/// <summary>
/// The Parameter array should be populated with default values here
/// </summary>
public override void Initialize()
{
_inputParam = new Parameter[7];
_inputParam[0] = new PointFeatureSetParam(TextStrings.PointFeatureSet);
_inputParam[1] = new ListParam(TextStrings.Zvalue)
{
HelpText = TextStrings.layercontainsvalues
};
_inputParam[2] = new DoubleParam(TextStrings.CellSize, 0, 0, double.MaxValue)
{
HelpText = TextStrings.Thecellsizeingeographicunits
};
_inputParam[3] = new DoubleParam(TextStrings.Power, 2, 1, double.MaxValue)
{
HelpText = TextStrings.Theinfluenceofdistance
};
_neighborhoodType = new List <string> {
TextStrings.FixedDistance, TextStrings.FixedCount
};
_inputParam[4] = new ListParam(TextStrings.NeighborhoodType, _neighborhoodType, 0)
{
HelpText = TextStrings.Selectthetypeofneighborhood
};
_inputParam[5] = new IntParam(TextStrings.MinMaxnumberofpoints, 12, 0, int.MaxValue)
{
HelpText = TextStrings.FixedDistanceHelpText
};
_inputParam[6] = new DoubleParam(TextStrings.MinMaxdistance, 0, 0, double.MaxValue)
{
HelpText = TextStrings.FixedDistanceHelpText
};
_outputParam = new Parameter[1];
_outputParam[0] = new RasterParam(TextStrings.Raster);
}
/// <summary>
/// Fires when one of the paramters value has beend changed, usually when a user changes a input or output Parameter value, this can be used to populate input2 Parameter default values.
/// </summary>
public override void ParameterChanged(Parameter sender)
{
// This will Diplay NoDataValue(Already exisit) in the Optional input box;
if (sender != _inputParam[0])
{
return;
}
IRaster inputTemp = _inputParam[0].Value as IRaster;
if (inputTemp == null)
{
return;
}
DoubleParam inParam1 = _inputParam[1] as DoubleParam;
if (inParam1 != null)
{
inParam1.Value = inputTemp.CellHeight;
}
DoubleParam inParam2 = _inputParam[2] as DoubleParam;
if (inParam2 != null)
{
inParam2.Value = inputTemp.CellWidth;
}
}
/// <summary>
/// Once the parameters have been configured, the Execute command can be called, it returns true if successful.
/// </summary>
/// <param name="cancelProgressHandler">The progress handler.</param>
/// <returns>True if executed successfully.</returns>
public override bool Execute(ICancelProgressHandler cancelProgressHandler)
{
// Get the needed input and output parameters
IFeatureSet inputFeatures = _inputParam[0].Value as IFeatureSet;
DoubleParam dp = _inputParam[1] as DoubleParam;
double bufferDistance = 1;
if (dp != null)
{
bufferDistance = dp.Value;
}
IFeatureSet outputFeatures = _outputParam[0].Value as IFeatureSet;
if (Buffer.AddBuffer(inputFeatures, bufferDistance, outputFeatures, cancelProgressHandler))
{
if (outputFeatures == null)
{
return(false);
}
outputFeatures.Save();
return(true);
}
_outputParam = null;
return(false);
}
public void TestDoubleParam()
{
DoubleParam sparam = new DoubleParam("myname", 42.0);
DoubleParam sparam2 = (DoubleParam)sparam.ToXmlAndBack();
Assert.AreEqual(sparam.Value, sparam2.Value);
Assert.AreEqual(sparam.Name, sparam2.Name);
}
public override void Initialize()
{
_inputParam = new Parameter[2];
_inputParam[0] = new LineFeatureSetParam(TextStrings.InputFeatureSet);
_inputParam[1] = new DoubleParam(TextStrings.LiLinePara, 10.0);
_outputParam = new Parameter[1];
_outputParam[0] = new LineFeatureSetParam(TextStrings.OutputFeatureSet);
}
/// <summary>
/// Inititalize input and output arrays with parameter types and default values.
/// </summary>
public override void Initialize()
{
_inputParam = new Parameter[2];
_inputParam[0] = new FeatureSetParam(TextStrings.InputFeatureSet);
_inputParam[1] = new DoubleParam(TextStrings.BufferDistance, 10.0);
_outputParam = new Parameter[1];
_outputParam[0] = new PolygonFeatureSetParam(TextStrings.OutputPolygonFeatureSet);
}
/// <summary>
/// Inititalize input and output arrays with parameter types and default values.
/// </summary>
public override void Initialize()
{
_inputParam = new Parameter[2];
_inputParam[0] = new FeatureSetParam(TextStrings.InputFeatureSet);
_inputParam[1] = new DoubleParam(TextStrings.BufferDistance, 10.0);
_outputParam = new Parameter[2];
_outputParam[0] = new PolygonFeatureSetParam(TextStrings.OutputPolygonFeatureSet);
_outputParam[1] = new BooleanParam(TextStrings.OutputParameter_AddToMap, TextStrings.OutputParameter_AddToMap_CheckboxText, true);
}
public object Convert(object value, Type targetType, object parameter, CultureInfo culture)
{
if (!(value is double))
{
return(null);
}
double v = (double)value;
double p = parameter as double? ?? 0;
return(SingleParam?.Invoke(v) ?? DoubleParam?.Invoke(v, p));
}
/// <summary>
/// Creates an instance of the dialog
/// </summary>
/// <param name="param">The parameter this element represents</param>
public DoubleElement(DoubleParam param)
{
//Needed by the designer
InitializeializeializeComponent();
GroupBox.Text = param.Name;
//We save the Parameter passed in
Param = param;
DoRefresh();
}
/// <summary>
/// The Parameter array should be populated with default values here
/// </summary>
public override void Initialize()
{
_inputParam = new Parameter[2];
_inputParam[0] = new LineFeatureSetParam(TextStrings.LineFeatureSet);
_inputParam[1] = new DoubleParam(TextStrings.Tolerance)
{
Value = 10.0
};
_outputParam = new Parameter[1];
_outputParam[0] = new LineFeatureSetParam(TextStrings.LineFeatureSet);
}
/// <summary>
/// Once the Parameter have been configured the Execute command can be called, it returns true if successful.
/// </summary>
/// <param name="cancelProgressHandler">The progress handler.</param>
/// <returns>Boolean, true if the method was successful.</returns>
public override bool Execute(ICancelProgressHandler cancelProgressHandler)
{
IRaster input1 = _inputParam[0].Value as IRaster;
DoubleParam dp1 = _inputParam[1] as DoubleParam;
DoubleParam dp2 = _inputParam[2] as DoubleParam;
double value1 = dp1?.Value ?? 0;
double value2 = dp2?.Value ?? 0;
IRaster output = _outputParam[0].Value as IRaster;
return(Execute(input1, value1, value2, output, cancelProgressHandler));
}
/// <summary>
/// The Parameter array should be populated with default values here
/// </summary>
public override void Initialize()
{
_inputParam = new Parameter[2];
_inputParam[0] = new LineFeatureSetParam(TextStrings.LineFeatureSet);
_inputParam[1] = new DoubleParam(TextStrings.Tolerance)
{
Value = 10.0
};
_outputParam = new Parameter[2];
_outputParam[0] = new LineFeatureSetParam(TextStrings.LineFeatureSet);
_outputParam[1] = new BooleanParam(TextStrings.OutputParameter_AddToMap, TextStrings.OutputParameter_AddToMap_CheckboxText, true);
}
/// <summary>
/// Once the Parameter have been configured the Execute command can be called, it returns true if succesful
/// </summary>
public override bool Execute(ICancelProgressHandler cancelProgressHandler)
{
IFeatureSet input = _inputParam[0].Value as IFeatureSet;
DoubleParam dp = _inputParam[1] as DoubleParam;
double bufferDistance = 1;
if (dp != null)
{
bufferDistance = dp.Value;
}
IFeatureSet output = _outputParam[0].Value as IFeatureSet;
return(Execute(input, bufferDistance, output, cancelProgressHandler));
}
/// <summary>
/// Once the parameters have been configured, the Execute command can be called, it returns true if succesful
/// </summary>
public override bool Execute(ICancelProgressHandler cancelProgressHandler)
{
//Get the needed input and output parameters
IFeatureSet inputFeatures = _inputParam[0].Value as IFeatureSet;
DoubleParam dp = _inputParam[1] as DoubleParam;
double bufferDistance = 1;
if (dp != null)
{
bufferDistance = dp.Value;
}
// IFeatureSet outputFeatures = _outputParam[0].Value as IFeatureSet;
return(true);
}
/// <summary>
/// The Parameter array should be populated with default values here
/// </summary>
public override void Initialize()
{
_inputParam = new Parameter[2];
_inputParam[0] = new RasterParam(TextStrings.inputRaster)
{
HelpText = TextStrings.InputRastercontainingtargetcells
};
_inputParam[1] = new DoubleParam(TextStrings.Maximumdistance, 100.0)
{
HelpText = TextStrings.Maximumdistancetobecalculated
};
_outputParam = new Parameter[1];
_outputParam[0] = new RasterParam(TextStrings.OutputRaster)
{
HelpText = TextStrings.SelectresultrasterfileName
};
}
public override void Initialize()
{
_inputParam = new Parameter[5];
_inputParam[0] = new LineFeatureSetParam(TextStrings.InputFeatureSet);
_inputParam[1] = new DoubleParam(TextStrings.LiCirclePara1, 60.0);
_inputParam[2] = new DoubleParam(TextStrings.LiCirclePara2, 3.0);
_inputParam[3] = new DoubleParam(TextStrings.LiCirclePara3, 5.0);
_inputParam[4] = new StringParam(TextStrings.LiCirclePara4, string.Empty);
#if DEBUG
_outputParam = new Parameter[2];
_outputParam[0] = new PointFeatureSetParam(TextStrings.OutputFeatureSet);
_outputParam[1] = new PolygonFeatureSetParam("DEBUG MODE OUTPUT");
#else
_outputParam = new Parameter[1];
_outputParam[0] = new PointFeatureSetParam(TextStrings.OutputFeatureSet);
#endif
}
/// <summary>
/// The Parameter array should be populated with default values here
/// </summary>
public override void Initialize()
{
_inputParam = new Parameter[4];
_inputParam[0] = new FeatureSetParam(TextStrings.input1polygontoRaster)
{
HelpText = TextStrings.InputPolygontochange
};
_inputParam[2] = new DoubleParam(TextStrings.DesiredCellSize)
{
HelpText = TextStrings.Themaximumnumber
};
_inputParam[1] = new ListParam(TextStrings.stringnameoffield)
{
HelpText = TextStrings.Thevalueofeachcell
};
_outputParam = new Parameter[1];
_outputParam[0] = new RasterParam(TextStrings.OutputRaster)
{
HelpText = TextStrings.Resultofaverageslope
};
}
/// <summary>
/// The Parameter array should be populated with default values here
/// </summary>
public override void Initialize()
{
_inputParam = new Parameter[3];
_inputParam[0] = new RasterParam(TextStrings.input1altitudeRaster)
{
HelpText = TextStrings.InputRasterforaverageslopecalculation
};
_inputParam[1] = new DoubleParam(TextStrings.inputZfactor, 1.0)
{
HelpText = TextStrings.InputZfactorforslopedisplay
};
_inputParam[2] = new BooleanParam(TextStrings.slopeinpercentage, TextStrings.boxSlopeInPercentage, false)
{
HelpText = TextStrings.slopeinpercentageindegree
};
_outputParam = new Parameter[1];
_outputParam[0] = new RasterParam(TextStrings.OutputslopeRaster)
{
HelpText = TextStrings.Resultofaverageslope
};
}
/// <summary>
/// The Parameter array should be populated with default values here
/// </summary>
public override void Initialize()
{
_inputParam = new Parameter[7];
_inputParam[0] = new RasterParam(TextStrings.input1altitudeRaster)
{
HelpText = TextStrings.InputRasterforaverageslopecalculation
};
_inputParam[1] = new DoubleParam(TextStrings.inputZfactor, 1.0)
{
HelpText = TextStrings.InputZfactorforslopedisplay
};
_inputParam[2] = new BooleanParam(TextStrings.slopeinpercentage, TextStrings.boxSlopeInPercentage, false)
{
HelpText = TextStrings.slopeinpercentage
};
_inputParam[3] = new FeatureSetParam(TextStrings.input1polygonfeatureset)
{
HelpText = TextStrings.averageslopeinarribute
};
_inputParam[4] = new FeatureSetParam(TextStrings.inputtheareaofinterest)
{
HelpText = TextStrings.featuresetcontainareainterest
};
_inputParam[5] = new IntParam(TextStrings.Indexofareaofinterestfeature, 0)
{
HelpText = TextStrings.indexspecificarea
};
_inputParam[6] = new StringParam(TextStrings.Fieldnameforavrageslope, TextStrings.AveSlope)
{
HelpText = TextStrings.Fieldnamecolomavrageslope
};
_outputParam = new Parameter[2];
_outputParam[0] = new FeatureSetParam(TextStrings.Outputwithaverageslope)
{
HelpText = TextStrings.SelecttheResultofOutput
};
_outputParam[2] = new BooleanParam(TextStrings.OutputParameter_AddToMap, TextStrings.OutputParameter_AddToMap_CheckboxText, true);
}
/// <summary>
/// The Parameter array should be populated with default values here
/// </summary>
public override void Initialize()
{
_inputParam = new Parameter[3];
_inputParam[0] = new RasterParam(TextStrings.inputRaster)
{
HelpText = TextStrings.InputtheRasterforCellsizeChange
};
_inputParam[1] = new DoubleParam(TextStrings.InputnewcellHight)
{
HelpText = TextStrings.DisplayingistheOldCellHight
};
_inputParam[2] = new DoubleParam(TextStrings.InputnewcellWidth)
{
HelpText = TextStrings.DisplayingistheOldCellHight
};
_outputParam = new Parameter[1];
_outputParam[0] = new RasterParam(TextStrings.OutputRaster)
{
HelpText = TextStrings.newrastername
};
}
/// <summary>
/// Once the Parameter have been configured the Execute command can be called, it returns true if succesful
/// </summary>
public override bool Execute(ICancelProgressHandler cancelProgressHandler)
{
IRaster input1 = _inputParam[0].Value as IRaster;
DoubleParam dp1 = _inputParam[1] as DoubleParam;
DoubleParam dp2 = _inputParam[2] as DoubleParam;
double value1 = 0;
double value2 = 0;
if (dp1 != null)
{
value1 = dp1.Value;
}
if (dp2 != null)
{
value2 = dp2.Value;
}
IRaster output = _outputParam[0].Value as IRaster;
return(Execute(input1, value1, value2, output, cancelProgressHandler));
}
/// <summary>
/// The Parameter array should be populated with default values here
/// </summary>
public override void Initialize()
{
_inputParam = new Parameter[3];
_inputParam[0] = new RasterParam(TextStrings.input1altitudeRaster)
{
HelpText = TextStrings.InputRasterforaverageslopecalculation
};
_inputParam[1] = new DoubleParam(TextStrings.inputZfactor, 1.0)
{
HelpText = TextStrings.InputZfactorforslopedisplay
};
_inputParam[2] = new PolygonFeatureSetParam(TextStrings.input1polygonfeatureset)
{
HelpText = TextStrings.FindAverageSlopeDescription
};
// _inputParam[2] = new FeatureSetParam(TextStrings."input1 polygon feature set");
_outputParam = new Parameter[1];
_outputParam[0] = new FeatureSetParam(TextStrings.Outputfeaturesetwithaverageslope)
{
HelpText = TextStrings.Resultofaverageslope
};
}
/// <summary>
/// The Parameter array should be populated with default values here.
/// </summary>
public override void Initialize()
{
_inputParam = new Parameter[3];
_inputParam[0] = new RasterParam(TextStrings.input1altitudeRaster)
{
HelpText = TextStrings.InputRasterforaverageslopecalculation
};
_inputParam[1] = new DoubleParam("Base value", 0)
{
HelpText = TextStrings.RasterBinTool_Initialize_BaseValueHelText
};
_inputParam[2] = new DoubleParam("Bin size", 10)
{
HelpText = TextStrings.RasterBinTool_Initialize_BinSizeHelpText
};
_outputParam = new Parameter[2];
_outputParam[0] = new RasterParam(TextStrings.OutputslopeRaster)
{
HelpText = TextStrings.Resultofaverageslope
};
_outputParam[1] = new BooleanParam(TextStrings.OutputParameter_AddToMap, TextStrings.OutputParameter_AddToMap_CheckboxText, true);
}
/// <summary>
/// The Parameter array should be populated with default values here
/// </summary>
public override void Initialize()
{
_inputParam = new Parameter[3];
_inputParam[0] = new RasterParam(TextStrings.input1altitudeRaster)
{
HelpText = TextStrings.InputRasterforaverageslopecalculation
};
_inputParam[1] = new DoubleParam("Base value", 0)
{
HelpText =
"The starting point for bin calculations. A base value of 10 with a bin size of 20 would give all values from 10 to 30 a value of 20."
};
_inputParam[2] = new DoubleParam("Bin size", 10)
{
HelpText =
"The size of the bins. A base value of 10 with a bin size of 20 would give all the values from 10 to 30 a value of 20."
};
_outputParam = new Parameter[1];
_outputParam[0] = new RasterParam(TextStrings.OutputslopeRaster)
{
HelpText = TextStrings.Resultofaverageslope
};
}
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,
});
}
private void buttonPrepareExport_Click(object sender, EventArgs e)
{
if (cbProcNames.Items.Count > 0)
{
List <ReportParamV2> paramList = new List <ReportParamV2>();
Dictionary <string, string> parameters =
ServicesProvider.GetInstance().GetAccountingServices().SelectExportAccountingProcParams("ExportAccounting_" + cbProcNames.Text);
if (parameters != null && parameters.Count > 0)
{
foreach (var parameter in parameters)
{
ReportParamV2 reportParam;
string paramName = parameter.Key.TrimStart('@');
if (paramName.Equals("branch_id", StringComparison.CurrentCultureIgnoreCase))
{
reportParam = new BranchParam(string.Empty);
}
else
{
string paramType = parameter.Value;
switch (paramType)
{
case "bit":
reportParam = new BoolParam(false);
break;
case "datetime":
reportParam = new DateParam(DateTime.Today);
break;
case "char":
reportParam = new CharParam(' ');
break;
case "nvarchar":
case "varchar":
case "text":
reportParam = new StringParam(string.Empty);
break;
case "int":
reportParam = new IntParam(1);
break;
case "float":
reportParam = new DoubleParam(1d);
break;
case "money":
reportParam = new DecimalParam(1m);
break;
default:
throw new NotImplementedException(string.Format("Sql type:{0} is not handled.", paramName));
}
}
reportParam.Label = paramName;
reportParam.Name = paramName;
paramList.Add(reportParam);
}
ReportParamsForm frm = new ReportParamsForm(paramList, cbProcNames.Text);
frm.ShowDialog();
}
_dataTable =
ServicesProvider.GetInstance().GetAccountingServices().FindElementaryMvtsToExport(
"ExportAccounting_"
+ cbProcNames.Text, paramList, out _idTable);
_total = _dataTable.Rows.Count;
_bwSelect = new BackgroundWorker {
WorkerSupportsCancellation = true
};
_bwSelect.DoWork += BwSelect_DoWork;
ExportBookings_Load(this, null);
}
}
/// <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");
}
private void DoubleParamTest( DoubleParam method, string command, string one, string two )
{
method(one, two );
Assertion.AssertEquals(command + " " + one + " " + two, BufferToString() );
try
{
method(null, two );
Assertion.Fail( "Null first parameter.");
}
catch( ArgumentException ae )
{
Assertion.Assert( true );
}
try
{
method(null, null);
Assertion.Fail( "Null first and second parameters.");
}
catch( ArgumentException ae )
{
Assertion.Assert( true );
}
try
{
method(one, null );
Assertion.Fail( "Null first parameter");
}
catch( ArgumentException ae )
{
Assertion.Assert( true );
}
try
{
method(one, "" );
Assertion.Fail( "Empty first parameter");
}
catch( ArgumentException ae )
{
Assertion.Assert( true );
}
try
{
method("", "" );
Assertion.Fail( "Empty first and second parameters");
}
catch( ArgumentException ae )
{
Assertion.Assert( true );
}
try
{
method("", two );
Assertion.Fail( "Empty second parameter");
}
catch( ArgumentException ae )
{
Assertion.Assert( true );
}
}
/// <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 SetParam(DoubleParam param, double value)
{
this._model.GetEnv().Set(param.param, value);
}
public void TestDoubleParam()
{
var sparam = new DoubleParam("myname", 42.0);
var sparam2 = (DoubleParam) sparam.ToXmlAndBack();
Assert.AreEqual(sparam.Value, sparam2.Value);
Assert.AreEqual(sparam.Name, sparam2.Name);
}
public double GetParam(DoubleParam param)
{
return this._model.GetEnv().Get(param.param);
}
