1 // This file is part of the Mussa source distribution.
2 // http://mussa.caltech.edu/
3 // Contact author: Tristan De Buysscher, tristan@caltech.edu
5 // This program and all associated source code files are Copyright (C) 2005
6 // the California Institute of Technology, Pasadena, CA, 91125 USA. It is
7 // under the GNU Public License; please see the included LICENSE.txt
8 // file for more information, or contact Tristan directly.
11 // ----------------------------------------
12 // ---------- flp_seqcomp.cc -----------
13 // ----------------------------------------
18 // Note one recording RC matches. This version of 'seqcomp' records RC matches
19 // as index of the window start in its nonRC form. However, past versions of
20 // the analysis recorded it as the index of the rear of the window, as the
21 // following legacy comment indicates. FR still uses this method
23 // Titus thinks the start of an RC window should be its "rear" in the
24 // normal version of the sequence. He's wrong, of course, and in the
25 // future my followers will annihilate his in the Final Battle, but for
26 // now I'll let him have his way.
28 // note seq2_i is actually the index of the leaving bp, so need to +1
31 FLPs::add(int seq1_i, int seq2_i, int a_score, int i2_offset)
36 if (a_score >= hard_threshold)
38 a_match.index = seq2_i + i2_offset;
39 a_match.score = a_score;
41 all_matches[seq1_i].push_back(a_match);
47 FLPs::seqcomp(string sseq1, string sseq2, bool is_RC)
49 int start_i, seq1_i, seq2_i, win_i; // loop variables
50 int matches; // number of matches in to a window
55 seq1 = (char *) sseq1.c_str();
56 seq2 = (char *) sseq2.c_str();
60 i2_offset = window_size - seq2_length;
65 // this does the "upper diagonals" of the search
67 // loop thru the start positions for sequence 1
68 for(start_i = 0; start_i < seq1_win_num; start_i++)
71 // compare initial window
72 for(win_i = 0; win_i < window_size; win_i++)
73 if ((seq1[start_i+win_i] == seq2[win_i]) &&
74 (seq1[start_i+win_i] != 'N')) // N's match nothing **
77 //seq2_i is always 0 for initial win
80 // call inlined function that adds match if it is above threshold
81 add(start_i, seq2_i, matches, i2_offset);
83 // run through rest of seq1 and seq2 with current seq1 offset (ie start_i)
84 // compare the bps leaving and entering the window and modify matches count
86 while( (seq1_i < seq1_win_num-1) && (seq2_i < seq2_win_num-1) )
88 // copmpare the bp leaving the window
89 if ((seq1[seq1_i] == seq2[seq2_i]) &&
90 (seq1[seq1_i] != 'N')) // N's match nothing
93 // compare the bp entering the window
94 if ((seq1[seq1_i+window_size] == seq2[seq2_i+window_size]) &&
95 (seq1[seq1_i+window_size] != 'N')) // N's match nothing
96 matches = matches + 1;
98 add(seq1_i + 1, seq2_i + 1, matches, i2_offset);
100 seq1_i = seq1_i + 1; // increment seq1_i to next window
101 seq2_i = seq2_i + 1; // increment seq2_i to next window
102 } // end of loop thru the current offset sequence
103 } // end of loop thru the start positions of seq1 sequence
106 // this does the "lower diagonals" of the search
108 // loop thru the start positions for sequence 1
109 for(start_i = 1; start_i < seq2_win_num; start_i++)
113 // compare initial window
114 for(win_i = 0; win_i < window_size; win_i++)
115 if ((seq2[start_i+win_i] == seq1[win_i]) &&
116 (seq2[start_i+win_i] != 'N')) // N's match nothing
119 //seq2_i is always start_i for initial window
122 add(0, seq2_i, matches, i2_offset);
124 // run through rest of seq1 and seq2 with current seq1 offset (ie start_i)
125 // compare the bps leaving and entering the window and modify matches count
127 while( (seq1_i < seq1_win_num-1) && (seq2_i < seq2_win_num-1) )
129 // copmpare the bp leaving the window
130 if ((seq1[seq1_i] == seq2[seq2_i]) &&
131 (seq1[seq1_i] != 'N')) // N's match nothing
132 matches = matches - 1;
134 // compare the bp entering the window
135 if ((seq1[seq1_i+window_size] == seq2[seq2_i+window_size]) &&
136 (seq1[seq1_i+window_size] != 'N')) // N's match nothing
137 matches = matches + 1;
139 add(seq1_i + 1, seq2_i + 1, matches, i2_offset);
141 seq1_i = seq1_i + 1; // increment seq1_i to next window
142 seq2_i = seq2_i + 1; // increment seq2_i to next window
143 } // end of loop thru the current offset sequence
144 } // end of loop thru the start positions of seq2 sequence