diff gene_fraction/src/FastaRecord.cpp @ 0:f95150c37d38 draft default tip

planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_fraction/src/FastaRecord.cpp	Sun Feb 21 23:31:55 2016 -0500
@@ -0,0 +1,62 @@
+#include "FastaRecord.h"
+
+#include <algorithm>
+
+FastaRecord::FastaRecord(std::string gene_id, std::string gene) :
+	_gene_id(gene_id), _gene(gene), _base_hits(_gene.length(), 0),
+	_gene_hits(0) {}
+
+std::string FastaRecord::gene_id() const { return _gene_id; }
+
+std::string FastaRecord::gene() const { return _gene; }
+
+void FastaRecord::update_gene_hits() {
+	_gene_hits++;
+}
+
+int FastaRecord::gene_hits() const {
+	return _gene_hits;
+}
+
+int FastaRecord::get_base_hits() const {
+	return static_cast<int>(count(_base_hits.begin(), _base_hits.end(), 1));
+}
+
+int FastaRecord::find_gene(const std::vector<FastaRecord> &records,
+			   const std::string &gene_id, std::string seq) {
+	int gene_index;
+
+	std::vector<FastaRecord>::const_iterator low;
+	// binary search for fasta record index
+	low = std::lower_bound(records.begin(), records.end(), FastaRecord(gene_id, seq),
+                                   [](const FastaRecord &a, const FastaRecord &b)
+                                   { return a.gene_id() < b.gene_id(); });
+	gene_index = (low - records.begin());
+
+	return gene_index;
+}
+
+void FastaRecord::sort_by_gene_id(std::vector<FastaRecord> &records) {
+	// sort records by gene id
+	sort(records.begin(), records.end(), [](const FastaRecord &a, const FastaRecord &b) { return a.gene_id() < b.gene_id(); });
+}
+
+void FastaRecord::reset_base_hits(std::vector<FastaRecord> &records) {
+	for_each(records.begin(), records.end(), [](FastaRecord &a) { std::fill(a.base_hits().begin(), a.base_hits().end(), 0); });
+}
+
+void FastaRecord::reset_gene_hits(std::vector<FastaRecord> &records) {
+	for_each(records.begin(), records.end(), [](FastaRecord &a) { a._gene_hits = 0; });
+}
+
+std::vector<int> &FastaRecord::base_hits() {
+        return _base_hits;
+}
+
+
+
+
+
+
+	
+