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 
41 class PedigreeDescription : public PedigreeGlobals
42 {
43 public:
44     int      columnCount;
45     IntArray columns, columnHash;
46 
47     PedigreeDescription();
48     ~PedigreeDescription();
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 
91