690da7ea38
biology/phrab biology/phred biology/consed Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to obtain the tarballs. PR: 191336 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer)
64 lines
1.7 KiB
C
64 lines
1.7 KiB
C
--- ./words.c.orig 2009-04-22 20:48:22.000000000 +0200
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+++ ./words.c 2014-08-02 12:39:30.000000000 +0200
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@@ -59,6 +59,12 @@
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static unsigned char *long_word_array;
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static int n_skips[3];
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+void print_word_counts();
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+void set_lower_upper();
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+void set_index_words(int,int,int);
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+void find_external_word_matches(int, unsigned char *);
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+void quicksort(SEQ_AREA, SEQ_AREA, int, int, SEQ_AREA *);
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+void new_lookup_words(unsigned char *, int, SEQ_AREA, SEQ_AREA, int, int);
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typedef struct sw_edge {
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int curr0, curr1, curr2;
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@@ -323,6 +329,7 @@
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/* only used when DNA_flag == 2 */
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+void
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set_lower_upper()
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{
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unsigned int word_int, word_reduced, last_word_reduced;
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@@ -540,6 +547,7 @@
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/*
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other input: total_length, num_entries, complexity_flag, alphabet_size, residues, minmatch, nlogn_diff, mod_value, index_shift */
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+void
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set_index_words(pass, trans_type, index_type)
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int pass, trans_type, index_type;
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{
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@@ -1070,7 +1078,7 @@
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refinement in Sedgwick, but using bookkeeping of matching leading parts
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of words in a block to substantially improve
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efficiency) */
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-
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+void
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quicksort(left, right, k_start, maxcheck, seq_offsets)
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SEQ_AREA left, right;
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int k_start, maxcheck;
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@@ -1532,6 +1540,7 @@
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*/
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+void
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find_external_word_matches(e1, seq)
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int e1;
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unsigned char *seq;
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@@ -1776,6 +1785,7 @@
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int known_match_size, target_match_size, offset1, sub_check, reuse;
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extern int num_pairs;
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+void
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new_lookup_words(seq1, trans_type, sa_l_lower, sa_u_upper, ss_displace, n_lc)
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int trans_type, ss_displace, n_lc;
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SEQ_AREA sa_l_lower, sa_u_upper;
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@@ -2850,6 +2860,7 @@
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for (i = 0; i < 5; i++) num_merge_words[i] = 0;
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}
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+void
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print_word_counts()
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{
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int i;
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