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• PerseusUtils

C# Class PerseusApi.Utils.PerseusUtils

Show file Open project: JurgenCox/perseus-plugins

Public Properties

Property	Type	Description
commentPrefix	HashSet
commentPrefixExceptions	HashSet

Public Methods

Method	Description
AddFilter ( List filters, Parameters p, int inds, string &errString ) : void
GetAvailableAnnots ( string &baseNames, AnnotType &types, string &files ) : string[][]
GetAvailableAnnots ( string &baseNames, AnnotType &types, string &files, List &badFiles ) : string[][]	Read-in all available annotations.
GetAvailableAnnots ( string &baseNames, string &files ) : string[][]
GetAvailableAnnots ( string &baseNames, string &files, List &badFiles ) : string[][]	Read-in all available annotations.
GetNumFilterParams ( string selection ) : BaseLibS.Param.Parameter[]
GetRelationsNumFilter ( Parameters param, string &errString, int &colInds, bool &and ) : Relation[]
GetRowCount ( StreamReader reader, StreamReader auxReader, int mainColIndices, List filters, char separator ) : int
HasAnyDescription ( IMatrixData data ) : bool
IsValidRowNumFilter ( double row, Relation relations, bool and ) : bool
LoadMatrixData ( string[]>.IDictionary annotationRows, int eInds, int cInds, int nInds, int tInds, int mInds, ProcessInfo processInfo, IList colNames, IMatrixData mdata, StreamReader reader, StreamReader auxReader, int nrows, string origin, char separator, bool shortenExpressionNames, List filters ) : void
ReadMatrixFromFile ( IMatrixData mdata, ProcessInfo processInfo, string filename, char separator ) : void
ReadMatrixFromFile ( IMatrixData mdata, ProcessInfo processInfo, string filename, int eInds, int nInds, int cInds, int tInds, int mInds, Parameters mainFilterParameters, Parameters numericalFilterParameters, bool shortenExpressionColumnNames ) : void
WriteMatrixToFile ( IMatrixData data, string filename, bool addtlMatrices = false ) : void	Write matrix to file with tab separation

Private Methods

Method	Description
ColumnIndices ( string typeRow, int &eInds, int &nInds, int &cInds, int &tInds, int &mInds ) : void
FromString1 ( string s ) : AnnotType
GetAnnotFiles ( ) : string[]
GetAvailableAnnots ( string file, string &baseName, AnnotType &types ) : string[]
GetColIndsNumFilter ( Parameters parameters, string &realVariableNames ) : int[]
GetColumnSelectionParameter ( string selection ) : BaseLibS.Param.Parameter
GetHasAddtlMatrices ( TextReader reader, IList expressionColIndices, char separator ) : bool
GetRelations ( Parameters parameters, string realVariableNames ) : Relation[]
GetRelationsParameter ( ) : BaseLibS.Param.Parameter
GetVariableName ( int i ) : string
IsValidLine ( string line, char separator, List filters, bool hasAddtlMatrices ) : bool
IsValidLine ( string line, char separator, List filters, string &split, bool hasAddtlMatrices ) : bool
LoadMatrixData ( IList colNames, IList colDescriptions, IList mainColIndices, IList catColIndices, IList numColIndices, IList textColIndices, IList multiNumColIndices, string origin, IMatrixData matrixData, string[]>.IDictionary annotationRows, Action progress, Action status, char separator, TextReader reader, StreamReader auxReader, int nrows, bool shortenExpressionNames, List filters ) : void
ParseExp ( string s, float &expressionValue, bool &isImputedValue, float &qualityValue ) : void
RemoveQuotes ( IEnumerable names ) : List
RemoveQuotes ( string name ) : string
RemoveSplitWhitespace ( string s ) : string
SplitAnnotRows ( string[]>.IDictionary annotRows, string[]>.Dictionary &catAnnotRows, string[]>.Dictionary &numAnnotRows ) : void
SplitLine ( string line, char separator ) : string[]
ToDoubles ( string s1, bool hasAddtlMatrices ) : double[]

Method Details

Property Details