sumalibs first commit

libfasta/sequence.h

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+/**
+ * FileName:    sequence.h
+ * Authors:      Tiayyba Riaz, Celine Mercier
+ * Description: Prototypes and other declarations for sequences
+ * **/
+#ifndef SEQUENCE_H_
+#define SEQUENCE_H_
+
+#include <stdint.h>
+#include <stdio.h>
+#include "../libutils/utilities.h"
+#include "fasta_header_parser.h"
+
+
+typedef struct {
+	char* accession_id;					// identifier
+	char *rawheader;					// not parsed header
+	element_from_header* header;		// parsed header
+	char *sequence;						// DNA sequence itself
+	int32_t length;						// DNA sequence's length
+	int32_t count;						// abundance of the sequence
+	unsigned char *table;      			// 4mer occurrence table build using function buildTable
+	int32_t over;              			// count of 4mer with occurrences greater than 255 (overflow)
+	struct fastaSeqPtr* next;			// next unique sequence for example
+	BOOL cluster_center;				// whether the sequence is a cluster center or not
+	int32_t cluster_weight;				// cluster weight when sequence is cluster center
+	int32_t cluster_weight_unique_ids;	// cluster weight when sequence is cluster center, counting the number sequence records
+	double score;						// score with cluster center for example
+	struct fastaSeqPtr* center;			// pointer to the sequence's cluster center
+	int32_t center_index;				// index of the sequence's cluster center
+	BOOL uniqHead;						// whether the sequence is a unique head or not
+	char* columns_BIOM;					// to print in BIOM format
+	int   columns_BIOM_size;			// size allocated for columns_BIOM
+	char* line_OTU_table;				// to print in OTU table format
+	int	  line_OTU_table_size;			// size allocated for line_OTU_table
+	struct hashtable *sample_counts;	// sample counts for sumaclean
+}fastaSeq,*fastaSeqPtr;
+
+
+typedef struct {
+	int32_t count;
+	fastaSeqPtr fastaSeqs;
+}fastaSeqCount, *fastaSeqCountPtr;
+
+
+fastaSeqPtr seq_getNext(FILE *fp, char *fieldDelim, BOOL isStandardSeq, BOOL onlyATGC);
+char *seq_readNextFromFilebyLine(FILE* fp);
+void seq_fillSeq(char *seq, fastaSeqPtr seqElem, int seqLen);
+void seq_fillSeqOnlyATGC(char *seq, fastaSeqPtr seqElem, int seqLen);
+void seq_fillDigitSeq(char *seq, fastaSeqPtr seqElem, int seqLen);
+void seq_fillHeader(char* header, char *fieldDelim, fastaSeqPtr seqElem);
+fastaSeqCount seq_readAllSeq2(char *fileName, BOOL isStandardSeq, BOOL onlyATGC);
+int32_t seq_findSeqByAccId (char *accid, fastaSeqCountPtr allseqs);
+void seq_printSeqs (fastaSeqCountPtr allseq);
+int cleanDB(fastaSeqCount);
+void addCounts(fastaSeqCount* db);
+int uniqSeqsVector(fastaSeqCount* db, fastaSeqPtr** uniqSeqs);
+void calculateMaxAndMinLen(fastaSeqPtr* db, int n, int* lmax, int* lmin);
+void calculateMaxAndMinLenDB(fastaSeqCount db, int* lmax, int* lmin);
+int sortSeqsWithCounts(const void **s1, const void **s2);
+int reverseSortSeqsWithCounts(const void **s1, const void **s2);
+void readSampleCounts(fastaSeqCount* db, char* key_name);
+
+#endif /*SEQUENCE_H_*/