/**
* For facing colunit definition line, for example:
* MTD colunit-protein retention_time=[UO, UO:000031, minute, ]
* after parse metadata and header lines, need calling
* {@link #refineColUnit(uk.ac.ebi.pride.jmztab.model.MZTabColumnFactory)} manually.
*/
public new void Parse(int lineNumber, string mtdLine, MZTabErrorList errorList)
{
base.Parse(lineNumber, mtdLine, errorList);
if (_items.Length != 3){
MZTabError error = new MZTabError(FormatErrorType.MTDLine, lineNumber, mtdLine);
throw new MZTabException(error);
}
string defineLabel = _items[1].Trim().ToLower();
string valueLabel = _items[2].Trim();
if (defineLabel.Contains("colunit")){
// ignore colunit parse. In the stage, just store them into colUnitMap<defineLabel, valueLabel>.
// after table section columns created, call checkColUnit manually.
_colUnitMap.Add(defineLabel, valueLabel);
if (! defineLabel.Equals("colunit-protein") &&
! defineLabel.Equals("colunit-peptide") &&
! defineLabel.Equals("colunit-psm") &&
! defineLabel.Equals("colunit-small_molecule")){
MZTabError error = new MZTabError(FormatErrorType.MTDDefineLabel, lineNumber, defineLabel);
throw new MZTabException(error);
}
}
else{
parseNormalMetadata(defineLabel, valueLabel);
}
}
/**
* We assume that user before call this method, have parse the raw line
* is not empty line and start with section prefix.
*/
protected void Parse(int lineNumber, string line, MZTabErrorList errorList)
{
_lineNumber = lineNumber;
_line = line;
_errorList = errorList ?? new MZTabErrorList();
_items = line.Split(MZTabConstants.TAB);
_items[0] = _items[0].Trim();
_items[_items.Length - 1] = _items[_items.Length - 1].Trim();
_section = Section.findSection(_items[0]);
if (_section == null){
MZTabError error = new MZTabError(FormatErrorType.LinePrefix, lineNumber, _items[0]);
_errorList.Add(error);
}
}
/**
* A limit max capacity list, if contains a couple of {@link MZTabError} objects.
* If overflow, system will raise {@link MZTabErrorOverflowException}. Besides this, during
* add a new {@link MZTabError} object, it's {@link MZTabErrorType#level} SHOULD equal or
* great than its level setting.
*
* @param error SHOULD NOT set null
*/
public bool Add(MZTabError error)
{
if (error == null){
throw new NullReferenceException("Can not add a null error into list.");
}
if (error.Type.Level.CompareTo(level) < 0){
return false;
}
if (_errorList.Count >= MZTabProperties.MAX_ERROR_COUNT){
throw new MZTabErrorOverflowException();
}
if (_errorList.Any(x => x.Type == error.Type && x.Message == error.Message)){
return false;
}
_errorList.Add(error);
return true;
}
private Url checkURL(string defineLabel, string valueLabel)
{
Url url = MZTabUtils.ParseUrl(valueLabel);
if (url == null){
MZTabError error = new MZTabError(FormatErrorType.URL, _lineNumber, Error_Header + defineLabel,
valueLabel);
throw new MZTabException(error);
}
return url;
}
private SplitList<PublicationItem> checkPublication(string defineLabel, string valueLabel)
{
SplitList<PublicationItem> publications = MZTabUtils.ParsePublicationItems(valueLabel);
if (publications.Count == 0){
MZTabError error = new MZTabError(FormatErrorType.Publication, _lineNumber, Error_Header + defineLabel,
valueLabel);
throw new MZTabException(error);
}
return publications;
}
private MetadataProperty checkProperty(MetadataSubElement subElement, string propertyName)
{
if (string.IsNullOrEmpty(propertyName)){
return null;
}
MetadataProperty property = MetadataProperty.FindProperty(subElement, propertyName);
if (property == null){
MZTabError error = new MZTabError(FormatErrorType.MTDDefineLabel, _lineNumber,
subElement.Name + "-" + propertyName);
throw new MZTabException(error);
}
return property;
}
private SplitList<Param> checkParamList(string defineLabel, string valueLabel)
{
SplitList<Param> paramList = MZTabUtils.ParseParamList(valueLabel);
if (paramList == null || paramList.Count == 0){
MZTabError error = new MZTabError(FormatErrorType.ParamList, _lineNumber, Error_Header + defineLabel,
valueLabel);
throw new MZTabException(error);
}
return paramList;
}
private Param checkParam(string defineLabel, string valueLabel)
{
Param param = MZTabUtils.ParseParam(valueLabel);
if (param == null){
MZTabError error = new MZTabError(FormatErrorType.Param, _lineNumber, Error_Header + defineLabel,
valueLabel);
throw new MZTabException(error);
}
return param;
}
/**
* Check XXXX_abundance_assay[id] column header. If parse error, stop validate and raise
* {@link MZTabException}.
*/
private void checkAbundanceAssayColumn(string abundanceHeader)
{
string valueLabel = checkAbundanceSection(abundanceHeader);
Regex regex = new Regex("assay\\[(\\d+)\\]");
Match match = regex.Match(valueLabel);
if (! match.Success){
MZTabError error = new MZTabError(FormatErrorType.AbundanceColumn, _lineNumber, abundanceHeader);
throw new MZTabException(error);
}
int id = checkIndex(abundanceHeader, match.Groups[1].Value);
Assay assay = null;
if (metadata.AssayMap.ContainsKey(id)){
assay = metadata.AssayMap[id];
}
if (assay == null){
MZTabError error = new MZTabError(LogicalErrorType.AssayNotDefined, _lineNumber, abundanceHeader);
throw new MZTabException(error);
}
factory.AddAbundanceOptionalColumn(assay);
}
// the id is not correct number in the define label.
private int checkIndex(string defineLabel, string id)
{
try{
int index = int.Parse(id);
if (index < 1){
throw new FormatException();
}
return index;
}
catch (FormatException){
MZTabError error = new MZTabError(LogicalErrorType.IdNumber, _lineNumber, Error_Header + defineLabel, id);
throw new MZTabException(error);
}
}
private string checkEmail(string defineLabel, string valueLabel)
{
string email = MZTabUtils.ParseEmail(valueLabel);
if (email == null){
MZTabError error = new MZTabError(FormatErrorType.Email, _lineNumber, Error_Header + defineLabel,
valueLabel);
throw new MZTabException(error);
}
return email;
}
/**
* Focus on validate and parse for stable columns and optional columns which have stable order;
* All of them defined in the {@link ProteinColumn}, {@link PeptideColumn}, {@link PSMColumn}
* or {@link SmallMoleculeColumn}.
*
* NOTICE: there not exist optional columns with stable order in {@link PSMColumn}
*/
private int parseStableOrderColumns()
{
List<string> headerList = _items.ToList();
// step 1: confirm stable columns have been included in the header line.
foreach (MZTabColumn column in factory.StableColumnMapping.Values){
if (! headerList.Contains(column.Header)){
MZTabError error = new MZTabError(FormatErrorType.StableColumn, _lineNumber, column.Header);
throw new MZTabException(error);
}
}
// step 2: checking some optional columns which have stable order.
foreach (string header in headerList){
if (header.Equals(ProteinColumn.GO_TERMS.Header)){
factory.addGoTermsOptionalColumn();
}
else if (header.Equals(ProteinColumn.RELIABILITY.Header)){
factory.addReliabilityOptionalColumn();
}
else if (header.Equals(ProteinColumn.URI.Header)){
factory.addURIOptionalColumn();
}
}
// step 3: checking some flexible optional columns which have stable order.
if (_items != null){
MZTabColumn column = null;
Regex regex = new Regex("(\\w+)_ms_run\\[(\\d+)\\]");
for (int i = 1; i < _items.Length; i++){
string header = _items[i];
Match match = regex.Match(header);
if (regex.IsMatch(header)){
int id = checkIndex(header, match.Groups[2].Value);
MsRun msRun = null;
if (metadata.MsRunMap.ContainsKey(id)){
msRun = metadata.MsRunMap[id];
}
if (msRun == null){
throw new MZTabException(new MZTabError(LogicalErrorType.MsRunNotDefined, _lineNumber,
header));
}
if (_section.Equals(Section.Protein_Header)){
if (header.StartsWith(ProteinColumn.SEARCH_ENGINE_SCORE.Name)){
column = ProteinColumn.SEARCH_ENGINE_SCORE;
}
else if (header.StartsWith(ProteinColumn.NUM_PSMS.Name)){
column = ProteinColumn.NUM_PSMS;
}
else if (header.StartsWith(ProteinColumn.NUM_PEPTIDES_DISTINCT.Name)){
column = ProteinColumn.NUM_PEPTIDES_DISTINCT;
}
else if (header.StartsWith(ProteinColumn.NUM_PEPTIDES_UNIQUE.Name)){
column = ProteinColumn.NUM_PEPTIDES_UNIQUE;
}
else if (header.StartsWith("opt_")){
// ignore opt_ms_run....
// This kind of optional columns will be processed in the parseOptionalColumns() method.
}
else{
throw new MZTabException(new MZTabError(FormatErrorType.MsRunOptionalColumn,
_lineNumber,
header, _section.Name));
}
}
else if (_section.Equals(Section.Peptide_Header)){
if (header.StartsWith(PeptideColumn.SEARCH_ENGINE_SCORE.Name)){
column = PeptideColumn.SEARCH_ENGINE_SCORE;
}
else if (header.StartsWith("opt_")){
// ignore opt_ms_run....
// This kind of optional columns will be processed in the parseOptionalColumns() method.
}
else{
throw new MZTabException(new MZTabError(FormatErrorType.MsRunOptionalColumn,
_lineNumber,
header, _section.Name));
}
}
else if (_section.Equals(Section.Small_Molecule_Header)){
if (header.StartsWith(SmallMoleculeColumn.SEARCH_ENGINE_SCORE.Name)){
column = SmallMoleculeColumn.SEARCH_ENGINE_SCORE;
}
else if (header.StartsWith("opt_")){
// ignore opt_ms_run....
// This kind of optional columns will be processed in the parseOptionalColumns() method.
}
else{
throw new MZTabException(new MZTabError(FormatErrorType.MsRunOptionalColumn,
_lineNumber,
header, _section.Name));
}
}
if (column != null){
factory.AddOptionalColumn(column, msRun);
}
}
}
}
return factory.StableColumnMapping.Values.Count;
}
/**
* Additional columns can be added to the end of the protein table. These column headers MUST start with the prefix "opt_".
* Column names MUST only contain the following characters: 'A’-'Z’, 'a’-'z’, '0’-'9’, '_’, '-’, '[’, ']’, and ':’.
*
* the format: opt_{IndexedElement[id]}_{value}. Spaces within the parameter's name MUST be replaced by '_'.
*/
private bool checkOptColumnName(string nameLabel)
{
nameLabel = nameLabel.Trim();
const string regexp = "opt_((assay|study_variable|ms_run)\\[(\\w+)\\]|global)_([A-Za-z0-9_\\-\\[\\]:\\.]+)";
Regex regex = new Regex(regexp);
Match match = regex.Match(nameLabel);
if (match.Success){
string object_id = match.Groups[1].Value;
string value = match.Groups[4].Value;
CVParam param = null;
if (value.StartsWith("cv_")){
param = checkCVParamOptColumnName(nameLabel, value);
}
Type dataType = getDataType(param);
if (object_id.Contains("global")){
if (param == null){
factory.AddOptionalColumn(value, dataType);
}
else{
factory.AddOptionalColumn(param, dataType);
}
}
else{
int id = checkIndex(nameLabel, match.Groups[3].Value);
MZTabError error;
if (object_id.Contains("assay")){
Assay element = null;
if (metadata.AssayMap.ContainsKey(id)){
element = metadata.AssayMap[id];
}
// not found assay_id in metadata.
if (element == null){
error = new MZTabError(LogicalErrorType.AssayNotDefined, _lineNumber, nameLabel);
throw new MZTabException(error);
}
if (param == null){
factory.AddOptionalColumn(element, value, dataType);
}
else{
factory.AddOptionalColumn(element, param, dataType);
}
}
else if (object_id.Contains("study_variable")){
StudyVariable element = null;
if (metadata.StudyVariableMap.ContainsKey(id)){
element = metadata.StudyVariableMap[id];
}
// not found study_variable_id in metadata.
if (element == null){
error = new MZTabError(LogicalErrorType.StudyVariableNotDefined, _lineNumber, nameLabel);
throw new MZTabException(error);
}
if (param == null){
factory.AddOptionalColumn(element, value, dataType);
}
else{
factory.AddOptionalColumn(element, param, dataType);
}
}
else if (object_id.Contains("ms_run")){
MsRun element = null;
if (metadata.MsRunMap.ContainsKey(id)){
element = metadata.MsRunMap[id];
}
// not found ms_run_id in metadata.
if (element == null){
error = new MZTabError(LogicalErrorType.MsRunNotDefined, _lineNumber, nameLabel);
throw new MZTabException(error);
}
if (param == null){
factory.AddOptionalColumn(element, value, dataType);
}
else{
factory.AddOptionalColumn(element, param, dataType);
}
}
}
return true;
}
throw new MZTabException(new MZTabError(FormatErrorType.OptionalCVParamColumn, _lineNumber, nameLabel));
}
/**
* Check XXXX_abundance_study_variable[id], XXXX_abundance_stdev_study_variable[id], XXXX_abundance_std_error_study_variable[id]
* column header. If parse error, stop validate and raise {@link MZTabException}.
*/
private void checkAbundanceStudyVariableColumns(string abundanceHeader, string abundanceStdevHeader,
string abundanceStdErrorHeader)
{
abundanceHeader = abundanceHeader.Trim().ToLower();
abundanceStdevHeader = abundanceStdevHeader.Trim().ToLower();
abundanceStdErrorHeader = abundanceStdErrorHeader.Trim().ToLower();
if (! abundanceHeader.Contains("_abundance_study_variable")){
string missHeader = Section.toDataSection(_section).Name + "_abundance_study_variable";
MZTabError error = new MZTabError(LogicalErrorType.AbundanceColumnTogether, _lineNumber, missHeader);
throw new MZTabException(error);
}
if (! abundanceStdevHeader.Contains("_abundance_stdev_study_variable")){
string missHeader = Section.toDataSection(_section).Name + "_abundance_stdev_study_variable";
MZTabError error = new MZTabError(LogicalErrorType.AbundanceColumnTogether, _lineNumber, missHeader);
throw new MZTabException(error);
}
if (! abundanceStdErrorHeader.Contains("_abundance_std_error_study_variable")){
string missHeader = Section.toDataSection(_section).Name + "_abundance_std_error_study_variable";
MZTabError error = new MZTabError(LogicalErrorType.AbundanceColumnTogether, _lineNumber, missHeader);
throw new MZTabException(error);
}
StudyVariable abundanceStudyVariable = checkAbundanceStudyVariableColumn(abundanceHeader);
StudyVariable abundanceStdevStudyVariable = checkAbundanceStudyVariableColumn(abundanceStdevHeader);
StudyVariable abundanceStdErrorStudyVariable = checkAbundanceStudyVariableColumn(abundanceStdErrorHeader);
if (abundanceStudyVariable != abundanceStdevStudyVariable ||
abundanceStudyVariable != abundanceStdErrorStudyVariable){
MZTabError error = new MZTabError(LogicalErrorType.AbundanceColumnSameId, _lineNumber, abundanceHeader,
abundanceStdevHeader, abundanceStdErrorHeader);
throw new MZTabException(error);
}
factory.AddAbundanceOptionalColumn(abundanceStudyVariable);
}
/**
* Check XXXX_abundance_study_variable[id], XXXX_abundance_stdev_study_variable[id], XXXX_abundance_std_error_study_variable[id]
* column header. If parse error, stop validate and raise {@link MZTabException}.
*/
private StudyVariable checkAbundanceStudyVariableColumn(string abundanceHeader)
{
string valueLabel = checkAbundanceSection(abundanceHeader);
Regex regex = new Regex("study_variable\\[(\\d+)\\]");
Match match = regex.Match(valueLabel);
if (! match.Success){
MZTabError error = new MZTabError(FormatErrorType.AbundanceColumn, _lineNumber, abundanceHeader);
throw new MZTabException(error);
}
int id = checkIndex(abundanceHeader, match.Groups[1].Value);
StudyVariable studyVariable = null;
if (metadata.StudyVariableMap.ContainsKey(id)){
studyVariable = metadata.StudyVariableMap[id];
}
if (studyVariable == null){
MZTabError error = new MZTabError(LogicalErrorType.StudyVariableNotDefined, _lineNumber, abundanceHeader);
throw new MZTabException(error);
}
return studyVariable;
}
/**
* Check (protein|peptide|smallmolecule)_abundance is correct, and return object value label.
* For example, protein_abundance_std_error_study_variable[id], return study_variable[id].
*/
private string checkAbundanceSection(string abundanceHeader)
{
abundanceHeader = abundanceHeader.Trim().ToLower();
Regex regex = new Regex("(protein|peptide|smallmolecule)_abundance_(.+)");
Match match = regex.Match(abundanceHeader);
if (match.Success){
string sectionName = translate(match.Groups[1].Value);
if (sectionName != null &&
!(sectionName.Equals(Section.Protein.Name) && _section != Section.Protein_Header) &&
!(sectionName.Equals(Section.Peptide.Name) && _section != Section.Peptide_Header) &&
!(sectionName.Equals(Section.Small_Molecule.Name) && _section != Section.Small_Molecule_Header)){
return match.Groups[2].Value;
}
MZTabError error = new MZTabError(FormatErrorType.AbundanceColumn, _lineNumber, abundanceHeader);
throw new MZTabException(error);
}
else{
MZTabError error = new MZTabError(FormatErrorType.AbundanceColumn, _lineNumber, abundanceHeader);
throw new MZTabException(error);
}
}
public MZTabException(MZTabError error)
: base(error.ToString())
{
_error = error;
}
private List<IndexedElement> checkIndexedElementList(string defineLabel, string valueLabel,
MetadataElement element)
{
List<IndexedElement> indexedElementList = MZTabUtils.ParseIndexedElementList(valueLabel, element);
if (indexedElementList == null || indexedElementList.Count == 0){
MZTabError error = new MZTabError(FormatErrorType.IndexedElement, _lineNumber,
Error_Header + defineLabel, valueLabel);
throw new MZTabException(error);
}
return indexedElementList;
}
/**
* Query {@link uk.ac.ebi.pride.jmztab.utils.errors.MZTabErrorList} to check exist errors or not.
* @throws java.io.IOException
* @throws uk.ac.ebi.pride.jmztab.utils.errors.MZTabException during parse metadata, protein/peptide/small_molecule header line, exists error.
* @throws uk.ac.ebi.pride.jmztab.utils.errors.MZTabErrorOverflowException reference mztab.properties file mztab.max_error_count parameter.
*/
public void check(StreamReader reader)
{
COMLineParser comParser = new COMLineParser();
MTDLineParser mtdParser = new MTDLineParser();
PRHLineParser prhParser = null;
PRTLineParser prtParser = null;
PEHLineParser pehParser = null;
PEPLineParser pepParser = null;
PSHLineParser pshParser = null;
PSMLineParser psmParser = null;
SMHLineParser smhParser = null;
SMLLineParser smlParser = null;
SortedDictionary<int, Comment> commentMap = new SortedDictionary<int, Comment>();
SortedDictionary<int, Protein> proteinMap = new SortedDictionary<int, Protein>();
SortedDictionary<int, Peptide> peptideMap = new SortedDictionary<int, Peptide>();
SortedDictionary<int, PSM> psmMap = new SortedDictionary<int, PSM>();
SortedDictionary<int, SmallMolecule> smallMoleculeMap = new SortedDictionary<int, SmallMolecule>();
PositionMapping prtPositionMapping = null;
PositionMapping pepPositionMapping = null;
PositionMapping psmPositionMapping = null;
PositionMapping smlPositionMapping = null;
string line;
int highWaterMark = 1;
int lineNumber = 0;
while ((line = reader.ReadLine()) != null){
lineNumber++;
if (string.IsNullOrEmpty(line) || line.StartsWith("MTH") || line.StartsWith("#")){
continue;
}
if (line.StartsWith(Section.Comment.Prefix)){
comParser.Parse(lineNumber, line, errorList);
commentMap.Add(lineNumber, comParser.getComment());
continue;
}
Section section = getSection(line);
MZTabError error;
if (section == null){
error = new MZTabError(FormatErrorType.LinePrefix, lineNumber, subString(line));
throw new MZTabException(error);
}
if (section.Level < highWaterMark){
Section currentSection = Section.FindSection(highWaterMark);
error = new MZTabError(LogicalErrorType.LineOrder, lineNumber, currentSection.Name, section.Name);
throw new MZTabException(error);
}
highWaterMark = section.Level;
// There exists errors during checking metadata section.
if (highWaterMark == 1 && ! errorList.IsNullOrEmpty()){
break;
}
switch (highWaterMark){
case 1:
// metadata section.
mtdParser.Parse(lineNumber, line, errorList);
break;
case 2:
if (prhParser != null){
// header line only display once!
error = new MZTabError(LogicalErrorType.HeaderLine, lineNumber, subString(line));
throw new MZTabException(error);
}
// protein header section
prhParser = new PRHLineParser(mtdParser.Metadata);
prhParser.Parse(lineNumber, line, errorList);
prtPositionMapping = new PositionMapping(prhParser.getFactory(), line);
// tell system to continue check protein data line.
highWaterMark = 3;
break;
case 3:
if (prhParser == null){
// header line should be check first.
error = new MZTabError(LogicalErrorType.NoHeaderLine, lineNumber, subString(line));
throw new MZTabException(error);
}
if (prtParser == null){
prtParser = new PRTLineParser(prhParser.getFactory(), prtPositionMapping, mtdParser.Metadata,
errorList);
}
prtParser.Parse(lineNumber, line, errorList);
proteinMap.Add(lineNumber, prtParser.getRecord(line));
break;
case 4:
if (pehParser != null){
// header line only display once!
error = new MZTabError(LogicalErrorType.HeaderLine, lineNumber, subString(line));
throw new MZTabException(error);
}
if (mtdParser.Metadata.MzTabType == MzTabType.Identification){
errorList.Add(new MZTabError(LogicalErrorType.PeptideSection, lineNumber, subString(line)));
}
// peptide header section
pehParser = new PEHLineParser(mtdParser.Metadata);
pehParser.Parse(lineNumber, line, errorList);
pepPositionMapping = new PositionMapping(pehParser.getFactory(), line);
// tell system to continue check peptide data line.
highWaterMark = 5;
break;
case 5:
if (pehParser == null){
// header line should be check first.
error = new MZTabError(LogicalErrorType.NoHeaderLine, lineNumber, subString(line));
throw new MZTabException(error);
}
if (pepParser == null){
pepParser = new PEPLineParser(pehParser.getFactory(), pepPositionMapping, mtdParser.Metadata,
errorList);
}
pepParser.Parse(lineNumber, line, errorList);
peptideMap.Add(lineNumber, pepParser.getRecord(line));
break;
case 6:
if (pshParser != null){
// header line only display once!
error = new MZTabError(LogicalErrorType.HeaderLine, lineNumber, subString(line));
throw new MZTabException(error);
}
// psm header section
pshParser = new PSHLineParser(mtdParser.Metadata);
pshParser.Parse(lineNumber, line, errorList);
psmPositionMapping = new PositionMapping(pshParser.getFactory(), line);
// tell system to continue check peptide data line.
highWaterMark = 7;
break;
case 7:
if (pshParser == null){
// header line should be check first.
error = new MZTabError(LogicalErrorType.NoHeaderLine, lineNumber, subString(line));
throw new MZTabException(error);
}
if (psmParser == null){
psmParser = new PSMLineParser(pshParser.getFactory(), psmPositionMapping, mtdParser.Metadata,
errorList);
}
psmParser.Parse(lineNumber, line, errorList);
psmMap.Add(lineNumber, psmParser.getRecord(line));
break;
case 8:
if (smhParser != null){
// header line only display once!
error = new MZTabError(LogicalErrorType.HeaderLine, lineNumber, subString(line));
throw new MZTabException(error);
}
// small molecule header section
smhParser = new SMHLineParser(mtdParser.Metadata);
smhParser.Parse(lineNumber, line, errorList);
smlPositionMapping = new PositionMapping(smhParser.getFactory(), line);
// tell system to continue check small molecule data line.
highWaterMark = 9;
break;
case 9:
if (smhParser == null){
// header line should be check first.
error = new MZTabError(LogicalErrorType.NoHeaderLine, lineNumber, subString(line));
throw new MZTabException(error);
}
if (smlParser == null){
smlParser = new SMLLineParser(smhParser.getFactory(), smlPositionMapping, mtdParser.Metadata,
errorList);
}
smlParser.Parse(lineNumber, line, errorList);
smallMoleculeMap.Add(lineNumber, smlParser.getRecord(line));
break;
}
}
if (reader != null){
reader.Close();
}
if (errorList.IsNullOrEmpty()){
_mzTabFile = new MZTabFile(mtdParser.Metadata);
foreach (int id in commentMap.Keys){
_mzTabFile.addComment(id, commentMap[id]);
}
if (prhParser != null){
MZTabColumnFactory proteinColumnFactory = prhParser.getFactory();
_mzTabFile.setProteinColumnFactory(proteinColumnFactory);
foreach (int id in proteinMap.Keys){
_mzTabFile.addProtein(id, proteinMap[id]);
}
}
if (pehParser != null){
MZTabColumnFactory peptideColumnFactory = pehParser.getFactory();
_mzTabFile.setPeptideColumnFactory(peptideColumnFactory);
foreach (int id in peptideMap.Keys){
_mzTabFile.addPeptide(id, peptideMap[id]);
}
}
if (pshParser != null){
MZTabColumnFactory psmColumnFactory = pshParser.getFactory();
_mzTabFile.setPSMColumnFactory(psmColumnFactory);
foreach (int id in psmMap.Keys){
_mzTabFile.addPSM(id, psmMap[id]);
}
}
if (smhParser != null){
MZTabColumnFactory smallMoleculeColumnFactory = smhParser.getFactory();
_mzTabFile.setSmallMoleculeColumnFactory(smallMoleculeColumnFactory);
foreach (int id in smallMoleculeMap.Keys){
_mzTabFile.addSmallMolecule(id, smallMoleculeMap[id]);
}
}
}
}
private MzTabType checkMZTabType(string defineLabel, string valueLabel)
{
try{
return (MzTabType) Enum.Parse(typeof (MzTabType), valueLabel);
}
catch (ArgumentException){
MZTabError error = new MZTabError(FormatErrorType.MZTabType, _lineNumber, Error_Header + defineLabel,
valueLabel);
throw new MZTabException(error);
}
}
