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void | Load (IFILE &Input, bool warnIfLinkage=false) |
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void | Load (const char *filename, bool warnIfLinkage=false) |
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void | LoadLinkageDataFile (IFILE &input) |
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void | LoadLinkageDataFile (const char *filename) |
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void | LoadMendelDataFile (IFILE &input) |
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void | LoadMendelDataFile (const char *filename) |
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void | LoadMap (IFILE &Input) |
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void | LoadMap (const char *filename) |
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PedigreeDescription & | operator= (PedigreeDescription &rhs) |
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int | CountTextColumns () |
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const char * | ColumnSummary (String &string) |
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void | AddMarkerColumn (const char *markerName) |
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void | AddTraitColumn (const char *traitName) |
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void | AddAffectionColumn (const char *affectionName) |
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void | AddCovariateColumn (const char *covariateName) |
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void | AddStringColumn (const char *stringName) |
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void | AddZygosityColumn () |
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void | AddSkippedColumn () |
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static int | GetTraitID (const char *name) |
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static int | GetMarkerID (const char *name) |
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static int | GetCovariateID (const char *name) |
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static int | GetAffectionID (const char *name) |
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static int | GetStringID (const char *name) |
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static int | LookupTrait (const char *name) |
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static int | LookupMarker (const char *name) |
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static int | LookupCovariate (const char *name) |
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static int | LookupAffection (const char *name) |
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static int | LookupString (const char *name) |
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static void | GrowMarkerInfo () |
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static MarkerInfo * | GetMarkerInfo (String &name) |
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static MarkerInfo * | GetMarkerInfo (int marker) |
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static int | SortMarkersInMapOrder (IntArray &markers, int chromosome=-1) |
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static void | GetOrderedMarkers (IntArray &markers) |
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static void | FlagMissingMarkers (IntArray &missingMarkers) |
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static bool | MarkerPositionsAvailable () |
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static bool | AlleleFrequenciesAvailable () |
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static void | VerifySexSpecificOrder () |
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static void | LoadAlleleFrequencies (const char *filename, bool required=false) |
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static void | LoadAlleleFrequencies (IFILE &file) |
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static void | LoadMarkerMap (const char *filename, bool filter=false) |
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static void | LoadMarkerMap (IFILE &file, bool filter=false) |
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static void | LoadBasepairMap (const char *filename) |
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static void | LoadBasepairMap (IFILE &file) |
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static void | WriteMapFile (const char *filename) |
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static void | WriteMapFile (FILE *file) |
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static void | WriteFreqFile (const char *filename, bool old_format=false) |
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static void | WriteFreqFile (FILE *file, bool old_format=false) |
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static int | LoadAllele (int marker, String &label) |
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static int | LoadAllele (MarkerInfo *info, String &label) |
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static int | traitCount = 0 |
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static int | markerCount = 0 |
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static int | affectionCount = 0 |
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static int | covariateCount = 0 |
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static int | stringCount = 0 |
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static bool | chromosomeX = false |
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static bool | sexSpecificMap = false |
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static StringArray | traitNames |
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static StringArray | covariateNames |
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static StringArray | affectionNames |
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static StringArray | markerNames |
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static StringArray | stringNames |
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static StringIntHash | markerLookup |
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static StringIntHash | traitLookup |
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static StringIntHash | affectionLookup |
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static StringIntHash | covariateLookup |
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static StringIntHash | stringLookup |
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static int | markerInfoCount = 0 |
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static int | markerInfoSize = 0 |
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static MarkerInfo ** | markerInfo = NULL |
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static StringHash | markerInfoByName |
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static MarkerInfo ** | markerInfoByInteger = NULL |
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Definition at line 41 of file PedigreeDescription.h.