libStatGen Software  1
PedigreeDescription.h
1 /*
2  * Copyright (C) 2010 Regents of the University of Michigan
3  *
4  * This program is free software: you can redistribute it and/or modify
5  * it under the terms of the GNU General Public License as published by
6  * the Free Software Foundation, either version 3 of the License, or
7  * (at your option) any later version.
8  *
9  * This program is distributed in the hope that it will be useful,
10  * but WITHOUT ANY WARRANTY; without even the implied warranty of
11  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12  * GNU General Public License for more details.
13  *
14  * You should have received a copy of the GNU General Public License
15  * along with this program. If not, see <http://www.gnu.org/licenses/>.
16  */
17 
18 #ifndef __PEDDESCRIBE_H__
19 #define __PEDDESCRIBE_H__
20 
21 #include "PedigreeGlobals.h"
22 #include "PedigreePerson.h"
23 #include "StringArray.h"
24 #include "IntArray.h"
25 
26 #include <stdio.h>
27 
28 // Possible pedigree columns
29 #define pcSkip 0
30 #define pcMarker 1
31 #define pcTrait 2
32 #define pcAffection 3
33 #define pcCovariate 4
34 #define pcString 5
35 #define pcZygosity 6
36 #define pcEnd 7
37 
38 // Undocumented pedigree column types -- not recommended
39 #define pcUndocumentedTraitCovariate 1001
40 
42 {
43 public:
44  int columnCount;
45  IntArray columns, columnHash;
46 
49 
50  void Load(IFILE & Input, bool warnIfLinkage = false);
51  void Load(const char * filename, bool warnIfLinkage = false);
52 
53  void LoadLinkageDataFile(IFILE & input);
54  void LoadLinkageDataFile(const char * filename);
55 
56  void LoadMendelDataFile(IFILE & input);
57  void LoadMendelDataFile(const char * filename);
58 
59  void LoadMap(IFILE & Input);
60  void LoadMap(const char * filename);
61 
62  PedigreeDescription & operator = (PedigreeDescription & rhs);
63 
64  int CountTextColumns();
65 
66  // returns a string summarizing column contents
67  const char * ColumnSummary(String & string);
68 
69  // Flag specifying Mendel format
70  bool mendelFormat;
71 
72  String filename;
73 
74  void AddMarkerColumn(const char * markerName);
75  void AddTraitColumn(const char * traitName);
76  void AddAffectionColumn(const char * affectionName);
77  void AddCovariateColumn(const char * covariateName);
78  void AddStringColumn(const char * stringName);
79  void AddZygosityColumn();
80  void AddSkippedColumn();
81 
82 private:
83  int ReadLineHelper(IFILE & input, String & buffer, StringArray & tokens);
84 
85  int CountColumns(int type);
86  void UpdateSummary(String & string, int type, const char * label);
87 };
88 
89 #endif
90 
Class for easily reading/writing files without having to worry about file type (uncompressed, gzip, bgzf) when reading.
Definition: InputFile.h:36