RNAlib-2.0.4
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00001 00006 #define PRIVATE static 00007 00008 PRIVATE char sep = ':'; 00009 PRIVATE char *coding = "Null:U:P:H:B:I:M:S:E:R"; 00010 00011 #define INF 10000 /* infinity */ 00012 00013 typedef int CostMatrix[10][10]; 00014 00015 PRIVATE CostMatrix *EditCost; /* will point to UsualCost or ShapiroCost */ 00016 00017 PRIVATE CostMatrix UsualCost = 00018 { 00019 00020 /* Null, U, P, H, B, I, M, S, E, R */ 00021 00022 { 0, 1, 2, 2, 2, 2, 2, 1, 1, INF}, /* Null replaced */ 00023 { 1, 0, 1, INF, INF, INF, INF, INF, INF, INF}, /* U replaced */ 00024 { 2, 1, 0, INF, INF, INF, INF, INF, INF, INF}, /* P replaced */ 00025 { 2, INF, INF, 0, 2, 2, 2, INF, INF, INF}, /* H replaced */ 00026 { 2, INF, INF, 2, 0, 1, 2, INF, INF, INF}, /* B replaced */ 00027 { 2, INF, INF, 2, 1, 0, 2, INF, INF, INF}, /* I replaced */ 00028 { 2, INF, INF, 2, 2, 2, 0, INF, INF, INF}, /* M replaced */ 00029 { 1, INF, INF, INF, INF, INF, INF, 0, INF, INF}, /* S replaced */ 00030 { 1, INF, INF, INF, INF, INF, INF, INF, 0, INF}, /* E replaced */ 00031 { INF, INF, INF, INF, INF, INF, INF, INF, INF, 0}, /* R replaced */ 00032 00033 }; 00034 00035 00036 PRIVATE CostMatrix ShapiroCost = 00037 { 00038 00039 /* Null, U, P, H, B, I, M, S, E, R */ 00040 00041 { 0, 1, 2, 100, 5, 5, 75, 5, 5, INF}, /* Null replaced */ 00042 { 1, 0, 1, INF, INF, INF, INF, INF, INF, INF}, /* U replaced */ 00043 { 2, 1, 0, INF, INF, INF, INF, INF, INF, INF}, /* P replaced */ 00044 { 100, INF, INF, 0, 8, 8, 8, INF, INF, INF}, /* H replaced */ 00045 { 5, INF, INF, 8, 0, 3, 8, INF, INF, INF}, /* B replaced */ 00046 { 5, INF, INF, 8, 3, 0, 8, INF, INF, INF}, /* I replaced */ 00047 { 75, INF, INF, 8, 8, 8, 0, INF, INF, INF}, /* M replaced */ 00048 { 5, INF, INF, INF, INF, INF, INF, 0, INF, INF}, /* S replaced */ 00049 { 5, INF, INF, INF, INF, INF, INF, INF, 0, INF}, /* E replaced */ 00050 { INF, INF, INF, INF, INF, INF, INF, INF, INF, 0}, /* R replaced */ 00051 00052 }; 00053