コード例 #1
0
ファイル: MzTabReader.cs プロジェクト: pcarvalho75/patternlab
 public string[] this[MzTabSection section, int index]
 {
     get
     {
         return(GetData(section, index));
     }
 }
コード例 #2
0
ファイル: MzTabReader.cs プロジェクト: pcarvalho75/patternlab
 public string this[MzTabSection section, int index, string columnName]
 {
     get
     {
         return(GetData(section, index, columnName));
     }
 }
コード例 #3
0
ファイル: MzTabReader.cs プロジェクト: yhayirsevertr/CSMSL
        public string[] GetColumns(MzTabSection section)
        {
            switch (section)
            {
            case MzTabSection.PSM:
                return(_psmDataTable != null?_psmDataTable.Columns.Cast <DataColumn>().Select(x => x.ColumnName).ToArray() : null);

            case MzTabSection.Peptide:
                return(_peptideDataTable != null?_peptideDataTable.Columns.Cast <DataColumn>().Select(x => x.ColumnName).ToArray() : null);

            case MzTabSection.Protein:
                return(_proteinDataTable != null?_proteinDataTable.Columns.Cast <DataColumn>().Select(x => x.ColumnName).ToArray() : null);

            case MzTabSection.SmallMolecule:
                return(_smallMoleculeDataTable != null?_smallMoleculeDataTable.Columns.Cast <DataColumn>().Select(x => x.ColumnName).ToArray() : null);

            default:
                return(null);
            }
        }
コード例 #4
0
ファイル: MzTabReader.cs プロジェクト: yhayirsevertr/CSMSL
        public string[] GetData(MzTabSection section, int index)
        {
            switch (section)
            {
            case MzTabSection.PSM:
                return(_psmDataTable != null ? (string[])_psmDataTable.Rows[index].ItemArray : null);

            case MzTabSection.Peptide:
                return(_peptideDataTable != null ? (string[])_peptideDataTable.Rows[index].ItemArray : null);

            case MzTabSection.Protein:
                return(_proteinDataTable != null ? (string[])_proteinDataTable.Rows[index].ItemArray : null);

            case MzTabSection.SmallMolecule:
                return(_smallMoleculeDataTable != null ? (string[])_smallMoleculeDataTable.Rows[index].ItemArray : null);

            default:
                return(null);
            }
        }
コード例 #5
0
ファイル: MzTabReader.cs プロジェクト: yhayirsevertr/CSMSL
        public string GetData(MzTabSection section, int index, string columnName)
        {
            switch (section)
            {
            case MzTabSection.PSM:
                return(_psmDataTable != null ? (string)_psmDataTable.Rows[index][columnName] : null);

            case MzTabSection.Peptide:
                return(_peptideDataTable != null ? (string)_peptideDataTable.Rows[index][columnName] : null);

            case MzTabSection.Protein:
                return(_proteinDataTable != null ? (string)_proteinDataTable.Rows[index][columnName] : null);

            case MzTabSection.SmallMolecule:
                return(_smallMoleculeDataTable != null ? (string)_smallMoleculeDataTable.Rows[index][columnName] : null);

            default:
                return(null);
            }
        }
コード例 #6
0
ファイル: MzTabReader.cs プロジェクト: yhayirsevertr/CSMSL
        public bool ContainsColumn(MzTabSection section, string columnName)
        {
            switch (section)
            {
            case MzTabSection.PSM:
                return(_psmDataTable != null && _psmDataTable.Columns.Contains(columnName));

            case MzTabSection.Peptide:
                return(_peptideDataTable != null && _peptideDataTable.Columns.Contains(columnName));

            case MzTabSection.Protein:
                return(_proteinDataTable != null && _proteinDataTable.Columns.Contains(columnName));

            case MzTabSection.SmallMolecule:
                return(_smallMoleculeDataTable != null && _smallMoleculeDataTable.Columns.Contains(columnName));

            default:
                return(false);
            }
        }
コード例 #7
0
ファイル: MzTabReader.cs プロジェクト: yhayirsevertr/CSMSL
        private IEnumerable <T> GetObjects <T>(MzTabSection section) where T : MzTabEntity, new()
        {
            DataTable table = null;

            switch (section)
            {
            case MzTabSection.PSM:
                table = _psmDataTable;
                break;

            case MzTabSection.Peptide:
                table = _peptideDataTable;
                break;

            case MzTabSection.SmallMolecule:
                table = _smallMoleculeDataTable;
                break;

            case MzTabSection.Protein:
                table = _proteinDataTable;
                break;
            }

            if (table == null || table.Rows.Count == 0)
            {
                yield break;
            }

            string[] columns = GetColumns(section);
            int      count   = columns.Length;

            foreach (DataRow row in table.Rows)
            {
                var item = new T();
                for (int i = 0; i < count; i++)
                {
                    item.SetValue(columns[i], (string)row.ItemArray[i]);
                }
                yield return(item);
            }
        }
コード例 #8
0
ファイル: MzTabWriter.cs プロジェクト: yhayirsevertr/CSMSL
        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);
            }
        }