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remove duplicated parts in the function convertStateBack()
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alignment/alignment.cpp

Lines changed: 7 additions & 61 deletions
Original file line numberDiff line numberDiff line change
@@ -2061,70 +2061,16 @@ char Alignment::convertStateBack(char state) {
20612061
} else {
20622062
return '-';
20632063
}
2064+
case SEQ_GENOTYPE:
2065+
// genotype state
2066+
if (state < strlen(symbols_genotype)) {
2067+
return symbols_genotype[(int)state];
2068+
} else {
2069+
return '-';
2070+
}
20642071
default:
20652072
return STATE_INVALID;
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}
2067-
case SEQ_DNA: // DNA
2068-
switch (state) {
2069-
case 0:
2070-
return 'A';
2071-
case 1:
2072-
return 'C';
2073-
case 2:
2074-
return 'G';
2075-
case 3:
2076-
return 'T';
2077-
case 1+4+3:
2078-
return 'R'; // A or G, Purine
2079-
case 2+8+3:
2080-
return 'Y'; // C or T, Pyrimidine
2081-
case 1+8+3:
2082-
return 'W'; // A or T, Weak
2083-
case 2+4+3:
2084-
return 'S'; // G or C, Strong
2085-
case 1+2+3:
2086-
return 'M'; // A or C, Amino
2087-
case 4+8+3:
2088-
return 'K'; // G or T, Keto
2089-
case 2+4+8+3:
2090-
return 'B'; // C or G or T
2091-
case 1+2+8+3:
2092-
return 'H'; // A or C or T
2093-
case 1+4+8+3:
2094-
return 'D'; // A or G or T
2095-
case 1+2+4+3:
2096-
return 'V'; // A or G or C
2097-
default:
2098-
return '?'; // unrecognize character
2099-
}
2100-
return state;
2101-
case SEQ_PROTEIN: // Protein
2102-
if (state < 20)
2103-
return symbols_protein[(int)state];
2104-
else if (state == 20) return 'B';
2105-
else if (state == 21) return 'Z';
2106-
else if (state == 22) return 'J';
2107-
// else if (state == 4+8+19) return 'B';
2108-
// else if (state == 32+64+19) return 'Z';
2109-
else
2110-
return '-';
2111-
case SEQ_MORPH:
2112-
// morphological state
2113-
if (state < strlen(symbols_morph))
2114-
return symbols_morph[(int)state];
2115-
else
2116-
return '-';
2117-
case SEQ_GENOTYPE:
2118-
// genotype state
2119-
if (state < strlen(symbols_genotype))
2120-
return symbols_genotype[(int)state];
2121-
else
2122-
return '-';
2123-
2124-
default:
2125-
// unknown
2126-
return '*';
2127-
}
21282074
}
21292075

21302076
string Alignment::convertStateBackStr(StateType state) {

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