Mercurial > repos > chrisd > testing
comparison gene_fraction/src/FastaRecord.cpp @ 0:f95150c37d38 draft default tip
planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
author | chrisd |
---|---|
date | Sun, 21 Feb 2016 23:31:55 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:f95150c37d38 |
---|---|
1 #include "FastaRecord.h" | |
2 | |
3 #include <algorithm> | |
4 | |
5 FastaRecord::FastaRecord(std::string gene_id, std::string gene) : | |
6 _gene_id(gene_id), _gene(gene), _base_hits(_gene.length(), 0), | |
7 _gene_hits(0) {} | |
8 | |
9 std::string FastaRecord::gene_id() const { return _gene_id; } | |
10 | |
11 std::string FastaRecord::gene() const { return _gene; } | |
12 | |
13 void FastaRecord::update_gene_hits() { | |
14 _gene_hits++; | |
15 } | |
16 | |
17 int FastaRecord::gene_hits() const { | |
18 return _gene_hits; | |
19 } | |
20 | |
21 int FastaRecord::get_base_hits() const { | |
22 return static_cast<int>(count(_base_hits.begin(), _base_hits.end(), 1)); | |
23 } | |
24 | |
25 int FastaRecord::find_gene(const std::vector<FastaRecord> &records, | |
26 const std::string &gene_id, std::string seq) { | |
27 int gene_index; | |
28 | |
29 std::vector<FastaRecord>::const_iterator low; | |
30 // binary search for fasta record index | |
31 low = std::lower_bound(records.begin(), records.end(), FastaRecord(gene_id, seq), | |
32 [](const FastaRecord &a, const FastaRecord &b) | |
33 { return a.gene_id() < b.gene_id(); }); | |
34 gene_index = (low - records.begin()); | |
35 | |
36 return gene_index; | |
37 } | |
38 | |
39 void FastaRecord::sort_by_gene_id(std::vector<FastaRecord> &records) { | |
40 // sort records by gene id | |
41 sort(records.begin(), records.end(), [](const FastaRecord &a, const FastaRecord &b) { return a.gene_id() < b.gene_id(); }); | |
42 } | |
43 | |
44 void FastaRecord::reset_base_hits(std::vector<FastaRecord> &records) { | |
45 for_each(records.begin(), records.end(), [](FastaRecord &a) { std::fill(a.base_hits().begin(), a.base_hits().end(), 0); }); | |
46 } | |
47 | |
48 void FastaRecord::reset_gene_hits(std::vector<FastaRecord> &records) { | |
49 for_each(records.begin(), records.end(), [](FastaRecord &a) { a._gene_hits = 0; }); | |
50 } | |
51 | |
52 std::vector<int> &FastaRecord::base_hits() { | |
53 return _base_hits; | |
54 } | |
55 | |
56 | |
57 | |
58 | |
59 | |
60 | |
61 | |
62 |