public TaxonomyItem(int taxId, int parentTaxId, TaxonomyRank rank, int divisionId, int geneticCodeId,
int mitoGeneticCodeId)
{
this.TaxId = taxId;
this.parentTaxId = parentTaxId;
this.Rank = rank;
this.divisionId = divisionId;
this.geneticCodeId = geneticCodeId;
this.mitoGeneticCodeId = mitoGeneticCodeId;
}
public static TaxonomyItem[] GetItemsOfRank(TaxonomyRank rank)
{
List<TaxonomyItem> x = new List<TaxonomyItem>();
foreach (TaxonomyItem ti in taxonomyItems){
if (ti.Rank == rank){
x.Add(ti);
}
}
return x.ToArray();
}
public TaxonomyItem(int taxId, int parentTaxId, TaxonomyRank rank, int divisionId, int geneticCodeId,
int mitoGeneticCodeId)
{
this.TaxId = taxId;
this.parentTaxId = parentTaxId;
this.Rank = rank;
this.divisionId = divisionId;
this.geneticCodeId = geneticCodeId;
this.mitoGeneticCodeId = mitoGeneticCodeId;
}
public TaxonomyItem GetParentOfRank(TaxonomyRank rank1)
{
if (rank1 == Rank){
return this;
}
if (!TaxonomyItems.taxId2Item.ContainsKey(parentTaxId)){
return null;
}
TaxonomyItem parent = TaxonomyItems.taxId2Item[parentTaxId];
return parent.GetParentOfRank(rank1);
}
public static string GetTaxonomyIdOfRank(string taxonomyId, TaxonomyRank rank)
{
int id;
if (!int.TryParse(taxonomyId, out id)){
return taxonomyId;
}
if (!taxId2Item.ContainsKey(id)){
return taxonomyId;
}
TaxonomyItem item = taxId2Item[id];
return "" + item.TaxId;
}
public static TaxonomyItem[] GetItemsOfRank(TaxonomyRank rank)
{
List <TaxonomyItem> x = new List <TaxonomyItem>();
foreach (TaxonomyItem ti in taxonomyItems)
{
if (ti.Rank == rank)
{
x.Add(ti);
}
}
return(x.ToArray());
}
public TaxonomyItem GetParentOfRank(TaxonomyItems taxonomyItems, TaxonomyRank rank1)
{
if (rank1 == Rank)
{
return(this);
}
if (!taxonomyItems.taxId2Item.ContainsKey(parentTaxId))
{
return(null);
}
TaxonomyItem parent = taxonomyItems.taxId2Item[parentTaxId];
return(parent.GetParentOfRank(taxonomyItems, rank1));
}
public static string GetTaxonomyIdOfRank(string taxonomyId, TaxonomyRank rank)
{
int id;
if (!int.TryParse(taxonomyId, out id))
{
return(taxonomyId);
}
if (!taxId2Item.ContainsKey(id))
{
return(taxonomyId);
}
TaxonomyItem item = taxId2Item[id];
return("" + item.TaxId);
}
public static TaxonomyItem[] Init()
{
StreamReader reader = GetReader(Resources.nodes_dmp);
string line;
List <TaxonomyItem> result = new List <TaxonomyItem>();
Dictionary <TaxonomyRank, List <TaxonomyItem> > counts = new Dictionary <TaxonomyRank, List <TaxonomyItem> >();
taxId2Item = new Dictionary <int, TaxonomyItem>();
name2Item = new Dictionary <string, TaxonomyItem>();
while ((line = reader.ReadLine()) != null)
{
string[] w = line.Split(new[] { "\t|\t" }, StringSplitOptions.None);
int taxId = int.Parse(w[0]);
int parentTaxId = int.Parse(w[1]);
TaxonomyRank rank = GetRank(w[2]);
int divisionId = int.Parse(w[4]);
int geneticCodeId = int.Parse(w[6]);
int mitoGeneticCodeId = int.Parse(w[8]);
TaxonomyItem ti = new TaxonomyItem(taxId, parentTaxId, rank, divisionId, geneticCodeId, mitoGeneticCodeId);
result.Add(ti);
if (!counts.ContainsKey(rank))
{
counts.Add(rank, new List <TaxonomyItem>());
}
counts[rank].Add(ti);
taxId2Item.Add(taxId, ti);
}
reader = GetReader(Resources.names_dmp);
while ((line = reader.ReadLine()) != null)
{
string[] w = line.Split(new[] { "\t|\t" }, StringSplitOptions.None);
int taxId = int.Parse(w[0]);
string name = w[1];
TaxonomyNameType nameType = GetNameType(w[3].Substring(0, w[3].Length - 2));
TaxonomyItem item = taxId2Item[taxId];
item.AddName(name, nameType);
string low = name.ToLower();
if (!name2Item.ContainsKey(low))
{
name2Item.Add(low, item);
}
}
return(result.ToArray());
}
