gclib/tophat_cpp/segments.h

/*
 *  segments.h
 *  TopHat
 *
 *  Created by Cole Trapnell on 2/11/09.
 *  Copyright 2009 __MyCompanyName__. All rights reserved.
 *
 */
#include <vector>
#include <map>
#include "bwt_map.h"

enum eREAD
  {
    READ_DONTCARE = 0,
    READ_LEFT,
    READ_RIGHT
  };

enum ePOINT_DIR
  {
    POINT_DIR_DONTCARE = 0,
    POINT_DIR_LEFT,
    POINT_DIR_RIGHT,
    POINT_DIR_BOTH
  };

struct RefSeg
{
RefSeg() :
  ref_id(0),
    points_where(POINT_DIR_DONTCARE),
    antisense(false),
    read(READ_DONTCARE),
    left(0),
    right(0),
    support_read("")
  {}
  
RefSeg(uint32_t i, ePOINT_DIR p, bool antisense, eREAD read, int l, int r, const string& support_read = "") :
  ref_id(i),
    points_where(p),
    antisense(antisense),
    read(read),
    left(l),
    right(r),
    support_read(support_read)
  {}
  
  bool operator<(const RefSeg& rhs) const
  {
    if (ref_id != rhs.ref_id)
      return ref_id < rhs.ref_id;
    if (left != rhs.left)
      return left < rhs.left;
    if (right != rhs.right)
      return right < rhs.right;
    return false;
  }
  
  bool operator==(const RefSeg& rhs) const
  {
    return (ref_id == rhs.ref_id &&
            left == rhs.left &&
            right == rhs.right && 
            points_where == rhs.points_where &&
            antisense == rhs.antisense &&
            read == rhs.read &&
            support_read == rhs.support_read);
  }
  
  uint32_t ref_id;
  ePOINT_DIR points_where;
  bool antisense;
  eREAD read;
  int left;
  int right;
  
  string support_read;
};      
Revision:	29
Committed:	Tue Aug 2 21:24:54 2011 UTC (13 years, 2 months ago) by gpertea
File size:	1483 byte(s)
Log Message:	adding tophat source work
Line	File contents
1	/*
2	* segments.h
3	* TopHat
4	*
5	* Created by Cole Trapnell on 2/11/09.
6	* Copyright 2009 __MyCompanyName__. All rights reserved.
7	*
8	*/
9	#include <vector>
10	#include <map>
11	#include "bwt_map.h"
12
13	enum eREAD
14	{
15	READ_DONTCARE = 0,
16	READ_LEFT,
17	READ_RIGHT
18	};
19
20	enum ePOINT_DIR
21	{
22	POINT_DIR_DONTCARE = 0,
23	POINT_DIR_LEFT,
24	POINT_DIR_RIGHT,
25	POINT_DIR_BOTH
26	};
27
28	struct RefSeg
29	{
30	RefSeg() :
31	ref_id(0),
32	points_where(POINT_DIR_DONTCARE),
33	antisense(false),
34	read(READ_DONTCARE),
35	left(0),
36	right(0),
37	support_read("")
38	{}
39
40	RefSeg(uint32_t i, ePOINT_DIR p, bool antisense, eREAD read, int l, int r, const string& support_read = "") :
41	ref_id(i),
42	points_where(p),
43	antisense(antisense),
44	read(read),
45	left(l),
46	right(r),
47	support_read(support_read)
48	{}
49
50	bool operator<(const RefSeg& rhs) const
51	{
52	if (ref_id != rhs.ref_id)
53	return ref_id < rhs.ref_id;
54	if (left != rhs.left)
55	return left < rhs.left;
56	if (right != rhs.right)
57	return right < rhs.right;
58	return false;
59	}
60
61	bool operator==(const RefSeg& rhs) const
62	{
63	return (ref_id == rhs.ref_id &&
64	left == rhs.left &&
65	right == rhs.right &&
66	points_where == rhs.points_where &&
67	antisense == rhs.antisense &&
68	read == rhs.read &&
69	support_read == rhs.support_read);
70	}
71
72	uint32_t ref_id;
73	ePOINT_DIR points_where;
74	bool antisense;
75	eREAD read;
76	int left;
77	int right;
78
79	string support_read;
80	};