70 lines
1.5 KiB
C
70 lines
1.5 KiB
C
#ifndef GODIST_H
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#define GODIST_H
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#include <search.h>
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#define MAX_NODES 15000
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#define MAX_PARENTS 100
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#define MAX_CHILDREN 100
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enum EVIDENCE { MP = 1,
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IGI = 1 << 1,
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IPI = 1 << 2,
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ISS = 1 << 3,
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IDA = 1 << 4,
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IEP = 1 << 5,
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IEA = 1 << 6,
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TAS = 1 << 7,
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NAS = 1 << 8,
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ND = 1 << 9,
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RCA = 1 << 10,
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IC = 1 << 11 };
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struct node;
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struct node {
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/* GO term id. E.g: "GO:0005180" */
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char term[11];
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/* Information content */
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float ic;
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/* Depth in tree */
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int depth;
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/* Evidence codes */
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int evidence[12];
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/* Accumulated evidence codes */
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int acc_evidence[12];
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/* Parent count and parents */
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int parentc;
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struct node *parents[MAX_PARENTS];
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/* Child count and children */
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int childrenc;
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struct node *children[MAX_CHILDREN];
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/* Flag to ensure that a node is only visited once in DAG operations */
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char visited;
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};
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struct node* term_array[MAX_NODES];
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long term_array_size;
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int link_count;
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int total_ann;
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int evidence; /* bitvector with one bit per evidence code */
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/* Ontology initialisation functions. */
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int godist_init();
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int godist_read_assoc(FILE *fd);
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int godist_read_term(FILE *fd);
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void accumulate_evidence(struct node*);
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/* Distance metric functions */
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float resnik_distance(char *term1, char *term2);
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float fussimeg_distance(char *term1, char *term2);
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void calc_ic(struct node *n, unsigned int evidence);
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void clear_flags(struct node *n);
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void print_term(struct node *n);
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#endif
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