public MsRunImpl(MsRun run)
: base(run.Id)
{
Format = run.Format;
IdFormat = run.IdFormat;
FragmentationMethod = run.FragmentationMethod;
Location = run.Location;
}
/**
* Creates a new SpectraRef object.
*
* @param reference The reference to the spectrum in the MS fiile.
*/
public SpectraRef(MsRun msRun, string reference)
{
if (msRun == null){
throw new NullReferenceException("msRun can not null!");
}
if (reference == null){
throw new NullReferenceException("msRun reference can not empty!");
}
this.msRun = msRun;
this.reference = reference;
}
private void addPeptideValue()
{
MsRun msRun1 = new MsRun(1);
Assay assay1 = new Assay(1);
Assay assay2 = new Assay(2);
StudyVariable studyVariable1 = new StudyVariable(1);
MZTabColumnFactory factory = MZTabColumnFactory.GetInstance(Section.Peptide_Header);
factory.AddOptionalColumn(PeptideColumn.SEARCH_ENGINE_SCORE, msRun1);
factory.AddAbundanceOptionalColumn(assay1);
factory.AddAbundanceOptionalColumn(studyVariable1);
factory.AddAbundanceOptionalColumn(assay2);
factory.AddOptionalColumn(msRun1, "my_value", typeof (string));
CVParam param = new CVParam("MS", "MS:1002217", "decoy peptide", null);
factory.AddOptionalColumn(param, typeof (string));
Metadata metadata = new Metadata();
metadata.AddMsRunLocation(2, new Url("file://C:\\path\\to\\my\\file"));
Console.WriteLine(factory);
Peptide peptide = new Peptide(factory, metadata);
peptide.Sequence = "KVPQVSTPTLVEVSR";
peptide.Accession = "P02768";
peptide.SetUnique("0");
peptide.Database = "UniProtKB";
peptide.DatabaseVersion = "2011_11";
peptide.SetSearchEngine("[MS,MS:1001207,Mascot,]|[MS,MS:1001208,Sequest,]");
peptide.SetBestSearchEngineScore("[MS,MS:1001155,Sequest:xcorr,2]");
peptide.Reliability = Reliability.findReliability("3");
peptide.SetModifications(
"3[MS,MS:1001876, modification probability, 0.8]|4[MS,MS:1001876, modification probability, 0.2]-MOD:00412,8[MS,MS:1001876, modification probability, 0.3]-MOD:00412");
peptide.AddRetentionTime(10.2);
peptide.AddRetentionTimeWindow(1123.2);
peptide.AddRetentionTimeWindow(1145.3);
peptide.Charge = new Integer(2);
peptide.MassToCharge = 1234.4;
peptide.URI = new Uri("http://www.ebi.ac.uk/pride/link/to/peptide");
peptide.SetSpectraRef("ms_run[2]:index=7|ms_run[2]:index=9");
Console.WriteLine(peptide);
}
public bool AddAssayMsRun(int id, MsRun msRun)
{
Assay assay;
if (!_assayMap.ContainsKey(id)){
assay = new Assay(id){MsRun = msRun};
_assayMap.Add(id, assay);
return true;
}
assay = _assayMap[id];
assay.MsRun = msRun;
return true;
}
public void AddMsRun(MsRun msRun)
{
_msRunMap.Add(msRun.Id, msRun);
}
public SplitList<Param> getSearchEngineScore(MsRun msRun)
{
return GetSplitList<Param>(getPosition(SmallMoleculeColumn.SEARCH_ENGINE_SCORE, msRun));
}
public void setNumPSMs(MsRun msRun, Integer numPSMs)
{
setNumPSMs(getLogicalPosition(ProteinColumn.NUM_PSMS, null, msRun), numPSMs.ToString());
}
/**
* The search engine score for the given protein in the defined ms run. The type of score
* MUST be defined in the metadata section. If the protein was not identified by the specified
* search engine “null” must be reported
*
* @param id protein_search_engine_score[id] which MUST be defined in the metadata section.
* @param msRun SHOULD NOT set null
*/
public Double getSearchEngineScore(Integer id, MsRun msRun)
{
return getDouble(getLogicalPosition(PeptideColumn.SEARCH_ENGINE_SCORE, id, msRun));
}
public void SetSearchEngineScore(MsRun msRun, SplitList<Param> searchEngineScore)
{
SetSearchEngineScore(getPosition(PeptideColumn.SEARCH_ENGINE_SCORE, msRun), searchEngineScore);
}
/**
* Add {@link CVParamOptionColumn} followed by ms_run into {@link #optionalColumnMapping} and {@link #columnMapping}.
* The header like: opt_ms_run[1]_cv_{accession}_{parameter name}
*
* @param msRun SHOULD NOT empty.
* @param param SHOULD NOT empty.
* @param columnType SHOULD NOT empty.
*/
public string AddOptionalColumn(MsRun msRun, CVParam param, Type columnType)
{
MZTabColumn column = new CVParamOptionColumn(msRun, param, columnType,
ParseColumnOrder(columnMapping.Last().Key));
return AddOptionColumn(column);
}
public bool AddMsRunLocation(int id, Url location)
{
MsRun msRun;
if (!_msRunMap.ContainsKey(id)){
msRun = new MsRun(id){Location = location};
_msRunMap.Add(id, msRun);
return true;
}
msRun = _msRunMap[id];
if (msRun.Location != null){
return false;
}
msRun.Location = location;
return true;
}
/**
* Add a optional column which has stable order and name, into {@link #optionalColumnMapping} and {@link #columnMapping}.
*
* @see MZTabColumn#createOptionalColumn(Section, MZTabColumn, IndexedElement)
*
* @exception ArgumentException: If user would like to add duplicate optional columns.
* @param column SHOULD NOT set null.
* @param msRun SHOULD NOT set null.
*/
public void AddOptionalColumn(MZTabColumn column, MsRun msRun)
{
string position = column.LogicPosition;
if (optionalColumnMapping.ContainsKey(position)){
throw new ArgumentException("There exists column " + optionalColumnMapping[position] + " in position " +
position);
}
MZTabColumn newColumn = null;
/*if (section.Equals(Section.Protein_Header)){
if (position.Equals("09") || position.Equals("11") || position.Equals("12") || position.Equals("13")){
newColumn = MZTabColumn.CreateOptionalColumn(section, column, msRun);
}
}
else if (section.Equals(Section.Peptide_Header)){
if (position.Equals("08")){
newColumn = MZTabColumn.CreateOptionalColumn(section, column, msRun);
}
}
else if (section.Equals(Section.Small_Molecule_Header)){
if (position.Equals("19")){
newColumn = MZTabColumn.CreateOptionalColumn(section, column, msRun);
}
}*/
if (section.Equals(Section.Protein_Header)) {
if (column.Name.Equals(ProteinColumn.NUM_PSMS.Name) || column.Name.Equals(ProteinColumn.NUM_PEPTIDES_DISTINCT.Name) || column.Name.Equals(ProteinColumn.NUM_PEPTIDES_UNIQUE.Name)) {
newColumn = MZTabColumn.CreateOptionalColumn(section, column, null, msRun);
}
}
if (newColumn != null){
optionalColumnMapping.Add(newColumn.LogicPosition, newColumn);
columnMapping.Add(newColumn.LogicPosition, newColumn);
}
}
/**
* Add {@link OptionColumn} followed by ms_run into {@link #optionalColumnMapping} and {@link #columnMapping}.
* The header like: opt_ms_run[1]_{name}
*
* @param msRun SHOULD NOT empty.
* @param name SHOULD NOT empty.
* @param columnType SHOULD NOT empty.
*/
public string AddOptionalColumn(MsRun msRun, String name, Type columnType)
{
MZTabColumn column = new OptionColumn(msRun, name, columnType, ParseColumnOrder(columnMapping.Last().Key));
return AddOptionColumn(column);
}
public void setSearchEngineScore(MsRun msRun, SplitList<Param> searchEngineScore)
{
setSearchEngineScore(getPosition(ProteinColumn.SEARCH_ENGINE_SCORE, msRun), searchEngineScore);
}
public void setNumPSMs(MsRun msRun, string numPSMsLabel)
{
setNumPSMs(msRun, MZTabUtils.ParseInteger(numPSMsLabel));
}
public void setNumPSMs(MsRun msRun, int numPSMs)
{
setNumPSMs(getPosition(ProteinColumn.NUM_PSMS, msRun), numPSMs);
}
public bool AddMsRunFragmentationMethod(int id, Param fragmentationMethod)
{
MsRun msRun;
if (!_msRunMap.ContainsKey(id)){
msRun = new MsRun(id){FragmentationMethod = fragmentationMethod};
_msRunMap.Add(id, msRun);
return true;
}
msRun = _msRunMap[id];
if (msRun.FragmentationMethod != null){
return false;
}
msRun.FragmentationMethod = fragmentationMethod;
return true;
}
/** Add {@link SearchEngineScore} followed by {@link MsRun} (MsRun will be null in the PSM section) which has stable order and name,
* into {@link #optionalColumnMapping} and {@link #columnMapping}.
*
* @param column search_engine_score column to add. SHOULD NOT set null.
* @param id of the {section}_search_engine_score[id] param defined in {@link Metadata} for this column. SHOULD NOT set null.
* @param msRun {@link MsRun} for this search_engine_score
*
* The header will be represented as: search_engine_score[id]{_ms_run[1-n]}
*/
public void AddSearchEngineScoreOptionalColumn(MZTabColumn column, Integer id, MsRun msRun)
{
String position = column.LogicPosition;
if (optionalColumnMapping.ContainsKey(position)) {
throw new ArgumentOutOfRangeException("There exists column " + optionalColumnMapping[position] + " in position " + position);
}
MZTabColumn newColumn = null;
if (section.Equals(Section.Protein_Header)){
if (column.Name.Equals(ProteinColumn.SEARCH_ENGINE_SCORE.Name)) {
newColumn = MZTabColumn.CreateOptionalColumn(section, column, id, msRun);
}
} else if (section.Equals(Section.Peptide_Header)){
if (column.Name.Equals(PeptideColumn.SEARCH_ENGINE_SCORE.Name)) {
newColumn = MZTabColumn.CreateOptionalColumn(section, column, id, msRun);
}
}else if (section.Equals(Section.Small_Molecule_Header)){
if (column.Name.Equals(SmallMoleculeColumn.SEARCH_ENGINE_SCORE.Name)) {
newColumn = MZTabColumn.CreateOptionalColumn(section, column, id, msRun);
}
}else if (section.Equals(Section.PSM_Header)){
if (column.Name.Equals(PSMColumn.SEARCH_ENGINE_SCORE.Name)) {
newColumn = MZTabColumn.CreateOptionalColumn(section, column, id, null);
}
}
if (newColumn != null) {
optionalColumnMapping.Add(newColumn.LogicPosition, newColumn);
columnMapping.Add(newColumn.LogicPosition, newColumn);
}
}
public bool AddMsRunIdFormat(int id, Param idFormat)
{
MsRun msRun;
if (!_msRunMap.ContainsKey(id)){
msRun = new MsRun(id){IdFormat = idFormat};
_msRunMap.Add(id, msRun);
return true;
}
msRun = _msRunMap[id];
if (msRun.IdFormat != null){
return false;
}
msRun.IdFormat = idFormat;
return true;
}
public void setNumPeptidesUnique(MsRun msRun, int numPeptidesUnique)
{
setNumPeptidesUnique(getPosition(ProteinColumn.NUM_PEPTIDES_UNIQUE, msRun), numPeptidesUnique);
}
public bool AddSearchEngineScore(MsRun msRun, CVParam param)
{
if (param == null){
return false;
}
SplitList<Param> searchparams = getSearchEngineScore(msRun);
if (searchparams == null){
searchparams = new SplitList<Param>(MZTabConstants.BAR);
SetSearchEngineScore(msRun, searchparams);
}
searchparams.Add(param);
return true;
}
private void addSmallMoleculeValue()
{
MsRun msRun1 = new MsRun(1);
Assay assay1 = new Assay(1);
Assay assay2 = new Assay(2);
StudyVariable studyVariable1 = new StudyVariable(1);
MZTabColumnFactory factory = MZTabColumnFactory.GetInstance(Section.Small_Molecule);
factory.AddAbundanceOptionalColumn(assay1);
factory.AddAbundanceOptionalColumn(studyVariable1);
factory.AddAbundanceOptionalColumn(assay2);
factory.AddOptionalColumn(msRun1, "my_value", typeof (string));
CVParam param = new CVParam("MS", "MS:1002217", "decoy peptide", null);
factory.AddOptionalColumn(param, typeof (string));
Metadata metadata = new Metadata();
metadata.AddMsRunLocation(2, new Url("file://C:\\path\\to\\my\\file"));
Console.WriteLine(factory);
/*TODO: SmallMolecule sm = new SmallMolecule(factory, metadata);
sm.setIdentifier("CID:00027395");
sm.setChemicalFormula("C17H20N4O2");
sm.setSmiles("C1=CC=C(C=C1)CCNC(=O)CCNNC(=O)C2=CC=NC=C2");
sm.setInchiKey("QXBMEGUKVLFJAM-UHFFFAOYSA-N");
sm.setDescription("N-(2-phenylethyl)-3-[2-(pyridine-4-carbonyl)hydrazinyl]propanamide");
sm.setExpMassToCharge("1234.4");
sm.setCalcMassToCharge("1234.5");
sm.setCharge("2");
sm.setRetentionTime("10.2|11.5");
sm.setTaxid("10116");
sm.setSpecies("Rattus norvegicus (Rat)");
sm.setDatabase("UniProtKB");
sm.setDatabaseVersion("2011_11");
sm.setReliability("2");
sm.setURI("http://www.ebi.ac.uk/pride/link/to/identification");
sm.setSpectraRef("ms_run[2]:index=7|ms_run[2]:index=9");
sm.setSearchEngine("[MS, MS:1001477, SpectraST,]");
sm.setBestSearchEngineScore("[MS, MS:1001419, SpectraST:discriminant score F, 0.7]");
sm.setModifications("CHEMMOD:+Na-H");
Console.WriteLine(sm);*/
}
/**
* The search engine score for the given protein in the defined ms run. The type of score
* MUST be defined in the metadata section. If the protein was not identified by the specified
* search engine “null” must be reported
*
* @param id protein_search_engine_score[id] which MUST be defined in the metadata section.
* @param msRun SHOULD NOT set null
*/
public void setSearchEngineScore(Integer id, MsRun msRun, double searchEngineScore)
{
setValue(getLogicalPosition(PeptideColumn.SEARCH_ENGINE_SCORE, id, msRun), searchEngineScore);
}
public void setSearchEngineScore(MsRun msRun, string paramsLabel)
{
setSearchEngineScore(msRun, MZTabUtils.ParseParamList(paramsLabel));
}
public bool addSearchEngineScore(MsRun msRun, CVParam param)
{
if (param == null){
return false;
}
SplitList<Param> paramList = getSearchEngineScore(msRun);
if (paramList == null){
paramList = new SplitList<Param>(MZTabConstants.BAR);
setSearchEngineScore(msRun, paramList);
}
paramList.Add(param);
return true;
}
public void setNumPeptidesDistinct(MsRun msRun, string numPeptidesDistinct)
{
setNumPeptidesDistinct(msRun, MZTabUtils.ParseInteger(numPeptidesDistinct));
}
public void setSearchEngineScore(MsRun msRun, SplitList<Param> searchEngineScore)
{
setValue(getPosition(SmallMoleculeColumn.SEARCH_ENGINE_SCORE, msRun), searchEngineScore);
}
public void setNumPeptidesUnique(MsRun msRun, string numPeptidesUnique)
{
setNumPeptidesUnique(msRun, MZTabUtils.ParseInteger(numPeptidesUnique));
}
private string MsRunToString(MsRun msrun)
{
return string.Format("[{0}] {1}", msrun.Id,
msrun is MsRunImpl
? (msrun as MsRunImpl).Description
: Path.GetFileNameWithoutExtension(msrun.Location.Value));
}
private void addProteinValue()
{
MsRun msRun1 = new MsRun(1);
MsRun msRun2 = new MsRun(2);
Assay assay1 = new Assay(1);
Assay assay2 = new Assay(2);
StudyVariable studyVariable1 = new StudyVariable(1);
MZTabColumnFactory factory = MZTabColumnFactory.GetInstance(Section.Protein_Header);
factory.AddOptionalColumn(ProteinColumn.SEARCH_ENGINE_SCORE, msRun1);
factory.AddOptionalColumn(ProteinColumn.NUM_PSMS, msRun1);
factory.AddOptionalColumn(ProteinColumn.NUM_PEPTIDES_DISTINCT, msRun1);
factory.AddOptionalColumn(ProteinColumn.NUM_PEPTIDES_UNIQUE, msRun1);
factory.AddOptionalColumn(ProteinColumn.NUM_PSMS, msRun2);
factory.AddOptionalColumn(ProteinColumn.NUM_PEPTIDES_DISTINCT, msRun2);
factory.AddAbundanceOptionalColumn(assay1);
factory.AddAbundanceOptionalColumn(studyVariable1);
factory.AddAbundanceOptionalColumn(assay2);
factory.AddOptionalColumn(assay1, "my_value", typeof (string));
CVParam param = new CVParam("MS", "MS:1002217", "decoy peptide", null);
factory.AddOptionalColumn(param, typeof (string));
Console.WriteLine(factory);
Protein protein = new Protein(factory);
// set stable columns data.
protein.Accession = "P12345";
protein.Description = "Aspartate aminotransferase, mitochondrial";
protein.SetTaxid("10116");
protein.Species = "Rattus norvegicus (Rat)";
protein.Database = "UniProtKB";
protein.DatabaseVersion = "2011_11";
protein.SetSearchEngine("[MS,MS:1001207,Mascot,]");
protein.AddSearchEngine("[MS,MS:1001208,Sequest,]");
protein.SetBestSearchEngineScore("[MS,MS:1001171,Mascot score,50]|[MS,MS:1001155,Sequest:xcorr,2]");
protein.Reliability = Reliability.High;
protein.SetAmbiguityMembers("P12347,P12348");
protein.SetModifications("3|4|8-MOD:00412, 3|4|8-MOD:00412");
protein.SetURI("http://www.ebi.ac.uk/pride/url/to/P12345");
protein.SetGOTerms("GO:0006457|GO:0005759|GO:0005886|GO:0004069");
protein.SetProteinCoverage("0.4");
Console.WriteLine(protein);
// set optional columns which have stable order.
protein.setSearchEngineScore(msRun1, "[MS,MS:1001171,Mascot score,50]|[MS,MS:1001155,Sequest:xcorr,2]");
protein.setNumPSMs(msRun1, 4);
protein.setNumPSMs(msRun2, 2);
protein.setNumPeptidesDistinct(msRun1, 3);
protein.setNumPeptidesUnique(msRun1, 2);
Console.WriteLine(protein);
// set abundance columns
protein.setAbundanceColumn(assay1, "0.4");
protein.setAbundanceColumn(assay2, "0.2");
protein.setAbundanceColumn(studyVariable1, "0.4");
protein.setAbundanceStdevColumn(studyVariable1, "0.3");
protein.setAbundanceStdErrorColumn(studyVariable1, "0.2");
Console.WriteLine(protein);
// set user defined optional columns
protein.setOptionColumn(assay1, "my_value", "My value about assay[1]");
protein.setOptionColumn(param, "TOM value");
Console.WriteLine(protein);
}