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