public string ToSerializableString()
{
// Replace tab with something that XML parsers won't mess with
var tsv = ToTSV();
return(AccessionNumbers.EscapeTabsForXML(tsv));
}
public List <string> AsFields()
{
var massOrFormula = !string.IsNullOrEmpty(Formula) ?
Formula :
string.Format(CultureInfo.InvariantCulture, "{0:F09}/{1:F09}", MonoisotopicMass, AverageMass); // Not L10N
var parts = new[] { Name, massOrFormula, AccessionNumbers.ToString() };
return((parts.All(string.IsNullOrEmpty) ? new[] { InvariantName } : parts).ToList());
}
public List <string> AsFields()
{
var massOrFormula = !string.IsNullOrEmpty(Formula) ?
Formula :
FormattedMasses(MonoisotopicMass, AverageMass);
var parts = new[] { Name, massOrFormula, AccessionNumbers.ToString() };
return((parts.All(string.IsNullOrEmpty) ? new[] { InvariantName } : parts).ToList());
}
public override int GetHashCode()
{
unchecked
{
int hashCode = (Formula != null ? Formula.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ (Name != null ? Name.GetHashCode() : 0);
hashCode = (hashCode * 397) ^ MonoisotopicMass.GetHashCode();
hashCode = (hashCode * 397) ^ AverageMass.GetHashCode();
hashCode = (hashCode * 397) ^ AccessionNumbers.GetHashCode();
return(hashCode);
}
}
public override string ToString()
{
var result = string.Empty;
if (AccessionNumbers != null && AccessionNumbers.Any())
{
foreach (var key in PREFERRED_ACCESSION_TYPE_ORDER)
{
string value;
if (AccessionNumbers.TryGetValue(key, out value) && !string.IsNullOrEmpty(value))
{
result += string.Format("{0}{1}:{2}", // Not L10N
string.IsNullOrEmpty(result) ? string.Empty : TextUtil.SEPARATOR_TSV_STR, key, value);
}
}
}
return(result);
}
public void WriteXml(XmlWriter writer, Adduct adduct)
{
if (adduct.IsEmpty)
{
writer.WriteAttributeIfString(ATTR.neutral_formula, Formula);
}
else
{
writer.WriteAttributeIfString(ATTR.ion_formula,
(Formula ?? string.Empty) +
(adduct.IsProteomic ? string.Empty : adduct.ToString()));
}
Assume.IsFalse(AverageMass.IsMassH()); // We're going to read these as neutral masses
Assume.IsFalse(MonoisotopicMass.IsMassH());
writer.WriteAttributeNullable(ATTR.neutral_mass_average, AverageMass);
writer.WriteAttributeNullable(ATTR.neutral_mass_monoisotopic, MonoisotopicMass);
if (!string.IsNullOrEmpty(Name))
{
writer.WriteAttribute(ATTR.custom_ion_name, Name);
}
writer.WriteAttributeIfString(ATTR.id, AccessionNumbers.ToSerializableString());
}
public int CompareTo(CustomMolecule other)
{
if (other == null)
{
return(1);
}
var result = string.CompareOrdinal(Name, other.Name);
if (result == 0)
{
result = string.CompareOrdinal(Formula, other.Formula);
if (result == 0)
{
result = AccessionNumbers.CompareTo(other.AccessionNumbers);
if (result == 0)
{
result = MonoisotopicMass.Equals(other.MonoisotopicMass, 5E-10) ? // Allow for float vs double serialization effects
0 : MonoisotopicMass.CompareTo(other.MonoisotopicMass);
}
}
}
return(result);
}
protected const string massFormatRegex = @"(?:[a-z][a-z]+)\s+\[([+-]?\d*\.\d+)(?![-+0-9\.])\/([+-]?\d*\.\d+)(?![-+0-9\.])\]"; // Not L10N
public SmallMoleculeLibraryAttributes GetSmallMoleculeLibraryAttributes()
{
return(SmallMoleculeLibraryAttributes.Create(Name, Formula,
AccessionNumbers.GetInChiKey(), AccessionNumbers.GetNonInChiKeys()));
}
public override int GetHashCode()
{
return((AccessionNumbers != null && AccessionNumbers.Any()) ? AccessionNumbers.GetHashCode() : 0);
}
public string GetSMILES()
{
string smiles;
return(AccessionNumbers != null && AccessionNumbers.TryGetValue(TagSMILES, out smiles) ? smiles : null);
}
public string GetSMILES()
{
string cas;
return(AccessionNumbers != null && AccessionNumbers.TryGetValue(TagSMILES, out cas) ? cas : null);
}
public string GetHMDB()
{
string cas;
return(AccessionNumbers != null && AccessionNumbers.TryGetValue(TagHMDB, out cas) ? cas : null);
}
public string GetInChI()
{
string inchikey;
return(AccessionNumbers != null && AccessionNumbers.TryGetValue(TagInChI, out inchikey) ? inchikey : null);
}
public SmallMoleculeLibraryAttributes GetSmallMoleculeLibraryAttributes()
{
return(SmallMoleculeLibraryAttributes.Create(Name, Formula,
MonoisotopicMass, AverageMass, // In case forumla is empty
AccessionNumbers.GetInChiKey(), AccessionNumbers.GetNonInChiKeys()));
}
public string GetKEGG()
{
string kegg;
return(AccessionNumbers != null && AccessionNumbers.TryGetValue(TagKEGG, out kegg) ? kegg : null);
}
public string GetNonInChiKeys()
{
return(AccessionNumbers != null && AccessionNumbers.Any() ?
AccessionNumbers.Where(k => k.Key != TagInChiKey).Select(kvp => string.Format("{0}:{1}", kvp.Key, kvp.Value)).ToDsvLine(TextUtil.SEPARATOR_TSV) : // Not L10N
null);
}
public string GetHMDB()
{
string hmdb;
return(AccessionNumbers != null && AccessionNumbers.TryGetValue(TagHMDB, out hmdb) ? hmdb : null);
}
