PedigreeGlobals.h
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00018 #ifndef __PEDGLOBALS_H__
00019 #define __PEDGLOBALS_H__
00020
00021 #include "Constant.h"
00022 #include "StringArray.h"
00023 #include "StringHash.h"
00024 #include "IntArray.h"
00025 #include "MathVector.h"
00026
00027 #include <iostream>
00028
00029 class MarkerInfo
00030 {
00031 public:
00032
00033 int chromosome;
00034
00035
00036 double position;
00037 double positionMale;
00038 double positionFemale;
00039
00040 Vector freq;
00041 String name;
00042 StringArray alleleLabels;
00043 StringIntHash alleleNumbers;
00044
00045 MarkerInfo(String & string)
00046 {
00047 serial = count++;
00048 name = string;
00049 chromosome = -1;
00050 position = 0.0;
00051 positionMale = 0.0;
00052 positionFemale = 0.0;
00053 }
00054
00055 bool AdjustFrequencies();
00056
00057 static int ComparePosition(MarkerInfo ** left, MarkerInfo ** right);
00058
00059 String GetAlleleLabel(int allele);
00060 int GetAlleleNumber(const String & label) const
00061 {
00062 return label == "0" ? 0 : alleleNumbers.Integer(label);
00063 }
00064
00065 int NewAllele(const String & label);
00066
00067
00068
00069 void UpdateSerial()
00070 {
00071 serial = count++;
00072 }
00073
00074 void IndexAlleles();
00075
00076 int CountAlleles()
00077 {
00078 return alleleLabels.Length() ? alleleLabels.Length() - 1 : 0;
00079 }
00080
00081 private:
00082
00083 static int count;
00084 static String label;
00085
00086
00087
00088
00089 int serial;
00090 };
00091
00092 std::ostream &operator << (std::ostream &stream, MarkerInfo &m);
00093
00094 class PedigreeGlobals
00095 {
00096 public:
00097 static int traitCount;
00098 static int markerCount;
00099 static int affectionCount;
00100 static int covariateCount;
00101
00102
00103 static bool chromosomeX;
00104
00105
00106 static bool sexSpecificMap;
00107
00108 static StringArray traitNames;
00109 static StringArray covariateNames;
00110 static StringArray affectionNames;
00111 static StringArray markerNames;
00112 static StringIntHash markerLookup;
00113 static StringIntHash traitLookup;
00114 static StringIntHash affectionLookup;
00115 static StringIntHash covariateLookup;
00116
00117
00118
00119
00120
00121 static int GetTraitID(const char * name);
00122 static int GetMarkerID(const char * name);
00123 static int GetCovariateID(const char * name);
00124 static int GetAffectionID(const char * name);
00125
00126
00127
00128
00129 static int LookupTrait(const char * name)
00130 {
00131 return traitLookup.Integer(name);
00132 }
00133 static int LookupMarker(const char * name)
00134 {
00135 return markerLookup.Integer(name);
00136 }
00137 static int LookupCovariate(const char * name)
00138 {
00139 return covariateLookup.Integer(name);
00140 }
00141 static int LookupAffection(const char * name)
00142 {
00143 return affectionLookup.Integer(name);
00144 }
00145
00146 static int markerInfoCount;
00147 static int markerInfoSize;
00148 static MarkerInfo ** markerInfo;
00149 static StringHash markerInfoByName;
00150 static MarkerInfo ** markerInfoByInteger;
00151
00152 static void GrowMarkerInfo();
00153 static MarkerInfo * GetMarkerInfo(String & name);
00154 static MarkerInfo * GetMarkerInfo(int marker);
00155
00156 static int SortMarkersInMapOrder(IntArray & markers, int chromosome = -1);
00157 static void GetOrderedMarkers(IntArray & markers);
00158 static void FlagMissingMarkers(IntArray & missingMarkers);
00159
00160 static bool MarkerPositionsAvailable();
00161 static bool AlleleFrequenciesAvailable();
00162
00163 static void VerifySexSpecificOrder();
00164
00165 static void LoadAlleleFrequencies(const char * filename, bool required = false);
00166 static void LoadAlleleFrequencies(IFILE & file);
00167
00168 static void LoadMarkerMap(const char * filename, bool filter = false);
00169 static void LoadMarkerMap(IFILE & file, bool filter = false);
00170
00171 static void LoadBasepairMap(const char * filename);
00172 static void LoadBasepairMap(IFILE & file);
00173
00174 static void WriteMapFile(const char * filename);
00175 static void WriteMapFile(FILE * file);
00176
00177 static void WriteFreqFile(const char * filename, bool old_format = false);
00178 static void WriteFreqFile(FILE * file, bool old_format = false);
00179
00180 static int LoadAllele(int marker, String & label);
00181 static int LoadAllele(MarkerInfo * info, String & label);
00182
00183 PedigreeGlobals()
00184 {
00185 instanceCount++;
00186 }
00187 ~PedigreeGlobals();
00188
00189 private:
00190 static int instanceCount;
00191
00192 };
00193
00194 #endif
00195