public MzTabWriter(string filePath)
{
FilePath = filePath;
_writer = new StreamWriter(FilePath, false, MzTab.DefaultEncoding);
IsOpen = true;
_currentState = MzTab.States.None;
}
public void WriteMetaData(string key, object value)
{
if (_currentState > MzTab.States.MetaData)
{
throw new ArgumentException("Unable to write Metadata, incorrect location. Only one Metadata section per file");
}
_currentState |= MzTab.States.MetaData;
WriteLine(MzTab.LinePrefix.MetaData, key, value);
}
private void ReadDataTable(MzTab.States dataState, object[] data, DataTable table)
{
if (table == null)
{
throw new ArgumentException("No header information loaded for " + dataState + ", unable to parse data");
}
// Set the we have entered the current state
_currentState |= dataState;
// Add the row to the Protein data table
table.Rows.Add(data.SubArray(1, table.Columns.Count));
}
private void ReadMetaData(string[] data, int lineNumber)
{
// Set that we have enter in Metadata section
_currentState |= MzTab.States.MetaData;
// Grab the key-value pair, which should correspond to index 1 and 2, respectively
string key = data[1];
string value = data[2];
if (string.IsNullOrWhiteSpace(key))
{
throw new ArgumentException("No key was specified in the metadata section at line #" + lineNumber);
}
MetaData.SetValue(key, value);
}
public void WriteMetaData(MzTabMetaData metaData)
{
if (_currentState > MzTab.States.MetaData)
{
throw new ArgumentException("Unable to write Metadata, incorrect location. Only one Metadata section per file");
}
_currentState |= MzTab.States.MetaData;
foreach (KeyValuePair <string, string> kvp in metaData.GetKeyValuePairs())
{
_writer.Write(MzTab.MetaDataLinePrefix);
_writer.Write(MzTab.FieldSeparator);
_writer.Write(kvp.Key);
_writer.Write(MzTab.FieldSeparator);
_writer.WriteLine(kvp.Value);
}
// Save meta data
_metaData = metaData;
}
private void ReadTableDefinition(MzTab.States headerState, string[] data, DataTable table)
{
if ((_currentState & MzTab.States.MetaData) != MzTab.States.MetaData)
{
throw new ArgumentException("The MetaData section MUST occur before the " + table.TableName + " Section. Invalid input file");
}
if ((_currentState & headerState) == headerState)
{
throw new ArgumentException("The " + table.TableName + " Table Header has already been parsed once, only one " + table.TableName + " section is allowed per mzTab file.");
}
// Set the we have entered the current state
_currentState |= headerState;
int i = 1;
while (i < data.Length && !string.IsNullOrWhiteSpace(data[i]))
{
table.Columns.Add(data[i].Trim());
i++;
}
}
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);
}
}
