protected override int loadStableData(MZTabRecord record, string line)
{
_items = line.Split(new[]{MZTabConstants.TAB}, StringSplitOptions.None);
_items[_items.Length - 1] = _items[_items.Length - 1].Trim();
PSM psm = (PSM) record;
SortedDictionary<string, MZTabColumn> columnMapping = factory.ColumnMapping;
int physicalPosition = 1;
string logicalPosition = positionMapping.get(physicalPosition);
MZTabColumn column = null;
if (columnMapping.ContainsKey(logicalPosition)){
column = columnMapping[logicalPosition];
}
while (column != null && column is PSMColumn){
string target;
try{
target = _items[physicalPosition];
}
catch (IndexOutOfRangeException e){
Console.Error.WriteLine(_lineNumber + ":\t" + line);
throw e;
}
string columnName = column.Name;
if (columnName.Equals(PSMColumn.SEQUENCE.Name)){
psm.Sequence = target;
}
else if (columnName.Equals(PSMColumn.PSM_ID.Name)){
psm.SetPSM_ID(target);
}
else if (columnName.Equals(PSMColumn.ACCESSION.Name)){
psm.Accession = target;
}
else if (columnName.Equals(PSMColumn.UNIQUE.Name)){
psm.setUnique(target);
}
else if (columnName.Equals(PSMColumn.DATABASE.Name)){
psm.Database = target;
}
else if (columnName.Equals(PSMColumn.DATABASE_VERSION.Name)){
psm.DatabaseVersion = target;
}
else if (columnName.Equals(PSMColumn.SEARCH_ENGINE.Name)){
psm.setSearchEngine(target);
}
else if (columnName.Equals(PSMColumn.SEARCH_ENGINE_SCORE.Name)){
psm.setSearchEngineScore(target);
}
else if (columnName.Equals(PSMColumn.RELIABILITY.Name)){
psm.setReliability(target);
}
else if (columnName.Equals(PSMColumn.MODIFICATIONS.Name)){
psm.setModifications(target);
}
else if (columnName.Equals(PSMColumn.RETENTION_TIME.Name)){
psm.setRetentionTime(target);
}
else if (columnName.Equals(PSMColumn.CHARGE.Name)){
psm.setCharge(target);
}
else if (columnName.Equals(PSMColumn.EXP_MASS_TO_CHARGE.Name)){
psm.SetExpMassToCharge(target);
}
else if (columnName.Equals(PSMColumn.CALC_MASS_TO_CHARGE.Name)){
psm.SetCalcMassToCharge(target);
}
else if (columnName.Equals(PSMColumn.URI.Name)){
psm.SetUri(target);
}
else if (columnName.Equals(PSMColumn.SPECTRA_REF.Name)){
psm.SetSpectraRef(target);
}
else if (columnName.Equals(PSMColumn.PRE.Name)){
psm.Pre = target;
}
else if (columnName.Equals(PSMColumn.POST.Name)){
psm.Post = target;
}
else if (columnName.Equals(PSMColumn.START.Name)){
psm.Start = target;
}
else if (columnName.Equals(PSMColumn.END.Name)){
psm.End = target;
}
physicalPosition++;
logicalPosition = positionMapping.get(physicalPosition);
column = logicalPosition != null && columnMapping.ContainsKey(logicalPosition)
? columnMapping[logicalPosition]
: null;
if (column == null){
break;
}
}
return physicalPosition;
}
private void loadOptionalData(MZTabRecord record, int physicalOffset)
{
for (int physicalPosition = physicalOffset; physicalPosition < _items.Length; physicalPosition++){
string target = _items[physicalPosition].Trim();
MZTabColumn column = null;
string key = positionMapping.get(physicalPosition);
if (factory.ColumnMapping.ContainsKey(key)){
column = factory.ColumnMapping[key];
}
if (column != null){
Type dataType = column.Type;
if (dataType == typeof (string)){
record.setValue(column.LogicPosition, checkString(column, target));
}
else if (dataType == typeof (double)){
record.setValue(column.LogicPosition, checkDouble(column, target));
}
else if (dataType == typeof (MZBoolean)){
record.setValue(column.LogicPosition, checkMZBoolean(column, target));
}
}
}
}
/**
* Load mzTab element and generate a {@link MZTabRecord}.
*/
protected abstract int loadStableData(MZTabRecord record, string line);
protected override int loadStableData(MZTabRecord record, string line)
{
_items = line.Split(new[]{MZTabConstants.TAB}, StringSplitOptions.None);
_items[_items.Length - 1] = _items[_items.Length - 1].Trim();
Protein protein = (Protein) record;
MZTabColumn column = null;
SortedDictionary<string, MZTabColumn> columnMapping = factory.ColumnMapping;
int physicalPosition = 1;
string logicalPosition = positionMapping.get(physicalPosition);
if (columnMapping.ContainsKey(logicalPosition)){
column = columnMapping[logicalPosition];
}
while (column != null && column is ProteinColumn){
string target = _items[physicalPosition].Trim();
string columnName = column.Name;
if (columnName.Equals(ProteinColumn.ACCESSION.Name)){
protein.Accession = target;
}
else if (columnName.Equals(ProteinColumn.DESCRIPTION.Name)){
protein.Description = target;
}
else if (columnName.Equals(ProteinColumn.TAXID.Name)){
protein.SetTaxid(target);
}
else if (columnName.Equals(ProteinColumn.SPECIES.Name)){
protein.Species = target;
}
else if (columnName.Equals(ProteinColumn.DATABASE.Name)){
protein.Database = target;
}
else if (columnName.Equals(ProteinColumn.DATABASE_VERSION.Name)){
protein.DatabaseVersion = target;
}
else if (columnName.Equals(ProteinColumn.SEARCH_ENGINE.Name)){
protein.SetSearchEngine(target);
}
else if (columnName.Equals(ProteinColumn.BEST_SEARCH_ENGINE_SCORE.Name)){
protein.SetBestSearchEngineScore(target);
}
else if (columnName.Equals(ProteinColumn.SEARCH_ENGINE_SCORE.Name)){
protein.setSearchEngineScore(logicalPosition, target);
}
else if (columnName.Equals(ProteinColumn.RELIABILITY.Name)){
protein.SetReliability(target);
}
else if (columnName.Equals(ProteinColumn.NUM_PSMS.Name)){
protein.setNumPSMs(logicalPosition, target);
}
else if (columnName.Equals(ProteinColumn.NUM_PEPTIDES_DISTINCT.Name)){
protein.setNumPeptidesDistinct(logicalPosition, target);
}
else if (columnName.Equals(ProteinColumn.NUM_PEPTIDES_UNIQUE.Name)){
protein.setNumPeptidesUnique(logicalPosition, target);
}
else if (columnName.Equals(ProteinColumn.AMBIGUITY_MEMBERS.Name)){
protein.SetAmbiguityMembers(target);
}
else if (columnName.Equals(ProteinColumn.MODIFICATIONS.Name)){
protein.SetModifications(target);
}
else if (columnName.Equals(ProteinColumn.URI.Name)){
protein.SetURI(target);
}
else if (columnName.Equals(ProteinColumn.GO_TERMS.Name)){
protein.SetGOTerms(target);
}
else if (columnName.Equals(ProteinColumn.PROTEIN_COVERAGE.Name)){
protein.SetProteinCoverage(target);
}
physicalPosition++;
logicalPosition = positionMapping.get(physicalPosition);
column = logicalPosition == null
? null
: columnMapping.ContainsKey(logicalPosition) ? columnMapping[logicalPosition] : null;
if (column == null){
break;
}
}
return physicalPosition;
}
protected override int loadStableData(MZTabRecord record, string line)
{
_items = line.Split(new[]{MZTabConstants.TAB}, StringSplitOptions.None);
_items[_items.Length - 1] = _items[_items.Length - 1].Trim();
SmallMolecule smallMolecule = (SmallMolecule) record;
SortedDictionary<string, MZTabColumn> columnMapping = factory.ColumnMapping;
int physicalPosition = 1;
string logicalPosition = positionMapping.get(physicalPosition);
MZTabColumn column = null;
if (columnMapping.ContainsKey(logicalPosition)){
column = columnMapping[logicalPosition];
}
while (column != null && column is SmallMoleculeColumn){
string target = _items[physicalPosition];
string columnName = column.Name;
if (columnName.Equals(SmallMoleculeColumn.IDENTIFIER.Name)){
smallMolecule.setIdentifier(target);
}
else if (columnName.Equals(SmallMoleculeColumn.CHEMICAL_FORMULA.Name)){
smallMolecule.ChemicalFormula = target;
}
else if (columnName.Equals(SmallMoleculeColumn.SMILES.Name)){
smallMolecule.Smiles = target;
}
else if (columnName.Equals(SmallMoleculeColumn.INCHI_KEY.Name)){
smallMolecule.InchiKey = target;
}
else if (columnName.Equals(SmallMoleculeColumn.DESCRIPTION.Name)){
smallMolecule.Description = target;
}
else if (columnName.Equals(SmallMoleculeColumn.EXP_MASS_TO_CHARGE.Name)){
smallMolecule.setExpMassToCharge(target);
}
else if (columnName.Equals(SmallMoleculeColumn.CALC_MASS_TO_CHARGE.Name)){
smallMolecule.setCalcMassToCharge(target);
}
else if (columnName.Equals(SmallMoleculeColumn.CHARGE.Name)){
smallMolecule.setCharge(target);
}
else if (columnName.Equals(SmallMoleculeColumn.RETENTION_TIME.Name)){
smallMolecule.setRetentionTime(target);
}
else if (columnName.Equals(SmallMoleculeColumn.TAXID.Name)){
smallMolecule.setTaxid(target);
}
else if (columnName.Equals(SmallMoleculeColumn.SPECIES.Name)){
smallMolecule.Species = target;
}
else if (columnName.Equals(SmallMoleculeColumn.DATABASE.Name)){
smallMolecule.Database = target;
}
else if (columnName.Equals(SmallMoleculeColumn.DATABASE_VERSION.Name)){
smallMolecule.DatabaseVersion = target;
}
else if (columnName.Equals(SmallMoleculeColumn.RELIABILITY.Name)){
smallMolecule.setReliability(target);
}
else if (columnName.Equals(SmallMoleculeColumn.URI.Name)){
smallMolecule.setURI(target);
}
else if (columnName.Equals(SmallMoleculeColumn.SPECTRA_REF.Name)){
smallMolecule.setSpectraRef(target);
}
else if (columnName.Equals(SmallMoleculeColumn.SEARCH_ENGINE.Name)){
smallMolecule.setSearchEngine(target);
}
else if (columnName.Equals(SmallMoleculeColumn.BEST_SEARCH_ENGINE_SCORE.Name)){
smallMolecule.setBestSearchEngineScore(target);
}
else if (columnName.Equals(SmallMoleculeColumn.SEARCH_ENGINE_SCORE.Name)){
smallMolecule.setSearchEngineScore(logicalPosition, target);
}
else if (columnName.Equals(SmallMoleculeColumn.MODIFICATIONS.Name)){
smallMolecule.setModifications(target);
}
physicalPosition++;
logicalPosition = positionMapping.get(physicalPosition);
column = logicalPosition != null && columnMapping.ContainsKey(logicalPosition)
? columnMapping[logicalPosition]
: null;
}
return physicalPosition;
}
protected override int loadStableData(MZTabRecord record, string line)
{
_items = line.Split(new[]{MZTabConstants.TAB}, StringSplitOptions.None);
_items[_items.Length - 1] = _items[_items.Length - 1].Trim();
Peptide peptide = (Peptide) record;
SortedDictionary<string, MZTabColumn> columnMapping = factory.ColumnMapping;
int physicalPosition = 1;
string logicalPosition = positionMapping.get(physicalPosition);
MZTabColumn column = null;
if (columnMapping.ContainsKey(logicalPosition)){
column = columnMapping[logicalPosition];
}
while (column != null && column is PeptideColumn){
string target = _items[physicalPosition];
string columnName = column.Name;
if (columnName.Equals(PeptideColumn.SEQUENCE.Name)){
peptide.Sequence = target;
}
else if (columnName.Equals(PeptideColumn.ACCESSION.Name)){
peptide.Accession = target;
}
else if (columnName.Equals(PeptideColumn.UNIQUE.Name)){
peptide.SetUnique(target);
}
else if (columnName.Equals(PeptideColumn.DATABASE.Name)){
peptide.Database = target;
}
else if (columnName.Equals(PeptideColumn.DATABASE_VERSION.Name)){
peptide.DatabaseVersion = target;
}
else if (columnName.Equals(PeptideColumn.SEARCH_ENGINE.Name)){
peptide.SetSearchEngine(target);
}
else if (columnName.Equals(PeptideColumn.BEST_SEARCH_ENGINE_SCORE.Name)){
peptide.SetBestSearchEngineScore(target);
}
else if (columnName.Equals(PeptideColumn.SEARCH_ENGINE_SCORE.Name)){
peptide.SetSearchEngineScore(logicalPosition, target);
}
else if (columnName.Equals(PeptideColumn.RELIABILITY.Name)){
peptide.SetReliability(target);
}
else if (columnName.Equals(PeptideColumn.MODIFICATIONS.Name)){
peptide.SetModifications(target);
}
else if (columnName.Equals(PeptideColumn.RETENTION_TIME.Name)){
peptide.SetRetentionTime(target);
}
else if (columnName.Equals(PeptideColumn.RETENTION_TIME_WINDOW.Name)){
peptide.SetRetentionTimeWindow(target);
}
else if (columnName.Equals(PeptideColumn.CHARGE.Name)){
peptide.SetCharge(target);
}
else if (columnName.Equals(PeptideColumn.MASS_TO_CHARGE.Name)){
peptide.SetMassToCharge(target);
}
else if (columnName.Equals(PeptideColumn.URI.Name)){
peptide.SetURI(target);
}
else if (columnName.Equals(PeptideColumn.SPECTRA_REF.Name)){
peptide.SetSpectraRef(target);
}
physicalPosition++;
logicalPosition = positionMapping.get(physicalPosition);
column = logicalPosition != null && columnMapping.ContainsKey(logicalPosition)
? columnMapping[logicalPosition]
: null;
if (column == null){
break;
}
}
return physicalPosition;
}
