term.ValuePairs != null)
{
foreach (OboTagValuePair pair in term.ValuePairs)
{
if (pair.Tag == "def")
{
definition = pair.Value.Replace("\\", string.Empty);
}
else if (pair.Tag == "xref" && pair.Value.StartsWith("delta_composition"))
{
diffFormula = pair.Value.Replace("\"", string.Empty).Substring(18);
}
else if (pair.Tag == "xref" && pair.Value.StartsWith("delta_mono_mass"))
{
diffMonoMass = Convert.ToDouble(pair.Value.Replace("\"", string.Empty).Substring(16));
}
else if (pair.Tag == "xref" && pair.Value.StartsWith("delta_avge_mass"))
{
diffAvMass = Convert.ToDouble(pair.Value.Replace("\"", string.Empty).Substring(16));
}
}
}
if (definition != null && diffFormula != null)
{
return(new UnimodModification(code, name, definition, diffFormula, diffMonoMass, diffAvMass));
}
throw new Exception("Could not find required 'definition' field.");
}
private XlmodTerm ConvertToModification(OboTerm oboTerm)
{
string?definition = null;
ICollection <XlmodSynonym>? synonyms = null;
ICollection <XlmodExternalReference>?externalReferences = null;
ICollection <XlmodProperty>? properties = null;
ICollection <XlmodRelationship>? relationships = null;
ICollection <string>?isA = null;
if (oboTerm.ValuePairs != null)
{
foreach (OboTagValuePair pair in oboTerm.ValuePairs)
{
var valueSpan = pair.Value.AsSpan();
switch (pair.Tag)
{
case "synonym":
// "Text" Score Type []
{
int endOfQuote = valueSpan.LastIndexOf('"');
var text = valueSpan.Slice(1, endOfQuote - 1);
var type = valueSpan.Slice(endOfQuote + 2, valueSpan.LastIndexOf('[') - endOfQuote - 3);
Utility.LazyCreateAndAdd(ref synonyms, new XlmodSynonym(type.ToString(), text.ToString()));
}
break;
case "def":
{
// "defString" [dbName1:acc1, dbName2:acc2]
int endOfQuote = valueSpan.LastIndexOf('"');
definition = valueSpan.Slice(1, endOfQuote - 1).ToString();
string refs = valueSpan.Slice(endOfQuote + 3, valueSpan.Length - endOfQuote - 4).ToString();
if (refs != "")
{
string[] splitComma = refs.Split(',');
foreach (string reference in splitComma.Select(s => s.Trim(' ')))
{
string[] splitColon2 = reference.Split(':');
Utility.LazyCreateAndAdd(ref externalReferences, new XlmodExternalReference(splitColon2[0], splitColon2[1]));
}
}
}
break;
case "property_value":
// property_value: doubletDeltaMass: "8.05016" xsd:double
{
int startOfQuote = valueSpan.IndexOf('"');
int endOfQuote = valueSpan.LastIndexOf('"');
var name = valueSpan.Slice(0, startOfQuote - 2);
var value = valueSpan.Slice(startOfQuote + 1, endOfQuote - startOfQuote - 1);
var dataType = valueSpan.Slice(endOfQuote + 2);
Utility.LazyCreateAndAdd(ref properties, new XlmodProperty(name.ToString(), value.ToString(), dataType.ToString()));
}
break;
case "relationship":
// relationship: has_property XLMOD:00014 ! hydrophilic
{
int spaceIndex = valueSpan.IndexOf(' ');
var type = valueSpan.Slice(0, spaceIndex);
var id = valueSpan.Slice(spaceIndex + 1, valueSpan.IndexOf('!') - spaceIndex - 2);
Utility.LazyCreateAndAdd(ref relationships, new XlmodRelationship(type.ToString(), id.ToString()));
}
break;
case "is_a":
// MOD:00000 ! description
string modNum = valueSpan.Slice(0, valueSpan.IndexOf(' ') - 1).ToString();
Utility.LazyCreateAndAdd(ref isA, modNum);
break;
}
}
}
if (definition != null)
{
return(new XlmodTerm(oboTerm.Id, oboTerm.Name, definition, externalReferences, isA,
relationships, synonyms, properties));
}
throw new Exception("Could not find required 'definition' field.");
}
private PsiModTerm ConvertToModification(OboTerm oboTerm)
{
string?definition = null;
ICollection <PsiModSynonym>? synonyms = null;
ICollection <PsiModExternalReference>?externalReferences = null;
ICollection <string>?isA = null;
string?comment = null;
bool isObsolete = false;
string?remap = null;
double?diffAvg = null;
string?diffFormula = null;
double?diffMono = null;
double?massAvg = null;
string?massFormula = null;
double?massMono = null;
int formalCharge = 0;
ICollection <char>?origin = null;
PsiModModificationSource?source = null;
Terminus?terminus = null;
if (oboTerm.ValuePairs != null)
{
foreach (OboTagValuePair pair in oboTerm.ValuePairs)
{
switch (pair.Tag)
{
case "synonym":
// "Text" Score Type []
string[] splitQuote = pair.Value.Trim('"').Split('"');
string text = splitQuote[0];
string[] split = splitQuote[1].Trim(' ').Split(' ');
string scope = split[0];
string type = split[1];
Utility.LazyCreateAndAdd(ref synonyms, new PsiModSynonym(type, text, scope));
break;
case "def":
// "defString" [dbName1:acc1, dbName2:acc2]
string[] splitQuot = pair.Value.Substring(1).Split('"');
definition = splitQuot[0];
string refs = splitQuot[1];
refs = refs.Trim(' ', '[', ']');
if (refs != "")
{
string[] splitComma = refs.Split(',');
foreach (string reference in splitComma.Select(s => s.Trim(' ')))
{
string[] splitColon2 = reference.Split(':');
Utility.LazyCreateAndAdd(ref externalReferences, new PsiModExternalReference(splitColon2[0], splitColon2[1]));
}
}
break;
case "comment":
comment = pair.Value;
break;
case "xref":
int colonIndex = pair.Value.IndexOf(':');
string key = pair.Value[0..colonIndex];
