Example Program
Interval Tree
Construction and usage demo for the interval tree.
An example for using interval trees.
| 1 | #include <iostream>
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| 2 | #include <seqan/graph_align.h>
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| 3 |
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| 4 | using namespace seqan;
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| 5 |
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| 6 | int main()
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| 7 | {
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| 8 |
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| 9 | typedef CharString TCargo; // id type
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| 10 | typedef int TValue; // position type
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| 11 |
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| 12 | typedef IntervalAndCargo<TValue, TCargo> TInterval;
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| 13 | typedef IntervalTree<TValue, TCargo> TIntervalTree;
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| 14 |
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| 15 | String<TInterval> intervals;
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| 16 | resize(intervals, 5);
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| 17 |
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| 18 | intervals[0].i1 = 5; intervals[0].i2 = 1000;
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| 19 | intervals[0].cargo = "gene";
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| 20 |
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| 21 | intervals[1].i1 = 50; intervals[1].i2 = 200;
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| 22 | intervals[1].cargo = "exon";
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| 23 |
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| 24 | intervals[2].i1 = 600; intervals[2].i2 = 800;
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| 25 | intervals[2].cargo = "exon";
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| 26 |
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| 27 | intervals[3].i1 = 100; intervals[3].i2 = 200;
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| 28 | intervals[3].cargo = "coding";
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| 29 |
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| 30 | intervals[4].i1 = 600; intervals[4].i2 = 700;
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| 31 | intervals[4].cargo = "coding";
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| 32 |
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| 33 | TIntervalTree tree(intervals);
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| 34 |
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| 35 | TInterval interval;
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| 36 | interval.i1 = 200; interval.i2 = 600;
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| 37 | interval.cargo = "intron";
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| 38 |
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| 39 | addInterval(tree, interval);
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| 40 |
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| 41 | TValue delBegin = 300;
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| 42 | TValue delEnd = 500;
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| 43 | String<TCargo> results;
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| 44 |
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| 45 | findIntervals(tree, delBegin, delEnd, results);
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| 46 |
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| 47 | std::cout << "Deletion " << delBegin << ".." << delEnd << " overlaps with ";
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| 48 | for (unsigned i = 0; i < length(results); ++i)
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| 49 | std::cout << results[i] << ",";
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| 50 | std::cout << std::endl;
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| 51 |
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| 52 | TValue snpPos = 150;
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| 53 | findIntervals(tree, snpPos, results);
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| 54 |
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| 55 | std::cout << "SNP " << snpPos << " overlaps with ";
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| 56 | for (unsigned i = 0; i < length(results); ++i)
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| 57 | std::cout << results[i] << ",";
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| 58 | std::cout << std::endl;
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| 59 |
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| 60 | CharString iCargo("exon");
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| 61 | bool res = removeInterval(tree, 50, 200, iCargo);
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| 62 | if (res)
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| 63 | std::cout << "Removed exon interval 50..200.\n";
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| 64 |
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| 65 | String<TCargo> results2;
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| 66 | findIntervals(tree, snpPos, results2);
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| 67 |
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| 68 | std::cout << "SNP " << snpPos << " overlaps with ";
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| 69 | for (unsigned i = 0; i < length(results2); ++i)
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| 70 | std::cout << results2[i] << ",";
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| 71 | std::cout << std::endl;
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| 72 |
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| 73 | return 0;
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| 74 | }
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