/**
* For proteins and peptides modifications SHOULD be reported using either UNIMOD or PSI-MOD accessions.
* As these two ontologies are not applicable to small molecules, so-called CHEMMODs can also be defined.
*
* Ambiguity of modification position MUST NOT be reported at the Protein level.
*/
protected SplitList<Modification> checkModifications(MZTabColumn column, string target)
{
SplitList<Modification> modificationList = checkModifications(_section, column, target);
foreach (Modification mod in modificationList){
if (mod.PositionMap.Count > 1){
// this is warn
_errorList.Add(new MZTabError(LogicalErrorType.AmbiguityMod, _lineNumber, column.Header,
mod.ToString()));
}
if (mod.Type == Modification.ModificationType.CHEMMOD){
// this is warn
_errorList.Add(new MZTabError(LogicalErrorType.CHEMMODS, _lineNumber, column.Header, mod.ToString()));
}
if (mod.Type == Modification.ModificationType.SUBST &&
parseSubstitutionIdentifier(mod.Accession) != null){
_errorList.Add(new MZTabError(LogicalErrorType.SubstituteIdentifier, _lineNumber, column.Header,
mod.ToString()));
return null;
}
}
return modificationList;
}
/**
* accession should not null.
* accession MUST be unique, otherwise raise {@link LogicalErrorType#DuplicationAccession} error.
*
* If check error return null, else return accession string.
*/
protected string checkAccession(MZTabColumn column, string accession)
{
string result_accession = checkData(column, accession, false);
if (result_accession == null){
return result_accession;
}
if (! accessionSet.Add(result_accession)){
_errorList.Add(new MZTabError(LogicalErrorType.DuplicationAccession, _lineNumber, column.Header,
result_accession));
return null;
}
return result_accession;
}
/**
* Defines the used unit for a column in the peptide/protein/small_molecule section.
* The format of the value has to be {column name}={Parameter defining the unit}
*/
internal ColUnit(MZTabColumn column, Param value)
{
if (column == null){
throw new NullReferenceException("MZTabColumn can not set null");
}
if (value == null){
throw new NullReferenceException("Param can not set null");
}
if (column is PluginMzTab.Lib.Model.AbundanceColumn){
throw new Exception("Colunit MUST NOT be used to define a unit for quantification columns.");
}
this.column = column;
this.value = value;
}
/**
* For proteins and peptides modifications SHOULD be reported using either UNIMOD or PSI-MOD accessions.
* As these two ontologies are not applicable to small molecules, so-called CHEMMODs can also be defined.
*/
protected SplitList<Modification> checkModifications(MZTabColumn column, string sequence, string target)
{
SplitList<Modification> modificationList = checkModifications(_section, column, target);
int terminal_position = sequence.Length + 1;
foreach (Modification mod in modificationList){
foreach (int position in mod.PositionMap.Keys){
if (position > terminal_position || position < 0){
_errorList.Add(new MZTabError(LogicalErrorType.ModificationPosition, _lineNumber, column.Header,
mod.ToString(), sequence));
return null;
}
}
if (mod.Type == Modification.ModificationType.CHEMMOD){
_errorList.Add(new MZTabError(LogicalErrorType.CHEMMODS, _lineNumber, column.Header, mod.ToString()));
}
}
return modificationList;
}
/**
* As these two ontologies are not applicable to small molecules, so-called CHEMMODs can also be defined.
* CHEMMODs MUST NOT be used if the modification can be reported using a PSI-MOD or UNIMOD accession.
* Mass deltas MUST NOT be used for CHEMMODs if the delta can be expressed through a known chemical formula .
*/
protected SplitList<Modification> checkModifications(MZTabColumn column, string target)
{
SplitList<Modification> modificationList = base.checkModifications(_section, column, target);
foreach (Modification mod in modificationList){
if (mod.Type == Modification.ModificationType.CHEMMOD){
if (target.Contains("-MOD:") || target.Contains("-UNIMOD:")){
_errorList.Add(new MZTabError(LogicalErrorType.CHEMMODS, _lineNumber, column.Header,
mod.ToString()));
}
if (parseChemmodAccession(mod.Accession) == null){
_errorList.Add(new MZTabError(FormatErrorType.CHEMMODSAccession, _lineNumber, column.Header,
mod.ToString()));
return null;
}
}
}
return modificationList;
}
/**
* Check and translate smiles string into parameter list which split by '|' character..
* If parse incorrect, raise {@link FormatErrorType#StringList} error.
* Normally, smiles can set "null", but in "Complete" file, in general "null" values SHOULD not be given.
*
* @param column SHOULD NOT set null
* @param smiles SHOULD NOT be empty.
*/
protected SplitList<string> checkSmiles(MZTabColumn column, string smiles)
{
return checkStringList(column, smiles, MZTabConstants.BAR);
}
/**
* Check and translate peptide sequence. 'O' and 'U' are encoded by codons that are usually interpreted as stop codons,
* which can not displayed in the sequence. So, if find it, system raise {@link FormatErrorType#Sequence} error.
*
* @param column SHOULD NOT set null
* @param sequence SHOULD NOT be empty.
*/
protected string checkSequence(MZTabColumn column, string sequence)
{
string result = checkData(column, sequence, true);
if (result == null){
return null;
}
result = result.ToUpper();
Regex regex = new Regex("[OU]");
Match match = regex.Match(result);
if (match.Success){
_errorList.Add(new MZTabError(FormatErrorType.Sequence, _lineNumber, column.Header, sequence));
}
return result;
}
/**
* Check and translate target to {@link MZBoolean}. Only "0" and "1" allow used in express Boolean (0/1).
* If parse incorrect, raise {@link FormatErrorType#MZBoolean} error.
*
* @param column SHOULD NOT set null
* @param target SHOULD NOT be empty.
*/
protected MZBoolean checkMZBoolean(MZTabColumn column, string target)
{
string result = checkData(column, target, true);
if (result == null || result.Equals("NULL", StringComparison.CurrentCultureIgnoreCase)){
return null;
}
MZBoolean value = MZBoolean.FindBoolean(result);
if (value == null){
_errorList.Add(new MZTabError(FormatErrorType.MZBoolean, _lineNumber, column.Header, result));
}
return value;
}
private string checkAccession(MZTabColumn column, string target)
{
return checkData(column, target, true);
}
/**
* Check and translate unique to {@link MZBoolean}. Only "0" and "1" allow used in express Boolean (0/1).
* If parse incorrect, raise {@link FormatErrorType#MZBoolean} error.
*
* @param column SHOULD NOT set null
* @param unique SHOULD NOT be empty.
*/
protected MZBoolean checkUnique(MZTabColumn column, string unique)
{
return checkMZBoolean(column, unique);
}
/**
* Check and translate target string into parameter list which split by splitChar character..
* If parse incorrect, raise {@link FormatErrorType#StringList} error.
*
* @param column SHOULD NOT set null
* @param target SHOULD NOT be empty.
*/
protected SplitList<string> checkStringList(MZTabColumn column, string target, char splitChar)
{
string result = checkData(column, target, true);
if (result == null || result.Equals("NULL", StringComparison.CurrentCultureIgnoreCase)){
return new SplitList<string>(splitChar);
}
SplitList<string> stringList = MZTabUtils.ParseStringList(splitChar, result);
if (stringList.Count == 0){
_errorList.Add(new MZTabError(FormatErrorType.StringList, _lineNumber, column.Header, result,
"" + splitChar));
}
return stringList;
}
/**
* Check target string. Normally, start can set "null". But
* in "Complete" file, in general "null" values SHOULD not be given.
*
* @see #checkData(uk.ac.ebi.pride.jmztab.model.MZTabColumn, string, boolean)
*
* @param column SHOULD NOT set null
* @param start SHOULD NOT be empty.
*/
protected string checkStart(MZTabColumn column, string start)
{
return checkData(column, start, true);
}
/**
* Check and translate protein_coverage string into double. If parse incorrect, raise {@link FormatErrorType#double} error.
* protein_coverage range should be in the [0, 1), otherwise raise {@link LogicalErrorType#ProteinCoverage} error.
*
* NOTICE: If ratios are included and the denominator is zero, the "INF" value MUST be used. If the result leads
* to calculation errors (for example 0/0), this MUST be reported as "not a number" ("NaN").
*
* @param column SHOULD NOT set null
* @param protein_coverage SHOULD NOT be empty.
*/
protected double checkProteinCoverage(MZTabColumn column, string protein_coverage)
{
double result = checkDouble(column, protein_coverage);
if (result.Equals(double.MinValue)){
return double.MinValue;
}
if (result < 0 || result > 1){
_errorList.Add(new MZTabError(LogicalErrorType.ProteinCoverage, _lineNumber, column.Header,
MZTabUtils.PrintDouble(result)));
return double.MinValue;
}
return result;
}
/**
* Check target string. Normally, pre can set "null". But
* in "Complete" file, in general "null" values SHOULD not be given.
*
* @see #checkData(uk.ac.ebi.pride.jmztab.model.MZTabColumn, string, boolean)
*
* @param column SHOULD NOT set null
* @param pre SHOULD NOT be empty.
*/
protected string checkPre(MZTabColumn column, string pre)
{
return checkData(column, pre, true);
}
/**
* Check target string. Normally, post can set "null". But
* in "Complete" file, in general "null" values SHOULD not be given.
*
* @see #checkData(uk.ac.ebi.pride.jmztab.model.MZTabColumn, string, boolean)
*
* @param column SHOULD NOT set null
* @param post SHOULD NOT be empty.
*/
protected string checkPost(MZTabColumn column, string post)
{
return checkData(column, post, true);
}
/**
* Check and translate target string into parameter list which split by '|' character..
* If parse incorrect, raise {@link FormatErrorType#ParamList} error.
*
* @param column SHOULD NOT set null
* @param target SHOULD NOT be empty.
*/
protected SplitList<Param> checkParamList(MZTabColumn column, string target)
{
string result = checkData(column, target, true);
if (result == null || result.Equals("NULL", StringComparison.CurrentCultureIgnoreCase)){
return new SplitList<Param>(MZTabConstants.BAR);
}
SplitList<Param> paramList = MZTabUtils.ParseParamList(result);
if (paramList.Count == 0){
_errorList.Add(new MZTabError(FormatErrorType.ParamList, _lineNumber, "Column " + column.Header, target));
}
return paramList;
}
/**
* Check and translate numPSMs string into int. If exists error during parse, raise {@link FormatErrorType#int} error.
* Normally, numPSMs can set "null", but in "Complete" file, in general "null" values SHOULD not be given.
*
* @param column SHOULD NOT set null
* @param numPSMs SHOULD NOT be empty.
*/
protected Integer checkNumPSMs(MZTabColumn column, string numPSMs)
{
return checkInteger(column, numPSMs);
}
/**
* Check and translate numPeptidesUnique string into int. If exists error during parse, raise {@link FormatErrorType#int} error.
* Normally, numPeptidesUnique can set "null", but in "Complete" file, in general "null" values SHOULD not be given.
*
* @param column SHOULD NOT set null
* @param numPeptidesUnique SHOULD NOT be empty.
*/
protected Integer checkNumPeptidesUnique(MZTabColumn column, string numPeptidesUnique)
{
return checkInteger(column, numPeptidesUnique);
}
/**
* Check and translate numPeptidesDistinct string into int. If exists error during parse, raise {@link FormatErrorType#int} error.
* Normally, numPeptidesDistinct can set "null", but in "Complete" file, in general "null" values SHOULD not be given.
*
* @param column SHOULD NOT set null
* @param numPeptidesDistinct SHOULD NOT be empty.
*/
protected Integer checkNumPeptidesDistinct(MZTabColumn column, string numPeptidesDistinct)
{
return checkInteger(column, numPeptidesDistinct);
}
/**
* Check target string. Normally, species can set "null". But
* in "Complete" file, in general "null" values SHOULD not be given.
*
* @see #checkData(uk.ac.ebi.pride.jmztab.model.MZTabColumn, string, boolean)
*
* @param column SHOULD NOT set null
* @param species SHOULD NOT be empty.
*/
protected string checkSpecies(MZTabColumn column, string species)
{
return checkData(column, species, true);
}
/**
* Check and translate spectraRef string into {@link SpectraRef} list.
* If parse incorrect, or ms_run not defined in metadata raise {@link FormatErrorType#SpectraRef} error.
* Normally, spectraRef can set "null", but in "Complete" file, in general "null" values SHOULD not be given.
*
* @param column SHOULD NOT set null
* @param spectraRef SHOULD NOT be empty.
*/
protected List<SpectraRef> checkSpectraRef(MZTabColumn column, string spectraRef)
{
string result_spectraRef = checkData(column, spectraRef, true);
if (result_spectraRef == null || result_spectraRef.Equals("NULL", StringComparison.CurrentCultureIgnoreCase)){
return new List<SpectraRef>();
}
List<SpectraRef> refList = MZTabUtils.ParseSpectraRefList(metadata, result_spectraRef);
if (refList.Count == 0){
_errorList.Add(new MZTabError(FormatErrorType.SpectraRef, _lineNumber, column.Header, result_spectraRef));
}
else{
foreach (SpectraRef reference in refList){
MsRun run = reference.MsRun;
if (run.Location == null){
_errorList.Add(new MZTabError(LogicalErrorType.SpectraRef, _lineNumber, column.Header,
result_spectraRef, "ms_run[" + run.Id + "]-location"));
refList.Clear();
break;
}
}
}
return refList;
}
/**
* Check and translate psm_id string into int. If exists error during parse, raise {@link FormatErrorType#int} error.
* Normally, psm_id can set "null", but in "Complete" file, in general "null" values SHOULD not be given.
*
* @param column SHOULD NOT set null
* @param psm_id SHOULD NOT be empty.
*/
protected Integer checkPSMID(MZTabColumn column, string psm_id)
{
return checkInteger(column, psm_id);
}
/**
* In the table-based sections (protein, peptide, and small molecule) there MUST NOT be any empty cells.
* Some field not allow "null" value, for example unit_id, accession and so on. In "Complete" file, in
* general "null" values SHOULD not be given.
*
* @param column SHOULD NOT set null
* @param target SHOULD NOT be empty.
*/
protected string checkString(MZTabColumn column, string target)
{
return checkData(column, target, true);
}
/**
* Check and translate reliability string into {@link Reliability}. Currently, only "1", "2", "3" and "null" are
* correct value, and others will raise {@link FormatErrorType#Reliability} error.
* But in "Complete" file, in general "null" values SHOULD not be given.
*
* @param column SHOULD NOT set null
* @param reliability SHOULD NOT be empty.
*/
protected Reliability checkReliability(MZTabColumn column, string reliability)
{
string result_reliaility = checkData(column, reliability, true);
if (result_reliaility == null || result_reliaility.Equals("NULL", StringComparison.CurrentCultureIgnoreCase)){
return null;
}
Reliability result = Reliability.findReliability(result_reliaility);
if (result == null){
_errorList.Add(new MZTabError(FormatErrorType.Reliability, _lineNumber, column.Header, result_reliaility));
}
return result;
}
/**
* Check and translate taxid string into int. If exists error during parse, raise {@link FormatErrorType#int} error.
* Normally, taxid can set "null", but in "Complete" file, in general "null" values SHOULD not be given.
*
* @param column SHOULD NOT set null
* @param taxid SHOULD NOT be empty.
*/
protected Integer checkTaxid(MZTabColumn column, string taxid)
{
return checkInteger(column, taxid);
}
/**
* Check and translate searchEngine string into parameter list which split by '|' character..
* If parse incorrect, raise {@link FormatErrorType#ParamList} error.
* Normally, searchEngine can set "null", but in "Complete" file, in general "null" values SHOULD not be given.
*
* @param column SHOULD NOT set null
* @param searchEngine SHOULD NOT be empty.
*/
protected SplitList<Param> checkSearchEngine(MZTabColumn column, string searchEngine)
{
return checkParamList(column, searchEngine);
}
protected Uri checkURI(MZTabColumn column, string uri)
{
string result_uri = checkData(column, uri, true);
if (result_uri == null || result_uri.Equals("NULL", StringComparison.CurrentCultureIgnoreCase)){
return null;
}
Uri result = MZTabUtils.ParseURI(result_uri);
if (result == null){
_errorList.Add(new MZTabError(FormatErrorType.URI, _lineNumber, "Column " + column.Header, result_uri));
}
return result;
}
/**
* Check and translate searchEngineScore string into parameter list which split by '|' character..
* If parse incorrect, raise {@link FormatErrorType#ParamList} error. If parameter is not {@link CVParam},
* or parameter value is empty (score should be provide), system raise {@link FormatErrorType#SearchEngineScore}.
* Normally, searchEngineScore can set "null", but in "Complete" file, in general "null" values SHOULD not be given.
*
* @param column SHOULD NOT set null
* @param searchEngineScore SHOULD NOT be empty.
*/
protected SplitList<Param> checkSearchEngineScore(MZTabColumn column, string searchEngineScore)
{
SplitList<Param> paramList = checkParamList(column, searchEngineScore);
foreach (Param param in paramList){
if (!(param is CVParam) || string.IsNullOrEmpty(param.Value)){
_errorList.Add(new MZTabError(FormatErrorType.SearchEngineScore, _lineNumber, column.Header,
searchEngineScore));
}
}
return paramList;
}
/**
* Check and translate retention_time_window string into double list which split by '|' character..
* If parse incorrect, raise {@link FormatErrorType#DoubleList} error.
* Normally, retention_time_window can set "null", but in "Complete" file, in general "null" values SHOULD not be given.
*
* @param column SHOULD NOT set null
* @param retention_time_window SHOULD NOT be empty.
*/
protected SplitList<double> checkRetentionTimeWindow(MZTabColumn column, string retention_time_window)
{
string result = checkData(column, retention_time_window, true);
if (result == null || result.Equals("NULL", StringComparison.CurrentCultureIgnoreCase)){
return new SplitList<double>(MZTabConstants.BAR);
}
SplitList<double> valueList = MZTabUtils.ParseDoubleList(result);
if (valueList.Count == 0){
_errorList.Add(new MZTabError(FormatErrorType.DoubleList, _lineNumber, column.Header, result,
"" + MZTabConstants.BAR));
}
return valueList;
}
/**
* Check and translate target string into {@link Modification} list which split by ',' character..
* If parse incorrect, raise {@link FormatErrorType#ModificationList} error.
* Normally, ambiguityMembers can set "null", but in "Complete" file, in general "null" values SHOULD not be given.
*
* If software cannot determine protein-level modifications, "null" MUST be used.
* If the software has determined that there are no modifications to a given protein "0" MUST be used.
*
* @param section SHOULD NOT set null
* @param column SHOULD NOT set null
* @param modificationsLabel SHOULD NOT be empty.
*/
protected SplitList<Modification> checkModifications(Section section, MZTabColumn column,
string modificationsLabel)
{
string result_modifications = checkData(column, modificationsLabel, true);
if (result_modifications == null ||
result_modifications.Equals("NULL", StringComparison.CurrentCultureIgnoreCase) ||
result_modifications.Equals("0")){
return new SplitList<Modification>(MZTabConstants.COMMA);
}
SplitList<Modification> modificationList = MZTabUtils.ParseModificationList(section, modificationsLabel);
if (modificationList.Count == 0){
_errorList.Add(new MZTabError(FormatErrorType.ModificationList, _lineNumber, column.Header,
result_modifications));
}
return modificationList;
}
