private static Parameter GetColumnSelectionParameter(string[] selection)
{
const int maxCols = 5;
string[] values = new string[maxCols];
Parameters[] subParams = new Parameters[maxCols];
for (int i = 1; i <= maxCols; i++)
{
values[i - 1] = "" + i;
Parameter[] px = new Parameter[i];
for (int j = 0; j < i; j++)
{
px[j] = new SingleChoiceParam(GetVariableName(j), j)
{
Values = selection
};
}
Parameters p = new Parameters(px);
subParams[i - 1] = p;
}
return(new SingleChoiceWithSubParams("Number of columns", 0)
{
Values = values,
SubParams = subParams,
ParamNameWidth = 120,
TotalWidth = 800
});
}
public void TestSingleChoiceParam()
{
SingleChoiceParam param = new SingleChoiceParam("choice", 1)
{
Values = new List <string> {
"c1", "b2"
}
};
SingleChoiceParam param2 = (SingleChoiceParam)param.ToXmlAndBack();
Assert.AreEqual(param.Name, param2.Name);
Assert.AreEqual(param.Value, param2.Value);
Assert.IsTrue(param.Values.SequenceEqual(param2.Values));
}
public Parameters GetParameters(IMatrixData mdata, ref string errorString)
{
string[] reducedExpColNames = ReduceNames(mdata.ColumnNames);
List <Parameter> p = new List <Parameter>();
for (int i = 0; i < mdata.ColumnCount; i++)
{
SingleChoiceParam scp = new SingleChoiceParam(mdata.ColumnNames[i])
{
Values = mdata.NumericColumnNames,
Value = GetSelectedValue(mdata.NumericColumnNames, reducedExpColNames[i])
};
p.Add(scp);
}
return(new Parameters(p));
}
public void TestSmallExample()
{
SingleChoiceParam matchColParam1 = (SingleChoiceParam)parameters.GetParam <int>("Matching column in table 1");
CollectionAssert.AreEqual(new [] { "pep_id", "pep_Protein group IDs", "pep_Intensity" }, matchColParam1.Values.ToArray());
matchColParam1.Value = 1;
Assert.AreEqual("pep_Protein group IDs", matchColParam1.StringValue);
IMatrixData[] supplTables = null;
IDocumentData[] documents = null;
IMatrixData matched = matching.ProcessData(new[] { expand, proteinMain }, parameters, ref supplTables, ref documents, BaseTest.CreateProcessInfo());
CollectionAssert.AreEqual(new [] { "pep_MS/MS Count", "pep_id", "pep_Protein group IDs", "pep_Intensity" },
matched.ColumnNames.Concat(matched.StringColumnNames).Concat(matched.NumericColumnNames).ToArray());
Assert.AreEqual(2, matched.RowCount);
Assert.AreEqual(1, matched.ColumnCount);
Assert.AreEqual(1, matched.NumericColumnCount);
}
protected override Parameter[] SpecificParameters(IMatrixData data, ref string errString)
{
if (data.StringColumnCount == 0)
{
errString = "Please add at least one string column";
return(null);
}
var ConditionColumn1Param = new SingleChoiceParam("Condition column, eg R.FileName")
{
Values = data.StringColumnNames,
Value = Math.Max(0, data.StringColumnNames.FindIndex(col => col.ToLower().Equals("r.filename"))),
Help = "Chose experimental condition column, such as R.FileName, which will be used to create wide-format intensity columns. Has to be a text column."
};
var PerlParam = new SingleChoiceWithSubParams("Condition grouping")
{
Values = new[] { "Group by condition column", "Skip" },
Value = 0,
Help = "Chose if input should be grouped from long-format (e.g. Spectronaut report or MaxQuant LFQ evidence) or mixed-format " +
"(e.g. MaxQuant TMT evidence with conditions) into wide-format required for this plugin. Chose skip if data is already in wide-format " +
"(e.g. MaxQuant TMT evidence without conditions).",
SubParams = new Parameters[] { // Define the different sub-parameter groups
new Parameters(ConditionColumn1Param), // condition grouping
new Parameters() // Skip
}
};
var Cutoff1aParam = new DoubleParam("Localization cutoff", 0.75)
{
Help = "Localization cutoff to be used to filter PTM localization. Can be between 0 and 1. Setting to 0 will not filter anything."
};
var Cutoff1bParam = new DoubleParam("Localization cutoff", 0.75)
{
Help = "Localization cutoff to be used to filter PTM localization. Can be between 0 and 1. Setting to 0 will not filter anything."
};
var Cutoff2aParam = new DoubleParam("Localization cutoff", 0.75)
{
Help = "Localization cutoff to be used to filter PTM localization. Can be between 0 and 1. Setting to 0 will not filter anything."
};
var Cutoff2bParam = new DoubleParam("Localization cutoff", 0.75)
{
Help = "Localization cutoff to be used to filter PTM localization. Can be between 0 and 1. Setting to 0 will not filter anything."
};
var Cutoff2cParam = new DoubleParam("Localization cutoff", 0.75)
{
Help = "Localization cutoff to be used to filter PTM localization. Can be between 0 and 1. Setting to 0 will not filter anything."
};
var Cutoff3aParam = new DoubleParam("Localization cutoff", 0.75)
{
Help = "Localization cutoff to be used to filter PTM localization. Can be between 0 and 1. Setting to 0 will not filter anything."
};
var Cutoff3bParam = new DoubleParam("Localization cutoff", 0.75)
{
Help = "Localization cutoff to be used to filter PTM localization. Can be between 0 and 1. Setting to 0 will not filter anything."
};
var PTMPosCol1Param = new SingleChoiceParam("PTM position column type")
{
Values = new[] { "EG.PTMLocalizationProbabilities (SN)", "EG.PrecursorId (SN)" },
Help = "Chose which column PTM positions should be extracted from. Requires respective columns."
};
var PTMPosCol2Param = new SingleChoiceParam("PTM position column type")
{
Values = new[] { "EG.PTMLocalizationProbabilities (SN)", "EG.PrecursorId (SN)", "Modified sequence (MQ)" },
Help = "Chose which column PTM positions should be extracted from. Requires respective columns."
};
var PTMPosCol3Param = new SingleChoiceParam("PTM position column type")
{
Values = new[] { "EG.PTMLocalizationProbabilities (SN)", "EG.PrecursorId (SN)" },
Help = "Chose which column PTM positions should be extracted from. Requires respective columns."
};
var PTMPosCol2cParam = new SingleChoiceParam("Target PTM Probabilities column")
{
Values = data.StringColumnNames,
Value = Math.Max(0, data.StringColumnNames.FindIndex(col => col.ToLower().Equals("phospho (sty) probabilities"))),
Help = "Chose which column PTM target probabilities should be extracted from. Requires respective columns."
};
var ProbType1Param = new SingleChoiceWithSubParams("Probability column type")
{
Values = new[] { "EG.PTMLocalizationProbabilities (SN)", "EG.PTMAssayProbability (SN)", "No probability column" },
Help = "Chose which column probabilities and PTM positions should be extracted from. Requires resepctive columns. " +
"EG.PTMAssayProbability will extract PTM positions from EG.PrecursorId.",
SubParams = new Parameters[] { // Define the different sub-parameter groups
new Parameters(Cutoff1aParam), // EG.PTMLocalizationProbabilities
new Parameters(Cutoff1bParam), // EG.PTMAssayProbability
new Parameters(PTMPosCol1Param) // Ignored
}
};
var ProbType2Param = new SingleChoiceWithSubParams("Probability column type")
{
Values = new[] { "EG.PTMLocalizationProbabilities (SN)", "EG.PTMAssayProbability (SN)",
"No probability column", "Modified sequence (MQ)" },
Help = "Chose which column probabilities and PTM positions should be extracted from. Requires resepctive columns. " +
"EG.PTMAssayProbability will extract PTM positions from EG.PrecursorId. Modified sequence will extract probabilities from provided PTM Probabilities columns.",
SubParams = new Parameters[] { // Define the different sub-parameter groups
new Parameters(Cutoff2aParam), // EG.PTMLocalizationProbabilities
new Parameters(Cutoff2bParam), // EG.PTMAssayProbability
new Parameters(PTMPosCol2Param), // Ignored
new Parameters(Cutoff2cParam, PTMPosCol2cParam) // Modified sequence
}
};
var ProbType3Param = new SingleChoiceWithSubParams("Probability column type")
{
Values = new[] { "EG.PTMLocalizationProbabilities (SN)", "EG.PTMAssayProbability (SN)", "No probability column" },
Help = "Chose which column probabilities and PTM positions should be extracted from. Requires resepctive columns. " +
"EG.PTMAssayProbability will extract PTM positions from EG.PrecursorId.",
SubParams = new Parameters[] { // Define the different sub-parameter groups
new Parameters(Cutoff3aParam), // EG.PTMLocalizationProbabilities
new Parameters(Cutoff3bParam), // EG.PTMAssayProbability
new Parameters(PTMPosCol3Param) // Ignored
}
};
var GenesParam = new SingleChoiceParam("Genes or protein groups")
{
Values = new[] { "PG.Genes", "PG.ProteinGroups" },
Help = "Chose if sites should be collapsed on gene or protein level."
};
var FastaFileParam = new FileParam("FASTA file (optional)")
{
Help = "Define file location of FASTA file for PTM motif sequence annotation. Leaving blank will skip annotation."
};
var FastaStringParam = new StringParam("FASTA identifier rule", ".*GN=([^ ]*) .*")
{
Help = "If FASTA file is provided, define identifier parsing rule. This is crucial to allow gene or protein name matching as defined above. Set e.g." +
".*GN=([^ ]*) .* for gene readout, or .*\\|(.*)\\|.* for protein readout"
};
var StoichParam = new SingleChoiceParam("Stoichiometry calculation")
{
Values = new[] { "Calculate stoichiometries", "Skip" },
Help = "Chose if target PTM stoichiometries should be calculated."
};
var CollapseParam = new SingleChoiceWithSubParams("Collapse level")
{
Values = new[] { "Target PTM site-level, e.g. ABC1_S15_M1", "Target PTM peptide-level, e.g. FS[ph]EAMST[ph]R (stoichiometry possible)",
"ModSpec peptide-level, e.g. FSEAMSTR_2[ph];1[ox]" },
Value = 0,
Help = "Chose if precursors should be collapsed on peptide- or site-level. Site-level requires PEP.PeptidePosition column.",
SubParams = new Parameters[] { // Define the different sub-parameter groups
new Parameters(ProbType1Param, GenesParam, FastaFileParam, FastaStringParam), // Localized Site
new Parameters(ProbType2Param, StoichParam), // Localized Peptide
new Parameters(ProbType3Param) // ModSpec Peptide
}
};
var PTMTypesParam = new StringParam("Variable PTMs, target PTM first", "[Phospho (STY)];[Deamidation (NQ)];[Oxidation (M)];[Carbamidomethyl (C)]")
{
Help = "List PTMs as listed in EG.PrecursorId, separated by semicolon. If target site- or target peptide-level collapse is performed, " +
"target PTM needs to be listed first."
};
var AggParam = new SingleChoiceParam("Aggregation type")
{
Values = new[] { "Linear modeling based", "Summing" },
Help = "Chose if peptide intensities should be aggregated based on a linear model or simply summed."
};
var NumberOfCoresParam = new IntParam("CPUcores", 8)
{
Help = "Number of CPU threads to be created by the plugin where possible. Set to 1 for lowest CPU usage. Do not set higher than actual number of available CPU threads."
};
return(new Parameter[]
{
PerlParam,
CollapseParam,
PTMTypesParam,
AggParam,
NumberOfCoresParam,
});
}
/// <summary>
/// Convert <see cref="BaseLib.Param"/> to <see cref="BaseLibS.Param"/>
/// </summary>
/// <param name="p"></param>
/// <returns></returns>
public static Parameter Convert(Parameter p)
{
if (p.Type == ParamType.Server)
{
return(p);
}
if (p is RegexReplaceParamWf)
{
RegexReplaceParamWf q = (RegexReplaceParamWf)p;
RegexReplaceParam b = new RegexReplaceParam(q.Name, q.Value.Item1, q.Value.Item2, q.Previews)
{
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is RegexMatchParamWf)
{
RegexMatchParamWf q = (RegexMatchParamWf)p;
RegexMatchParam b = new RegexMatchParam(q.Name, q.Value, q.Previews)
{
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is BoolParamWf)
{
BoolParamWf q = (BoolParamWf)p;
BoolParam b = new BoolParam(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is BoolWithSubParamsWf)
{
BoolWithSubParamsWf q = (BoolWithSubParamsWf)p;
q.SubParamsFalse?.Convert(Convert);
q.SubParamsTrue?.Convert(Convert);
BoolWithSubParams b = new BoolWithSubParams(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
SubParamsFalse = q.SubParamsFalse,
SubParamsTrue = q.SubParamsTrue,
Default = q.Default,
ParamNameWidth = q.ParamNameWidth,
TotalWidth = q.TotalWidth,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is DictionaryIntValueParamWf)
{
DictionaryIntValueParamWf q = (DictionaryIntValueParamWf)p;
DictionaryIntValueParam b = new DictionaryIntValueParam(q.Name, q.Value, q.Keys)
{
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is DoubleParamWf)
{
DoubleParamWf q = (DoubleParamWf)p;
DoubleParam b = new DoubleParam(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is FileParamWf)
{
FileParamWf q = (FileParamWf)p;
FileParam b = new FileParam(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Filter = q.Filter,
ProcessFileName = q.ProcessFileName,
Save = q.Save,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is FolderParamWf)
{
FolderParamWf q = (FolderParamWf)p;
FolderParam b = new FolderParam(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is IntParamWf)
{
IntParamWf q = (IntParamWf)p;
IntParam b = new IntParam(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is LabelParamWf)
{
LabelParamWf q = (LabelParamWf)p;
LabelParam b = new LabelParam(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is MultiChoiceMultiBinParamWf)
{
MultiChoiceMultiBinParamWf q = (MultiChoiceMultiBinParamWf)p;
MultiChoiceMultiBinParam b = new MultiChoiceMultiBinParam(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
Values = q.Values,
Bins = q.Bins,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is MultiChoiceParamWf)
{
MultiChoiceParamWf q = (MultiChoiceParamWf)p;
MultiChoiceParam b = new MultiChoiceParam(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
Repeats = q.Repeats,
Values = q.Values,
Default = q.Default,
DefaultSelections = q.DefaultSelections,
DefaultSelectionNames = q.DefaultSelectionNames,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is MultiFileParamWf)
{
MultiFileParamWf q = (MultiFileParamWf)p;
MultiFileParam b = new MultiFileParam(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
Filter = q.Filter,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is MultiStringParamWf)
{
MultiStringParamWf q = (MultiStringParamWf)p;
MultiStringParam b = new MultiStringParam(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is SingleChoiceParamWf)
{
SingleChoiceParamWf q = (SingleChoiceParamWf)p;
SingleChoiceParam b = new SingleChoiceParam(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
Values = q.Values,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is SingleChoiceWithSubParamsWf)
{
SingleChoiceWithSubParamsWf q = (SingleChoiceWithSubParamsWf)p;
foreach (Parameters param in q.SubParams)
{
param?.Convert(Convert);
}
SingleChoiceWithSubParams b = new SingleChoiceWithSubParams(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
Values = q.Values,
Default = q.Default,
SubParams = new Parameters[q.SubParams.Count],
ParamNameWidth = q.ParamNameWidth,
TotalWidth = q.TotalWidth,
Url = q.Url
};
for (int i = 0; i < q.SubParams.Count; i++)
{
b.SubParams[i] = q.SubParams[i];
}
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is StringParamWf)
{
StringParamWf q = (StringParamWf)p;
StringParam b = new StringParam(q.Name, q.Value)
{
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
if (p is Ms1LabelParamWf)
{
Ms1LabelParamWf q = (Ms1LabelParamWf)p;
Ms1LabelParam b = new Ms1LabelParam(q.Name, q.Value)
{
Values = q.Values,
Multiplicity = q.Multiplicity,
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers())
{
b.ValueChanged += act;
}
return(b);
}
throw new Exception("Could not convert ParamWfeter");
}
public void TestSingleChoiceParam()
{
var param = new SingleChoiceParam("choice", 1) { Values = new List<string> {"c1", "b2"} };
var param2 = (SingleChoiceParam) param.ToXmlAndBack();
Assert.AreEqual(param.Name, param2.Name);
Assert.AreEqual(param.Value, param2.Value);
Assert.IsTrue(param.Values.SequenceEqual(param2.Values));
}
private static Parameter GetColumnSelectionParameter(string[] selection)
{
const int maxCols = 5;
string[] values = new string[maxCols];
Parameters[] subParams = new Parameters[maxCols];
for (int i = 1; i <= maxCols; i++){
values[i - 1] = "" + i;
Parameter[] px = new Parameter[i];
for (int j = 0; j < i; j++){
px[j] = new SingleChoiceParam(GetVariableName(j), j){Values = selection};
}
Parameters p = new Parameters(px);
subParams[i - 1] = p;
}
return new SingleChoiceWithSubParams("Number of columns", 0){
Values = values,
SubParams = subParams,
ParamNameWidth = 120,
TotalWidth = 800
};
}
private void AddQuantificationParameters(IList<Parameter> list, Lib.Model.Param quantificationMethod,
Lib.Model.Param protUnit, Lib.Model.Param pepUnit,
IList<ParameterDescription> help)
{
string name = MetadataElement.QUANTIFICATION_METHOD.Name;
string desc = null;
name = CheckIfDescriptionExists(help, name, ref desc, null);
IList<string> values = cv.GetOnlyChildNamesOfTerm("MS:1001833", "MS");
values.Add("");
int index = -1;
if (quantificationMethod != null){
index = MzTabMatrixUtils.GetSelectedIndex(quantificationMethod.Name, values);
}
SingleChoiceParam method = new SingleChoiceParam(name, index){
Help = desc,
Values = values
};
list.Add(method);
values = cv.GetOnlyChildNamesOfTerm("PRIDE:0000392", "PRIDE");
name = string.Format("{0}{1}{2}", MetadataElement.PROTEIN, MZTabConstants.MINUS,
MetadataProperty.PROTEIN_QUANTIFICATION_UNIT);
desc = null;
name = CheckIfDescriptionExists(help, name, ref desc, null);
index =
MzTabMatrixUtils.GetSelectedIndex(
protUnit == null ? cv.GetParam("Ratio", "PRIDE").Name : protUnit.Name, values);
SingleChoiceParam protein_unit = new SingleChoiceParam(name, index){Help = desc, Values = values};
list.Add(protein_unit);
name = string.Format("{0}{1}{2}", MetadataElement.PEPTIDE, MZTabConstants.MINUS,
MetadataProperty.PEPTIDE_QUANTIFICATION_UNIT);
desc = null;
name = CheckIfDescriptionExists(help, name, ref desc, null);
index =
MzTabMatrixUtils.GetSelectedIndex(pepUnit == null ? cv.GetParam("Ratio", "PRIDE").Name : pepUnit.Name,
values);
SingleChoiceParam peptide_unit = new SingleChoiceParam(name, index){Help = desc, Values = values};
list.Add(peptide_unit);
}
private void AddMzParameters(IList<Parameter> list, IList<ParameterDescription> help, Metadata mtd)
{
string name = string.Format("{0}{1}{2}", MetadataElement.MZTAB, MZTabConstants.MINUS,
MetadataProperty.MZTAB_VERSION);
string desc = null;
name = CheckIfDescriptionExists(help, name, ref desc, mtd);
StringParam version = new StringParam(name, Constants.versions.Last()){
Help = desc
};
list.Add(version);
IList<string> values = Enum.GetNames(typeof (MzTabMode));
name = string.Format("{0}{1}{2}", MetadataElement.MZTAB, MZTabConstants.MINUS, MetadataProperty.MZTAB_MODE);
desc = null;
name = CheckIfDescriptionExists(help, name, ref desc, mtd);
SingleChoiceParam mode = new SingleChoiceParam(name){
Values = values,
Value = values.IndexOf(mtd.TabDescription.MzTabMode.ToString()),
Help = desc
};
list.Add(mode);
values = Enum.GetNames(typeof (MzTabType));
name = string.Format("{0}{1}{2}", MetadataElement.MZTAB, MZTabConstants.MINUS, MetadataProperty.MZTAB_TYPE);
desc = null;
name = CheckIfDescriptionExists(help, name, ref desc, mtd);
SingleChoiceParam type = new SingleChoiceParam(name){
Values = values,
Value = values.IndexOf(mtd.TabDescription.MzTabType.ToString()),
Help = desc
};
list.Add(type);
name = string.Format("{0}{1}{2}", MetadataElement.MZTAB, MZTabConstants.MINUS, MetadataProperty.MZTAB_ID);
desc = null;
name = CheckIfDescriptionExists(help, name, ref desc, mtd);
StringParam id = new StringParam(name){Value = mtd.TabDescription.Id, Help = desc};
list.Add(id);
}
protected override Parameter[] SpecificParameters(IMatrixData data, ref string errString)
{
if (data.StringColumnCount == 0)
{
errString = "Please add at least one string column";
return(null);
}
if (data.CategoryColumnCount == 0)
{
errString = "Please add at least one categorical column";
return(null);
}
var NumberOfCoresParam = new StringParam("CPUcores", "8")
{
Help = "Number of CPU cores to be used by the plugin in certain steps, set to 1 for lowest CPU usage."
};
var ConditionColumnParam = new SingleChoiceParam("Condition column, eg R.FileName")
{
Values = data.CategoryColumnNames,
Value = Math.Max(0, data.CategoryColumnNames.FindIndex(col => col.ToLower().Equals("r.filename"))),
Help = "Chose experimental condition column, such as R.FileName. Has to be a categorical column."
};
var ConditionOldParam = new StringParam("Rename condition old", "20171125_QE7_nLC14_DBJ_SA_DIAphos_RPE1_pilot2_")
{
Help = "Write parsing rule of condition column to be changed from. Leave blank if no change wanted."
};
var ConditionNewParam = new StringParam("Rename condition new", "DIA_")
{
Help = "Write parsing rule of condition column to be changed into. Leave blank if no change wanted."
};
var PerlParam = new SingleChoiceParam("Parsing type")
{
Values = new[] { "fixed", "perl" },
Help = "Chose if perl compatibility should be enabled for parsing."
};
var ProbParam = new SingleChoiceWithSubParams("Prob param") // Hierarchical parameter with sub parameters
{
Values = new [] { "Local", "Global" }, // Name the different sub-parameter groups
SubParams = new Parameters[] { // Define the different sub-parameter groups
new Parameters(ConditionColumnParam, ConditionOldParam, ConditionNewParam, PerlParam), // Local
new Parameters(PTMProbParam) // Global
}
};
var PTMProbParam = new SingleChoiceParam("EG.PTMLocalizationProbabilities")
{
Values = data.StringColumnNames,
Value = Math.Max(0, data.StringColumnNames.FindIndex(col => col.ToLower().Equals("eg.ptmlocalizationprobabilities"))),
Help = "Chose localization probability column, such as EG.PTMLocalizationProbabilities. Has to be a string column."
};
var PTMSeqParam = new SingleChoiceParam("EG.PrecursorId")
{
Values = data.StringColumnNames,
Value = Math.Max(0, data.StringColumnNames.FindIndex(col => col.ToLower().Equals("eg.precursorid"))),
Help = "Chose sequence column, such as EG.PrecursorId. Has to be a string column."
};
var GenesParam = new SingleChoiceParam("PG.Genes or PG.ProteinGroups")
{
Values = data.StringColumnNames,
Value = Math.Max(0, data.StringColumnNames.FindIndex(col => col.ToLower().Equals("pg.genes"))),
Help = "Chose gene or protein group column. Has to be a string column."
};
var PeptidePosParam = new SingleChoiceParam("PEP.PeptidePosition")
{
Values = data.StringColumnNames,
Value = Math.Max(0, data.StringColumnNames.FindIndex(col => col.ToLower().Equals("pep.peptideposition"))),
Help = "Chose peptide position column, such as PEP.PeptidePosition. Has to be a string column."
};
var AggParam = new SingleChoiceParam("Aggregation type")
{
Values = new[] { "Linear modeling based", "Summing" },
Help = "Chose if peptide intensities should be aggregated based on a linear model or simply summed."
};
var CutoffParam = new StringParam("Localization cutoff", "0")
{
Help = "Localization cutoff to be used to filter PTM localization. Can be between 0 and 1. Setting to 0 will not filter anything."
};
return(new Parameter[]
{
NumberOfCoresParam,
ProbParam, // Use ProbParam instead of other parameters.
PTMSeqParam,
GenesParam,
PeptidePosParam,
AggParam,
CutoffParam,
});
}
/// <summary>
/// Convert <see cref="BaseLib.Param"/> to <see cref="BaseLibS.Param"/>
/// </summary>
/// <param name="p"></param>
/// <returns></returns>
public static Parameter Convert(Parameter p)
{
if (p.Type == ParamType.Server){
return p;
}
if (p is RegexReplaceParamWf){
RegexReplaceParamWf q = (RegexReplaceParamWf) p;
RegexReplaceParam b = new RegexReplaceParam(q.Name, q.Value.Item1, q.Value.Item2, q.Previews){
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is RegexMatchParamWf){
RegexMatchParamWf q = (RegexMatchParamWf) p;
RegexMatchParam b = new RegexMatchParam(q.Name, q.Value, q.Previews){
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is BoolParamWf){
BoolParamWf q = (BoolParamWf) p;
BoolParam b = new BoolParam(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is BoolWithSubParamsWf){
BoolWithSubParamsWf q = (BoolWithSubParamsWf) p;
q.SubParamsFalse?.Convert(Convert);
q.SubParamsTrue?.Convert(Convert);
BoolWithSubParams b = new BoolWithSubParams(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
SubParamsFalse = q.SubParamsFalse,
SubParamsTrue = q.SubParamsTrue,
Default = q.Default,
ParamNameWidth = q.ParamNameWidth,
TotalWidth = q.TotalWidth,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is DictionaryIntValueParamWf){
DictionaryIntValueParamWf q = (DictionaryIntValueParamWf) p;
DictionaryIntValueParam b = new DictionaryIntValueParam(q.Name, q.Value, q.Keys){
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is DoubleParamWf){
DoubleParamWf q = (DoubleParamWf) p;
DoubleParam b = new DoubleParam(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is FileParamWf){
FileParamWf q = (FileParamWf) p;
FileParam b = new FileParam(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Filter = q.Filter,
ProcessFileName = q.ProcessFileName,
Save = q.Save,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is FolderParamWf){
FolderParamWf q = (FolderParamWf) p;
FolderParam b = new FolderParam(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is IntParamWf){
IntParamWf q = (IntParamWf) p;
IntParam b = new IntParam(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is LabelParamWf){
LabelParamWf q = (LabelParamWf) p;
LabelParam b = new LabelParam(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is MultiChoiceMultiBinParamWf){
MultiChoiceMultiBinParamWf q = (MultiChoiceMultiBinParamWf) p;
MultiChoiceMultiBinParam b = new MultiChoiceMultiBinParam(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
Values = q.Values,
Bins = q.Bins,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is MultiChoiceParamWf){
MultiChoiceParamWf q = (MultiChoiceParamWf) p;
MultiChoiceParam b = new MultiChoiceParam(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
Repeats = q.Repeats,
Values = q.Values,
Default = q.Default,
DefaultSelections = q.DefaultSelections,
DefaultSelectionNames = q.DefaultSelectionNames,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is MultiFileParamWf){
MultiFileParamWf q = (MultiFileParamWf) p;
MultiFileParam b = new MultiFileParam(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
Filter = q.Filter,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is MultiStringParamWf){
MultiStringParamWf q = (MultiStringParamWf) p;
MultiStringParam b = new MultiStringParam(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is SingleChoiceParamWf){
SingleChoiceParamWf q = (SingleChoiceParamWf) p;
SingleChoiceParam b = new SingleChoiceParam(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
Values = q.Values,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is SingleChoiceWithSubParamsWf){
SingleChoiceWithSubParamsWf q = (SingleChoiceWithSubParamsWf) p;
foreach (Parameters param in q.SubParams){
param?.Convert(Convert);
}
SingleChoiceWithSubParams b = new SingleChoiceWithSubParams(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
Values = q.Values,
Default = q.Default,
SubParams = new Parameters[q.SubParams.Count],
ParamNameWidth = q.ParamNameWidth,
TotalWidth = q.TotalWidth,
Url = q.Url
};
for (int i = 0; i < q.SubParams.Count; i++){
b.SubParams[i] = q.SubParams[i];
}
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is StringParamWf){
StringParamWf q = (StringParamWf) p;
StringParam b = new StringParam(q.Name, q.Value){
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
if (p is Ms1LabelParamWf){
Ms1LabelParamWf q = (Ms1LabelParamWf) p;
Ms1LabelParam b = new Ms1LabelParam(q.Name, q.Value){
Values = q.Values,
Multiplicity = q.Multiplicity,
Help = q.Help,
Visible = q.Visible,
Default = q.Default,
Url = q.Url
};
foreach (ValueChangedHandler act in q.GetPropertyChangedHandlers()){
b.ValueChanged += act;
}
return b;
}
throw new Exception("Could not convert ParamWfeter");
}
