public string[] this[MzTabSection section, int index]
{
get
{
return(GetData(section, index));
}
}
public string this[MzTabSection section, int index, string columnName]
{
get
{
return(GetData(section, index, columnName));
}
}
public string[] GetColumns(MzTabSection section)
{
switch (section)
{
case MzTabSection.PSM:
return(_psmDataTable != null?_psmDataTable.Columns.Cast <DataColumn>().Select(x => x.ColumnName).ToArray() : null);
case MzTabSection.Peptide:
return(_peptideDataTable != null?_peptideDataTable.Columns.Cast <DataColumn>().Select(x => x.ColumnName).ToArray() : null);
case MzTabSection.Protein:
return(_proteinDataTable != null?_proteinDataTable.Columns.Cast <DataColumn>().Select(x => x.ColumnName).ToArray() : null);
case MzTabSection.SmallMolecule:
return(_smallMoleculeDataTable != null?_smallMoleculeDataTable.Columns.Cast <DataColumn>().Select(x => x.ColumnName).ToArray() : null);
default:
return(null);
}
}
public string[] GetData(MzTabSection section, int index)
{
switch (section)
{
case MzTabSection.PSM:
return(_psmDataTable != null ? (string[])_psmDataTable.Rows[index].ItemArray : null);
case MzTabSection.Peptide:
return(_peptideDataTable != null ? (string[])_peptideDataTable.Rows[index].ItemArray : null);
case MzTabSection.Protein:
return(_proteinDataTable != null ? (string[])_proteinDataTable.Rows[index].ItemArray : null);
case MzTabSection.SmallMolecule:
return(_smallMoleculeDataTable != null ? (string[])_smallMoleculeDataTable.Rows[index].ItemArray : null);
default:
return(null);
}
}
public string GetData(MzTabSection section, int index, string columnName)
{
switch (section)
{
case MzTabSection.PSM:
return(_psmDataTable != null ? (string)_psmDataTable.Rows[index][columnName] : null);
case MzTabSection.Peptide:
return(_peptideDataTable != null ? (string)_peptideDataTable.Rows[index][columnName] : null);
case MzTabSection.Protein:
return(_proteinDataTable != null ? (string)_proteinDataTable.Rows[index][columnName] : null);
case MzTabSection.SmallMolecule:
return(_smallMoleculeDataTable != null ? (string)_smallMoleculeDataTable.Rows[index][columnName] : null);
default:
return(null);
}
}
public bool ContainsColumn(MzTabSection section, string columnName)
{
switch (section)
{
case MzTabSection.PSM:
return(_psmDataTable != null && _psmDataTable.Columns.Contains(columnName));
case MzTabSection.Peptide:
return(_peptideDataTable != null && _peptideDataTable.Columns.Contains(columnName));
case MzTabSection.Protein:
return(_proteinDataTable != null && _proteinDataTable.Columns.Contains(columnName));
case MzTabSection.SmallMolecule:
return(_smallMoleculeDataTable != null && _smallMoleculeDataTable.Columns.Contains(columnName));
default:
return(false);
}
}
private IEnumerable <T> GetObjects <T>(MzTabSection section) where T : MzTabEntity, new()
{
DataTable table = null;
switch (section)
{
case MzTabSection.PSM:
table = _psmDataTable;
break;
case MzTabSection.Peptide:
table = _peptideDataTable;
break;
case MzTabSection.SmallMolecule:
table = _smallMoleculeDataTable;
break;
case MzTabSection.Protein:
table = _proteinDataTable;
break;
}
if (table == null || table.Rows.Count == 0)
{
yield break;
}
string[] columns = GetColumns(section);
int count = columns.Length;
foreach (DataRow row in table.Rows)
{
var item = new T();
for (int i = 0; i < count; i++)
{
item.SetValue(columns[i], (string)row.ItemArray[i]);
}
yield return(item);
}
}
private void WriteData <T>(MzTabSection section, IEnumerable <T> data, bool includeCommentLine = false) where T : MzTabEntity
{
if ((_currentState & MzTab.States.MetaData) != MzTab.States.MetaData)
{
throw new ArgumentException("Unable to write the " + section + " section, incorrect location. The Meta Data section must come first.");
}
List <T> objects = data.ToList();
if (objects.Count == 0)
{
return;
}
MzTab.LinePrefix headerPrefix = MzTab.LinePrefix.Comment;
MzTab.LinePrefix prefix = MzTab.LinePrefix.Comment;
switch (section)
{
case MzTabSection.SmallMolecule:
headerPrefix = MzTab.LinePrefix.SmallMoleculeTable;
prefix = MzTab.LinePrefix.SmallMoleculeData;
_currentState |= MzTab.States.SmallMoleculeData;
_currentState |= MzTab.States.SmallMoleculeHeader;
break;
case MzTabSection.Peptide:
headerPrefix = MzTab.LinePrefix.PeptideTable;
prefix = MzTab.LinePrefix.PeptideData;
_currentState |= MzTab.States.PeptideData;
_currentState |= MzTab.States.PeptideHeader;
break;
case MzTabSection.PSM:
headerPrefix = MzTab.LinePrefix.PsmTable;
prefix = MzTab.LinePrefix.PsmData;
_currentState |= MzTab.States.PsmData;
_currentState |= MzTab.States.PsmHeader;
break;
case MzTabSection.Protein:
headerPrefix = MzTab.LinePrefix.ProteinTable;
prefix = MzTab.LinePrefix.ProteinData;
_currentState |= MzTab.States.ProteinData;
_currentState |= MzTab.States.ProteinHeader;
break;
}
// Write Header
string[] header = MzTabEntity.GetHeader(objects).ToArray();
WriteLine(headerPrefix, header);
if (includeCommentLine)
{
WriteComment(string.Join("\t", header));
}
// Write table
foreach (string[] values in objects.Select(datum => datum.GetStringValues(header).ToArray()))
{
WriteLine(prefix, values);
}
}
