Example Program
Interval Tree
Construction and usage demo for the interval tree.
File "interval_tree.cpp"
An example for using interval trees.

1 | #include <iostream>
2 | #include <seqan/graph_align.h>
3 |
4 | using namespace seqan;
5 |
6 | int main()
7 | {
8 |
9 | typedef CharString TCargo; // id type
10 | typedef int TValue; // position type
11 |
12 | typedef IntervalAndCargo<TValue, TCargo> TInterval;
13 | typedef IntervalTree<TValue, TCargo> TIntervalTree;
14 |
15 | String<TInterval> intervals;
16 | resize(intervals, 5);
17 |

Store gene annotation in intervals.

18 | intervals[0].i1 = 5; intervals[0].i2 = 1000;
19 | intervals[0].cargo = "gene";
20 |
21 | intervals[1].i1 = 50; intervals[1].i2 = 200;
22 | intervals[1].cargo = "exon";
23 |
24 | intervals[2].i1 = 600; intervals[2].i2 = 800;
25 | intervals[2].cargo = "exon";
26 |
27 | intervals[3].i1 = 100; intervals[3].i2 = 200;
28 | intervals[3].cargo = "coding";
29 |
30 | intervals[4].i1 = 600; intervals[4].i2 = 700;
31 | intervals[4].cargo = "coding";
32 |
33 | TIntervalTree tree(intervals);
34 |

Add another interval.

35 | TInterval interval;
36 | interval.i1 = 200; interval.i2 = 600;
37 | interval.cargo = "intron";
38 |
39 | addInterval(tree, interval);
40 |

Query a genomic region.

41 | TValue delBegin = 300;
42 | TValue delEnd = 500;
43 | String<TCargo> results;
44 |
45 | findIntervals(tree, delBegin, delEnd, results);
46 |
47 | std::cout << "Deletion " << delBegin << ".." << delEnd << " overlaps with ";
48 | for (unsigned i = 0; i < length(results); ++i)
49 | std::cout << results[i] << ",";
50 | std::cout << std::endl;
51 |

Query a single position.

52 | TValue snpPos = 150;
53 | findIntervals(tree, snpPos, results);
54 |
55 | std::cout << "SNP " << snpPos << " overlaps with ";
56 | for (unsigned i = 0; i < length(results); ++i)
57 | std::cout << results[i] << ",";
58 | std::cout << std::endl;
59 |
60 | CharString iCargo("exon");
61 | bool res = removeInterval(tree, 50, 200, iCargo);
62 | if (res)
63 | std::cout << "Removed exon interval 50..200.\n";
64 |

Now, redo the query. This time one interval less should be returned.

65 | String<TCargo> results2;
66 | findIntervals(tree, snpPos, results2);
67 |
68 | std::cout << "SNP " << snpPos << " overlaps with ";
69 | for (unsigned i = 0; i < length(results2); ++i)
70 | std::cout << results2[i] << ",";
71 | std::cout << std::endl;
72 |
73 | return 0;
74 | }

See
addInterval, findIntervals, removeInterval, IntervalTree, IntervalAndCargo, createIntervalTree
SeqAn - Sequence Analysis Library - www.seqan.de

Page built @2014/10/13 16:12:57