public Parameters GetParameters(IMatrixData mdata, ref string errorString)
{
var parameter = new SingleChoiceWithSubParams("Column type")
{
Values = new [] { "Main", "Text", "Numeric", "Category" },
SubParams = new []
{
new RegexReplaceParam("Regex", new Regex("Column (.*)"), "$1", mdata.ColumnNames),
new RegexReplaceParam("Regex", new Regex("Column (.*)"), "$1", mdata.StringColumnNames),
new RegexReplaceParam("Regex", new Regex("Column (.*)"), "$1", mdata.NumericColumnNames),
new RegexReplaceParam("Regex", new Regex("Column (.*)"), "$1", mdata.CategoryColumnNames),
}.Select(param => new Parameters(param)).ToArray()
};
return(new Parameters(parameter));
}
public Parameters GetParameters(IMatrixData mdata, ref string errorString)
{
SingleChoiceWithSubParams scwsp = new SingleChoiceWithSubParams("Action")
{
Values =
new[] { "Create", "Create from experiment name", "Edit", "Rename", "Delete", "Write template file", "Read from file" },
SubParams =
new[] {
GetCreateParameters(mdata), GetCreateFromExperimentNamesParameters(mdata, ref errorString),
GetEditParameters(mdata), GetRenameParameters(mdata), GetDeleteParameters(mdata),
GetWriteTemplateFileParameters(mdata), GetReadFromFileParameters(mdata)
},
ParamNameWidth = 136,
TotalWidth = 731
};
return(new Parameters(new Parameter[] { scwsp }));
}
public void TestSingleChoiceWithSubParamsInParameters()
{
SingleChoiceWithSubParams param = new SingleChoiceWithSubParams("choice", 1)
{
Values = new List <string> {
"c1", "b2"
}, SubParams = new []
{
new Parameters(new Parameter[0]),
new Parameters(new IntParam("sub2", 82))
}
};
SingleChoiceWithSubParams param2 = (SingleChoiceWithSubParams)param.ToXmlAndBack();
Assert.AreEqual(param.Name, param2.Name);
Assert.AreEqual(param.Value, param2.Value);
Assert.IsTrue(param.Values.SequenceEqual(param2.Values));
Assert.IsNotNull(param2.SubParams[0]);
Assert.AreEqual(82, param2.SubParams[1].GetParam <int>("sub2").Value);
}
public Parameters GetParameters(IMatrixData mdata, ref string errorString)
{
SingleChoiceWithSubParams scwsp = new SingleChoiceWithSubParams("Action"){
Values = new[]{"Create", "Edit", "Rename", "Delete"},
SubParams =
new[]{GetCreateParameters(mdata), GetEditParameters(mdata), GetRenameParameters(mdata), GetDeleteParameters(mdata)},
ParamNameWidth = 136, TotalWidth = 731
};
return new Parameters(new Parameter[]{scwsp});
}
protected void AddStudyVariableParameters(IList<Parameter> list, IList<StudyVariable> studyVariables,
IList<ParameterDescription> help, bool defineNumber)
{
StudyVariable[] array = studyVariables.Any() ? studyVariables.ToArray() : null;
if (defineNumber) {
SingleChoiceWithSubParams group = new SingleChoiceWithSubParams(MetadataElement.STUDY_VARIABLE.Name) {
ParamNameWidth = 0,
TotalWidth = 700
};
int count = array == null ? 10 : array.Length;
group.Values = new List<string>();
group.SubParams = new List<Parameters>();
int[] temp = new[] { count };
foreach (int n in temp){
if (n < 1) {
continue;
}
@group.Values.Add(n.ToString(CultureInfo.InvariantCulture));
@group.SubParams.Add(new Parameters(new StudyVariableParam(array != null && array.Length >= n
? ArrayUtils.SubArray(array, n)
: new StudyVariable[n], true, cv)));
}
if (array != null && group.SubParams.Count >= array.Length) {
group.Value = group.Values.IndexOf(array.Length.ToString(CultureInfo.InvariantCulture));
}
list.Add(group);
} else {
list.Add(new StudyVariableParam(array, false, cv, MetadataElement.STUDY_VARIABLE.Name));
}
}
protected void AddMsRunParameters(IList<Parameter> list, IList<MsRunImpl> runs, IList<ParameterDescription> help,
bool defineGroupNumber)
{
string name = MetadataElement.MS_RUN.Name;
string desc = null;
CheckIfDescriptionExists(help, name, ref desc, null);
MsRunImpl[] array = runs.Any() ? runs.ToArray() : null;
IList<MsRunImpl> groups = MsRunPanel.UniqueGroups(runs);
if (defineGroupNumber) {
SingleChoiceWithSubParams group = new SingleChoiceWithSubParams(name) {
ParamNameWidth = 0,
TotalWidth = 700,
Help = desc
};
int count = groups == null ? 5 : groups.Count;
group.Values = new List<string>();
group.SubParams = new List<Parameters>();
for (int i = 1; i < count; i++) {
int n = i + 1;
if (n < 1) {
continue;
}
group.Values.Add(n.ToString(CultureInfo.InvariantCulture));
group.SubParams.Add(new Parameters(new MsRunParam(n, array, cv, true)));
}
if (groups != null && group.SubParams.Count >= groups.Count) {
group.Value = group.Values.IndexOf(groups.Count.ToString(CultureInfo.InvariantCulture));
}
list.Add(group);
} else {
list.Add(new MsRunParam(groups.Count, array, cv, false, name) { Help = desc });
}
}
/// <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");
}
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,
});
}
public Parameters GetParameters(IMatrixData mdata, ref string errorString)
{
SingleChoiceWithSubParams scwsp = new SingleChoiceWithSubParams("Action"){
Values = new[]{"Create", "Create from experiment name", "Edit", "Rename", "Delete", "Write template file", "Read from file"},
SubParams =
new[]{
GetCreateParameters(mdata), GetCreateFromExperimentNamesParameters(mdata, ref errorString), GetEditParameters(mdata),
GetRenameParameters(mdata), GetDeleteParameters(mdata),
GetWriteTemplateFileParameters(mdata), GetReadFromFileParameters(mdata)
},
ParamNameWidth = 136, TotalWidth = 731
};
return new Parameters(new Parameter[]{scwsp});
}
private void AddSoftware(IList<Parameter> list, List<Software> software, Dictionary<string, string> parameters,
IList<ParameterDescription> help)
{
string name = MetadataElement.SOFTWARE.Name;
string desc = null;
name = CheckIfDescriptionExists(help, name, ref desc, null);
Software[] array = software.Any() ? software.ToArray() : null;
SingleChoiceWithSubParams group = new SingleChoiceWithSubParams(name){
Help = desc,
ParamNameWidth = 0,
TotalWidth = 800,
Value = 0,
Values = new[]{"1", "2", "3"},
SubParams = new Parameters[3]
};
group.SubParams[0] =
new Parameters(new Parameter[]{
new SoftwareParam(
array != null && array.Length >= 1 ? ArrayUtils.SubArray(array, 1) : new Software[1],
cv, parameters)
});
group.SubParams[1] = new Parameters(new Parameter[]{
new SoftwareParam(array != null && array.Length >= 2
? ArrayUtils.SubArray(array, 2)
: new Software[2], cv, parameters)
});
group.SubParams[2] = new Parameters(new Parameter[]{
new SoftwareParam(array != null && array.Length >= 3
? ArrayUtils.SubArray(array, 3)
: new Software[3], cv, parameters)
});
if (array != null && group.SubParams.Count >= array.Length){
group.Value = array.Length - 1;
}
list.Add(group);
}
private void AddSampleProcessingParameters(IList<Parameter> list, IList<ParameterDescription> help,
IList<SplitList<Lib.Model.Param>> steps)
{
string name = MetadataElement.SAMPLE_PROCESSING.Name;
string desc = null;
name = CheckIfDescriptionExists(help, name, ref desc, null);
SplitList<Lib.Model.Param>[] array = steps.Any() ? steps.ToArray() : null;
SingleChoiceWithSubParams group = new SingleChoiceWithSubParams(name){
Help = desc,
ParamNameWidth = 0,
TotalWidth = 800,
Value = 0,
Values = new[]{"1", "2", "3"},
SubParams =
new[]{
new Parameters(new Parameter[]{
new SampleProcessingParam(
array != null && array.Length >= 1
? ArrayUtils.SubArray(array, 1)
: new SplitList<Lib.Model.Param>[1], cv)
}),
new Parameters(new Parameter[]{
new SampleProcessingParam(array != null && array.Length >= 2
? ArrayUtils.SubArray(array, 2)
: new SplitList<Lib.Model.Param>[2], cv)
}),
new Parameters(new Parameter[]{
new SampleProcessingParam(array != null && array.Length >= 3
? ArrayUtils.SubArray(array, 3)
: new SplitList<Lib.Model.Param>[3], cv)
})
}
};
if (array != null && group.SubParams.Count >= array.Length){
group.Value = array.Length - 1;
}
list.Add(group);
}
private void AddPublicationParameters(IList<Parameter> list, IList<Publication> publications,
IList<ParameterDescription> help)
{
string name = MetadataElement.PUBLICATION.Name;
string desc = null;
name = CheckIfDescriptionExists(help, name, ref desc, null);
Publication[] array = publications.Any() ? publications.ToArray() : null;
SingleChoiceWithSubParams group = new SingleChoiceWithSubParams(name){
Help = desc,
ParamNameWidth = 0,
TotalWidth = 800
};
int count = array == null ? 3 : array.Length;
group.Values = new string[count];
group.SubParams = new Parameters[count];
for (int i = 0; i < count; i++){
int n = i + 1;
group.Values[i] = n.ToString(CultureInfo.InvariantCulture);
group.SubParams[i] = new Parameters(new PublicationParam(array != null && array.Length >= n
? ArrayUtils.SubArray(array, n)
: new Publication[n], cv));
}
group.Value = 0;
if (array != null && group.SubParams.Count >= array.Length){
group.Value = array.Length - 1;
}
list.Add(group);
}
private void AddDatabaseParameters(IList<Parameter> list, IList<Database> databases,
IList<ParameterDescription> help)
{
string name = "database";
string desc = null;
name = CheckIfDescriptionExists(help, name, ref desc, null);
Database[] array = databases.Any() ? databases.ToArray() : null;
SingleChoiceWithSubParams group = new SingleChoiceWithSubParams(name){
Help = desc,
ParamNameWidth = 0,
TotalWidth = 800
};
int count = array == null ? 3 : Math.Max(array.Length + 1, 3);
group.Values = new string[count];
group.SubParams = new Parameters[count];
for (int i = 0; i < count; i++){
int n = i + 1;
group.Values[i] = n.ToString(CultureInfo.InvariantCulture);
group.SubParams[i] = new Parameters(new DatabaseParam(array != null && array.Length >= n
? ArrayUtils.SubArray(array, n)
: new Database[n]));
}
group.Value = 0;
if (array != null && group.SubParams.Count >= array.Length){
group.Value = array.Length - 1;
}
list.Add(group);
}
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,
});
}
public void TestSingleChoiceWithSubParamsInParameters()
{
var param = new SingleChoiceWithSubParams("choice", 1) { Values = new List<string> {"c1", "b2"}, SubParams = new []
{
new Parameters(new Parameter[0]),
new Parameters(new IntParam("sub2", 82))
}};
var param2 = (SingleChoiceWithSubParams) param.ToXmlAndBack();
Assert.AreEqual(param.Name, param2.Name);
Assert.AreEqual(param.Value, param2.Value);
Assert.IsTrue(param.Values.SequenceEqual(param2.Values));
Assert.IsNotNull(param2.SubParams[0]);
Assert.AreEqual(82, param2.SubParams[1].GetParam<int>("sub2").Value );
}
/// <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");
}
protected void AddAssayParameters(IList<Parameter> list, IList<Assay> assays, IList<ParameterDescription> help,
bool defineGroupNumber)
{
Assay[] array = assays.Any() ? assays.ToArray() : null;
IList<Assay> groups = AssayPanel.UniqueGroups(assays);
if (defineGroupNumber) {
SingleChoiceWithSubParams group = new SingleChoiceWithSubParams(MetadataElement.ASSAY.Name) {
ParamNameWidth = 0,
TotalWidth = 700
};
int count = groups == null ? 5 : groups.Count < 3 ? 3 : groups.Count + 1;
@group.Values = new string[count];
@group.SubParams = new Parameters[count];
for (int i = 0; i < count; i++) {
int n = i + 1;
@group.Values[i] = n.ToString(CultureInfo.InvariantCulture);
@group.SubParams[i] = new Parameters(new AssayParam(n, array, true, cv));
}
@group.Value = 0;
if (groups != null && @group.SubParams.Count >= groups.Count) {
@group.Value = groups.Count - 1;
}
list.Add(@group);
} else {
list.Add(new AssayParam(groups.Count, array, false, cv, MetadataElement.ASSAY.Name));
}
}
internal static SingleChoiceWithSubParams GetFilterModeParamNew()
{
SingleChoiceWithSubParams p = new SingleChoiceWithSubParams("Filter mode"){
Values = new[]{"Reduce matrix", "Add categorical column", "Split matrix"},
SubParams =
new List<Parameters>(new[]{new Parameters(GetModeParam1()), new Parameters(GetModeParam2()), new Parameters()})
};
return p;
}
protected void AddInstrumentParameters(IList<Parameter> list, IList<Instrument> instruments,
IList<ParameterDescription> help)
{
string name = MetadataElement.INSTRUMENT.Name;
string desc = null;
name = CheckIfDescriptionExists(help, name, ref desc, null);
Instrument[] array = instruments.Any() ? instruments.ToArray() : null;
SingleChoiceWithSubParams group = new SingleChoiceWithSubParams(name) {
Help = desc,
ParamNameWidth = 0,
TotalWidth = 800,
Value = 0,
Values = new[] { "1", "2", "3" },
SubParams =
new[]{
new Parameters(new Parameter[]{
new InstrumentParam(array != null && array.Length >= 1
? ArrayUtils.SubArray(array, 1)
: new Instrument[1], cv)
}),
new Parameters(new Parameter[]{
new InstrumentParam(array != null && array.Length >= 2
? ArrayUtils.SubArray(array, 2)
: new Instrument[2], cv)
}),
new Parameters(new Parameter[]{
new InstrumentParam(array != null && array.Length >= 3
? ArrayUtils.SubArray(array, 3)
: new Instrument[3], cv)
})
}
};
if (array != null && group.SubParams.Count >= array.Length) {
group.Value = array.Length - 1;
}
list.Add(group);
}
