Lines Matching refs:j
737 int i, j, k; in get_ribosum() local
748 for (j = 0; j < n_seq - 1; j++) in get_ribosum()
749 for (k = j + 1; k < n_seq; k++) { in get_ribosum()
750 ident = length - vrna_hamming_distance(Alseq[k], Alseq[j]); in get_ribosum()
764 for (j = 0; j < 7; j++) in get_ribosum()
765 ribo[i][j] = 0.; in get_ribosum()
786 for (j = 0; j < 7; j++) in get_ribosum()
787 ribo[i][j] = dm_12_5[i][j]; in get_ribosum()
791 for (j = 0; j < 7; j++) in get_ribosum()
792 ribo[i][j] = dm_12_6[i][j]; in get_ribosum()
796 for (j = 0; j < 7; j++) in get_ribosum()
797 ribo[i][j] = dm_12_7[i][j]; in get_ribosum()
801 for (j = 0; j < 7; j++) in get_ribosum()
802 ribo[i][j] = dm_12_8[i][j]; in get_ribosum()
806 for (j = 0; j < 7; j++) in get_ribosum()
807 ribo[i][j] = dm_12_9[i][j]; in get_ribosum()
811 for (j = 0; j < 7; j++) in get_ribosum()
812 ribo[i][j] = dm_12_10[i][j]; in get_ribosum()
816 for (j = 0; j < 7; j++) in get_ribosum()
817 ribo[i][j] = dm_12_11[i][j]; in get_ribosum()
827 for (j = 0; j < 7; j++) in get_ribosum()
828 ribo[i][j] = dm_13_5[i][j]; in get_ribosum()
832 for (j = 0; j < 7; j++) in get_ribosum()
833 ribo[i][j] = dm_13_6[i][j]; in get_ribosum()
837 for (j = 0; j < 7; j++) in get_ribosum()
838 ribo[i][j] = dm_13_7[i][j]; in get_ribosum()
842 for (j = 0; j < 7; j++) in get_ribosum()
843 ribo[i][j] = dm_13_8[i][j]; in get_ribosum()
847 for (j = 0; j < 7; j++) in get_ribosum()
848 ribo[i][j] = dm_13_9[i][j]; in get_ribosum()
852 for (j = 0; j < 7; j++) in get_ribosum()
853 ribo[i][j] = dm_13_10[i][j]; in get_ribosum()
857 for (j = 0; j < 7; j++) in get_ribosum()
858 ribo[i][j] = dm_13_11[i][j]; in get_ribosum()
862 for (j = 0; j < 7; j++) in get_ribosum()
863 ribo[i][j] = dm_13_12[i][j]; in get_ribosum()
873 for (j = 0; j < 7; j++) in get_ribosum()
874 ribo[i][j] = dm_14_5[i][j]; in get_ribosum()
878 for (j = 0; j < 7; j++) in get_ribosum()
879 ribo[i][j] = dm_14_6[i][j]; in get_ribosum()
883 for (j = 0; j < 7; j++) in get_ribosum()
884 ribo[i][j] = dm_14_7[i][j]; in get_ribosum()
888 for (j = 0; j < 7; j++) in get_ribosum()
889 ribo[i][j] = dm_14_8[i][j]; in get_ribosum()
893 for (j = 0; j < 7; j++) in get_ribosum()
894 ribo[i][j] = dm_14_9[i][j]; in get_ribosum()
898 for (j = 0; j < 7; j++) in get_ribosum()
899 ribo[i][j] = dm_14_10[i][j]; in get_ribosum()
903 for (j = 0; j < 7; j++) in get_ribosum()
904 ribo[i][j] = dm_14_11[i][j]; in get_ribosum()
908 for (j = 0; j < 7; j++) in get_ribosum()
909 ribo[i][j] = dm_14_12[i][j]; in get_ribosum()
913 for (j = 0; j < 7; j++) in get_ribosum()
914 ribo[i][j] = dm_14_13[i][j]; in get_ribosum()
924 for (j = 0; j < 7; j++) in get_ribosum()
925 ribo[i][j] = dm_15_5[i][j]; in get_ribosum()
929 for (j = 0; j < 7; j++) in get_ribosum()
930 ribo[i][j] = dm_15_6[i][j]; in get_ribosum()
934 for (j = 0; j < 7; j++) in get_ribosum()
935 ribo[i][j] = dm_15_7[i][j]; in get_ribosum()
939 for (j = 0; j < 7; j++) in get_ribosum()
940 ribo[i][j] = dm_15_8[i][j]; in get_ribosum()
944 for (j = 0; j < 7; j++) in get_ribosum()
945 ribo[i][j] = dm_15_9[i][j]; in get_ribosum()
949 for (j = 0; j < 7; j++) in get_ribosum()
950 ribo[i][j] = dm_15_10[i][j]; in get_ribosum()
954 for (j = 0; j < 7; j++) in get_ribosum()
955 ribo[i][j] = dm_15_11[i][j]; in get_ribosum()
959 for (j = 0; j < 7; j++) in get_ribosum()
960 ribo[i][j] = dm_15_12[i][j]; in get_ribosum()
964 for (j = 0; j < 7; j++) in get_ribosum()
965 ribo[i][j] = dm_15_13[i][j]; in get_ribosum()
969 for (j = 0; j < 7; j++) in get_ribosum()
970 ribo[i][j] = dm_15_14[i][j]; in get_ribosum()
980 for (j = 0; j < 7; j++) in get_ribosum()
981 ribo[i][j] = dm_16_5[i][j]; in get_ribosum()
985 for (j = 0; j < 7; j++) in get_ribosum()
986 ribo[i][j] = dm_16_6[i][j]; in get_ribosum()
990 for (j = 0; j < 7; j++) in get_ribosum()
991 ribo[i][j] = dm_16_7[i][j]; in get_ribosum()
995 for (j = 0; j < 7; j++) in get_ribosum()
996 ribo[i][j] = dm_16_8[i][j]; in get_ribosum()
1000 for (j = 0; j < 7; j++) in get_ribosum()
1001 ribo[i][j] = dm_16_9[i][j]; in get_ribosum()
1005 for (j = 0; j < 7; j++) in get_ribosum()
1006 ribo[i][j] = dm_16_10[i][j]; in get_ribosum()
1010 for (j = 0; j < 7; j++) in get_ribosum()
1011 ribo[i][j] = dm_16_11[i][j]; in get_ribosum()
1015 for (j = 0; j < 7; j++) in get_ribosum()
1016 ribo[i][j] = dm_16_12[i][j]; in get_ribosum()
1020 for (j = 0; j < 7; j++) in get_ribosum()
1021 ribo[i][j] = dm_16_13[i][j]; in get_ribosum()
1025 for (j = 0; j < 7; j++) in get_ribosum()
1026 ribo[i][j] = dm_16_14[i][j]; in get_ribosum()
1030 for (j = 0; j < 7; j++) in get_ribosum()
1031 ribo[i][j] = dm_16_15[i][j]; in get_ribosum()
1041 for (j = 0; j < 7; j++) in get_ribosum()
1042 ribo[i][j] = dm_17_5[i][j]; in get_ribosum()
1046 for (j = 0; j < 7; j++) in get_ribosum()
1047 ribo[i][j] = dm_17_6[i][j]; in get_ribosum()
1051 for (j = 0; j < 7; j++) in get_ribosum()
1052 ribo[i][j] = dm_17_7[i][j]; in get_ribosum()
1056 for (j = 0; j < 7; j++) in get_ribosum()
1057 ribo[i][j] = dm_17_8[i][j]; in get_ribosum()
1061 for (j = 0; j < 7; j++) in get_ribosum()
1062 ribo[i][j] = dm_17_9[i][j]; in get_ribosum()
1066 for (j = 0; j < 7; j++) in get_ribosum()
1067 ribo[i][j] = dm_17_10[i][j]; in get_ribosum()
1071 for (j = 0; j < 7; j++) in get_ribosum()
1072 ribo[i][j] = dm_17_11[i][j]; in get_ribosum()
1076 for (j = 0; j < 7; j++) in get_ribosum()
1077 ribo[i][j] = dm_17_12[i][j]; in get_ribosum()
1081 for (j = 0; j < 7; j++) in get_ribosum()
1082 ribo[i][j] = dm_17_13[i][j]; in get_ribosum()
1086 for (j = 0; j < 7; j++) in get_ribosum()
1087 ribo[i][j] = dm_17_14[i][j]; in get_ribosum()
1091 for (j = 0; j < 7; j++) in get_ribosum()
1092 ribo[i][j] = dm_17_15[i][j]; in get_ribosum()
1096 for (j = 0; j < 7; j++) in get_ribosum()
1097 ribo[i][j] = dm_17_16[i][j]; in get_ribosum()
1107 for (j = 0; j < 7; j++) in get_ribosum()
1108 ribo[i][j] = dm_18_5[i][j]; in get_ribosum()
1112 for (j = 0; j < 7; j++) in get_ribosum()
1113 ribo[i][j] = dm_18_6[i][j]; in get_ribosum()
1117 for (j = 0; j < 7; j++) in get_ribosum()
1118 ribo[i][j] = dm_18_7[i][j]; in get_ribosum()
1122 for (j = 0; j < 7; j++) in get_ribosum()
1123 ribo[i][j] = dm_18_8[i][j]; in get_ribosum()
1127 for (j = 0; j < 7; j++) in get_ribosum()
1128 ribo[i][j] = dm_18_9[i][j]; in get_ribosum()
1132 for (j = 0; j < 7; j++) in get_ribosum()
1133 ribo[i][j] = dm_18_10[i][j]; in get_ribosum()
1137 for (j = 0; j < 7; j++) in get_ribosum()
1138 ribo[i][j] = dm_18_11[i][j]; in get_ribosum()
1142 for (j = 0; j < 7; j++) in get_ribosum()
1143 ribo[i][j] = dm_18_12[i][j]; in get_ribosum()
1147 for (j = 0; j < 7; j++) in get_ribosum()
1148 ribo[i][j] = dm_18_13[i][j]; in get_ribosum()
1152 for (j = 0; j < 7; j++) in get_ribosum()
1153 ribo[i][j] = dm_18_14[i][j]; in get_ribosum()
1157 for (j = 0; j < 7; j++) in get_ribosum()
1158 ribo[i][j] = dm_18_15[i][j]; in get_ribosum()
1162 for (j = 0; j < 7; j++) in get_ribosum()
1163 ribo[i][j] = dm_18_16[i][j]; in get_ribosum()
1167 for (j = 0; j < 7; j++) in get_ribosum()
1168 ribo[i][j] = dm_18_17[i][j]; in get_ribosum()
1178 for (j = 0; j < 7; j++) in get_ribosum()
1179 ribo[i][j] = dm_19_5[i][j]; in get_ribosum()
1183 for (j = 0; j < 7; j++) in get_ribosum()
1184 ribo[i][j] = dm_19_6[i][j]; in get_ribosum()
1188 for (j = 0; j < 7; j++) in get_ribosum()
1189 ribo[i][j] = dm_19_7[i][j]; in get_ribosum()
1193 for (j = 0; j < 7; j++) in get_ribosum()
1194 ribo[i][j] = dm_19_8[i][j]; in get_ribosum()
1198 for (j = 0; j < 7; j++) in get_ribosum()
1199 ribo[i][j] = dm_19_9[i][j]; in get_ribosum()
1203 for (j = 0; j < 7; j++) in get_ribosum()
1204 ribo[i][j] = dm_19_10[i][j]; in get_ribosum()
1208 for (j = 0; j < 7; j++) in get_ribosum()
1209 ribo[i][j] = dm_19_11[i][j]; in get_ribosum()
1213 for (j = 0; j < 7; j++) in get_ribosum()
1214 ribo[i][j] = dm_19_12[i][j]; in get_ribosum()
1218 for (j = 0; j < 7; j++) in get_ribosum()
1219 ribo[i][j] = dm_19_13[i][j]; in get_ribosum()
1223 for (j = 0; j < 7; j++) in get_ribosum()
1224 ribo[i][j] = dm_19_14[i][j]; in get_ribosum()
1228 for (j = 0; j < 7; j++) in get_ribosum()
1229 ribo[i][j] = dm_19_15[i][j]; in get_ribosum()
1233 for (j = 0; j < 7; j++) in get_ribosum()
1234 ribo[i][j] = dm_19_16[i][j]; in get_ribosum()
1238 for (j = 0; j < 7; j++) in get_ribosum()
1239 ribo[i][j] = dm_19_17[i][j]; in get_ribosum()
1243 for (j = 0; j < 7; j++) in get_ribosum()
1244 ribo[i][j] = dm_19_18[i][j]; in get_ribosum()
1254 for (j = 0; j < 7; j++) in get_ribosum()
1255 ribo[i][j] = dm_20_5[i][j]; in get_ribosum()
1259 for (j = 0; j < 7; j++) in get_ribosum()
1260 ribo[i][j] = dm_20_6[i][j]; in get_ribosum()
1264 for (j = 0; j < 7; j++) in get_ribosum()
1265 ribo[i][j] = dm_20_7[i][j]; in get_ribosum()
1269 for (j = 0; j < 7; j++) in get_ribosum()
1270 ribo[i][j] = dm_20_8[i][j]; in get_ribosum()
1274 for (j = 0; j < 7; j++) in get_ribosum()
1275 ribo[i][j] = dm_20_9[i][j]; in get_ribosum()
1279 for (j = 0; j < 7; j++) in get_ribosum()
1280 ribo[i][j] = dm_20_10[i][j]; in get_ribosum()
1284 for (j = 0; j < 7; j++) in get_ribosum()
1285 ribo[i][j] = dm_20_11[i][j]; in get_ribosum()
1289 for (j = 0; j < 7; j++) in get_ribosum()
1290 ribo[i][j] = dm_20_12[i][j]; in get_ribosum()
1294 for (j = 0; j < 7; j++) in get_ribosum()
1295 ribo[i][j] = dm_20_13[i][j]; in get_ribosum()
1299 for (j = 0; j < 7; j++) in get_ribosum()
1300 ribo[i][j] = dm_20_14[i][j]; in get_ribosum()
1304 for (j = 0; j < 7; j++) in get_ribosum()
1305 ribo[i][j] = dm_20_15[i][j]; in get_ribosum()
1309 for (j = 0; j < 7; j++) in get_ribosum()
1310 ribo[i][j] = dm_20_16[i][j]; in get_ribosum()
1314 for (j = 0; j < 7; j++) in get_ribosum()
1315 ribo[i][j] = dm_20_17[i][j]; in get_ribosum()
1319 for (j = 0; j < 7; j++) in get_ribosum()
1320 ribo[i][j] = dm_20_18[i][j]; in get_ribosum()
1324 for (j = 0; j < 7; j++) in get_ribosum()
1325 ribo[i][j] = dm_20_19[i][j]; in get_ribosum()