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