diff gene_fraction/src/FastaRecord.h @ 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.h	Sun Feb 21 23:31:55 2016 -0500
@@ -0,0 +1,86 @@
+#ifndef FASTA_RECORD_H
+#define FASTA_RECORD_H
+
+#include <string>
+#include <vector>
+
+/**
+ * Class for dealing with fasta records
+ */
+class FastaRecord {
+public:
+	/**
+ 	 * Ctor that initializes gene id and gene
+ 	 */ 
+	FastaRecord(std::string gene_id, std::string gene);
+
+	/**
+ 	 * Returns a string gene id
+ 	 */
+	std::string gene_id() const;
+
+	/**
+ 	 * Returns the gene associated with gene id
+ 	 */
+	std::string gene() const;
+
+	/**
+ 	 * Returns the total base hits for a gene
+ 	 */ 
+	int get_base_hits() const;
+
+	/**
+ 	 * Returns the amount of genes that were hit
+ 	 * during the gene fraction calculation
+ 	 */ 
+	int gene_hits() const;
+	
+	/**
+ 	 *
+ 	 */ 
+	void update_base_hits(const int &index);
+
+	/**
+ 	 *
+ 	 */ 
+	void update_gene_hits();
+
+	/**
+ 	 * Searches for a fasta record corresponding
+ 	 * to gene id
+ 	 */ 
+	static int find_gene(const std::vector<FastaRecord> &records, 
+			     const std::string &gene_id, 
+                             std::string seq = "");
+
+	/**
+ 	 * Sorts fasta records by gene id
+ 	 */ 
+	static void sort_by_gene_id(std::vector<FastaRecord> &records);
+
+	/**
+ 	 * Resets base hits vector to 0's. 
+ 	 * This occurs after each sample is processed
+ 	 */ 
+	static void reset_base_hits(std::vector<FastaRecord> &records);
+
+	/**
+ 	 * Resets gene hits primitive to 0.
+ 	 * This happens after each sample is processed 
+ 	 */
+	static void reset_gene_hits(std::vector<FastaRecord> &records);
+
+	std::vector<int> &base_hits();
+
+	std::string _gene_id;
+	std::string _gene;
+	std::vector<int> _base_hits;
+
+private:
+	int _gene_hits;
+};
+
+
+
+
+#endif /* FASTA_RECORD_H */