public static GORecord[] FromDataTable(DataTable dt)
{
GORecord[] array = new GORecord[dt.Rows.Count];
for (int i = 0; i < array.Length; i++)
{
array[i] = GORecord.FromDataRow(dt.Rows[i]);
}
return(array);
}
public GORecord[] GetGORecordsFromECNumber(string ecNumber)
{
DataTable tableGO = GetGOFromECNumber(ecNumber);
ArrayList listTerms = new ArrayList();
foreach (DataRow rowGO in tableGO.Rows)
{
listTerms.Add(GORecord.FromDataRow(rowGO));
}
return((GORecord[])listTerms.ToArray(typeof(GORecord)));
}
// public void AddMetaRecord(string key, string val)
// {
// _meta.Add(new string[]{key, val});
// }
//
// public string[][] GetMetaRecords()
// {
// return (string[][])_meta.ToArray(typeof(string[]));
// }
//
// public void AddMetaRecords(string[][] records)
// {
// foreach(string[] pair in records)
// AddMetaRecord(pair[0], pair[1]);
// }
public static GORecord FromDataRow(DataRow dr)
{
GORecord rec = new GORecord();
if (dr.Table.Columns.Contains("GOID"))
{
rec._id = (string)dr["GOID"];
if (rec._id.StartsWith("GO:"))
{
rec._id = rec._id.Substring("GO:".Length);
}
}
if (dr.Table.Columns.Contains("GOName"))
{
rec._name = (string)dr["GOName"];
}
//put the rest of the DataRow information into the meta dictionary
// int colID = dr.Table.Columns["GOID"].Ordinal;
// int colName = dr.Table.Columns["GOName"].Ordinal;
// for(int i=0; i<dr.Table.Columns.Count; i++)
// {
// if( i == colID || i == colName) continue;
// string key = dr.Table.Columns[i].ColumnName;
// string val = dr[i].ToString();
// rec.AddMetaRecord(key, val);
// }
if (dr.Table.Columns.Contains("SwissProID"))
{
rec._notes = "linked through Protein: " + (string)dr["protein_name"];
}
if (dr.Table.Columns.Contains("ECNumber"))
{
string ec = (string)dr["ECNumber"];
rec._notes = "linked through EC: " + ec;
rec._ecNumber = ec;
}
if (dr.Table.Columns.Contains("process_ID") && !dr.IsNull("process_ID"))
{
rec._processID = (Guid)dr["process_ID"];
}
if (dr.Table.Columns.Contains("process_name") && !dr.IsNull("process_name"))
{
rec._processName = (string)dr["process_name"];
}
if (dr.Table.Columns.Contains("TermLevel") && !dr.IsNull("TermLevel"))
{
rec._treeLevel = (int)dr["TermLevel"];
}
return(rec);
}
public override bool Equals(object obj)
{
if (obj.GetType() != typeof(GORecord))
{
return(base.Equals(obj));
}
GORecord rec = obj as GORecord;
return
(this.ID == rec.ID &&
this.ECNumber == rec.ECNumber &&
this.Name == rec.Name &&
this.Notes == rec.Notes &&
this.ProcessID == rec.ProcessID &&
this.ProcessName == rec.ProcessName);
}
public GORecord[] GetGORecordsFromProcessID_EC(Guid processID)
{
//find the GO Terms through EC Numbers
// PathwaysLib.ServerObjects.ServerProcess sp = PathwaysLib.ServerObjects.ServerProcess.Load(processID);
// Guid gProcessID = sp.GenericProcessID;
DataTable dtGO_EC = GetGOFromProcessID_ECNumber(processID);
ArrayList goRecords = new ArrayList();
foreach (DataRow dr in dtGO_EC.Rows)
{
GORecord rec = GORecord.FromDataRow(dr);
rec.TreeLevel = GetMaxMaxTreeLevelOfGOTerm(rec.ID);
goRecords.Add(rec);
}
return((GORecord[])goRecords.ToArray(typeof(GORecord)));
}
public GORecord[] TransposeGOTermUpToLevel(GORecord record, int treeLevel)
{
if (GetMinTreeLevelOfGOTerm_UnderCatalyticActivity(record.ID) <= treeLevel)
{
return new GORecord[] { record }
}
;
//a queue to aid in BFS
Queue goTerms = new Queue(new GORecord[] { record });
ArrayList listLevelXAnnotations = new ArrayList();
//keep track of all categories so we don't go up a path multiple times
ArrayList listTouchedCategories = new ArrayList();
while (goTerms.Count > 0)
{
GORecord rec = (GORecord)goTerms.Dequeue();
//if this is at the correct level or above, add it to the annotation list
int minLevel = GetMaxMaxTreeLevelOfGOTerm(rec.ID);
if (minLevel <= treeLevel)
{
rec.TreeLevel = minLevel;
listLevelXAnnotations.Add(rec);
}
else
{
//find it's parents who are under Catalytic Activity and add those to the Queue
SqlConnection con = new SqlConnection(CONNECTION_STRING);
try
{
con.Open();
string command =
"select ParentName = terms.[Name], tt.* from " +
" (select * from Pubmed.dbo.GOTermsTree where ChildID=@childID and OnPathUnderCatalyticActivity=1) tt "+
" inner join "+
" Pubmed.dbo.GOTerms terms "+
" on tt.ParentID = terms.[ID] ";
SqlCommand com = new SqlCommand(command, con);
com.Parameters.Add("@childID", rec.ID);
SqlDataReader dr = com.ExecuteReader();
while (dr.Read())
{
//add a modified version of this same record to the queue
string GOID = (string)dr["ParentID"];
string GOName = (string)dr["ParentName"];
int nextLevel = (int)dr["TermLevel"];
GORecord newRec = new GORecord();
newRec.ECNumber = rec.ECNumber;
newRec.Notes = rec.Notes;
newRec.ProcessID = rec.ProcessID;
newRec.ProcessName = rec.ProcessName;
newRec.TreeLevel = nextLevel;
newRec.ID = GOID;
newRec.Name = GOName;
//only add this category if we haven't been up this path
if (!listTouchedCategories.Contains(newRec.ID))
{
goTerms.Enqueue(newRec);
listTouchedCategories.Add(newRec.ID);
}
}
dr.Close();
}
catch (Exception se) { throw se; }
finally{ con.Close(); }
}
}
return((GORecord[])listLevelXAnnotations.ToArray(typeof(GORecord)));
}
