| 1 | /*** |
|---|
| 2 | Conservation value for a column in an MSA is defined as the number |
|---|
| 3 | of times the most common letter appears divided by the number of |
|---|
| 4 | sequences. |
|---|
| 5 | ***/ |
|---|
| 6 | |
|---|
| 7 | #include "muscle.h" |
|---|
| 8 | #include "msa.h" |
|---|
| 9 | #include <math.h> |
|---|
| 10 | |
|---|
| 11 | double MSA::GetAvgCons() const |
|---|
| 12 | { |
|---|
| 13 | assert(GetSeqCount() > 0); |
|---|
| 14 | double dSum = 0; |
|---|
| 15 | unsigned uNonGapColCount = 0; |
|---|
| 16 | for (unsigned uColIndex = 0; uColIndex < GetColCount(); ++uColIndex) |
|---|
| 17 | { |
|---|
| 18 | if (!IsGapColumn(uColIndex)) |
|---|
| 19 | { |
|---|
| 20 | dSum += GetCons(uColIndex); |
|---|
| 21 | ++uNonGapColCount; |
|---|
| 22 | } |
|---|
| 23 | } |
|---|
| 24 | assert(uNonGapColCount > 0); |
|---|
| 25 | double dAvg = dSum / uNonGapColCount; |
|---|
| 26 | assert(dAvg > 0 && dAvg <= 1); |
|---|
| 27 | return dAvg; |
|---|
| 28 | } |
|---|
| 29 | |
|---|
| 30 | double MSA::GetCons(unsigned uColIndex) const |
|---|
| 31 | { |
|---|
| 32 | unsigned Counts[MAX_ALPHA]; |
|---|
| 33 | for (unsigned uLetter = 0; uLetter < g_AlphaSize; ++uLetter) |
|---|
| 34 | Counts[uLetter] = 0; |
|---|
| 35 | |
|---|
| 36 | unsigned uMaxCount = 0; |
|---|
| 37 | for (unsigned uSeqIndex = 0; uSeqIndex < GetSeqCount(); ++uSeqIndex) |
|---|
| 38 | { |
|---|
| 39 | if (IsGap(uSeqIndex, uColIndex)) |
|---|
| 40 | continue; |
|---|
| 41 | char c = GetChar(uSeqIndex, uColIndex); |
|---|
| 42 | c = toupper(c); |
|---|
| 43 | if ('X' == c || 'B' == c || 'Z' == c) |
|---|
| 44 | continue; |
|---|
| 45 | unsigned uLetter = GetLetter(uSeqIndex, uColIndex); |
|---|
| 46 | unsigned uCount = Counts[uLetter] + 1; |
|---|
| 47 | if (uCount > uMaxCount) |
|---|
| 48 | uMaxCount = uCount; |
|---|
| 49 | Counts[uLetter] = uCount; |
|---|
| 50 | } |
|---|
| 51 | |
|---|
| 52 | // Cons is undefined for all-gap column |
|---|
| 53 | if (0 == uMaxCount) |
|---|
| 54 | { |
|---|
| 55 | // assert(false); |
|---|
| 56 | return 1; |
|---|
| 57 | } |
|---|
| 58 | |
|---|
| 59 | double dCons = (double) uMaxCount / (double) GetSeqCount(); |
|---|
| 60 | assert(dCons > 0 && dCons <= 1); |
|---|
| 61 | return dCons; |
|---|
| 62 | } |
|---|
| 63 | |
|---|
| 64 | // Perecent identity of a pair of sequences. |
|---|
| 65 | // Positions with one or both gapped are ignored. |
|---|
| 66 | double MSA::GetPctIdentityPair(unsigned uSeqIndex1, unsigned uSeqIndex2) const |
|---|
| 67 | { |
|---|
| 68 | const unsigned uColCount = GetColCount(); |
|---|
| 69 | unsigned uPosCount = 0; |
|---|
| 70 | unsigned uSameCount = 0; |
|---|
| 71 | for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) |
|---|
| 72 | { |
|---|
| 73 | const char c1 = GetChar(uSeqIndex1, uColIndex); |
|---|
| 74 | const char c2 = GetChar(uSeqIndex2, uColIndex); |
|---|
| 75 | if (IsGapChar(c1) || IsGapChar(c2)) |
|---|
| 76 | continue; |
|---|
| 77 | if (c1 == c2) |
|---|
| 78 | ++uSameCount; |
|---|
| 79 | ++uPosCount; |
|---|
| 80 | } |
|---|
| 81 | if (0 == uPosCount) |
|---|
| 82 | return 0; |
|---|
| 83 | return (double) uSameCount / (double) uPosCount; |
|---|
| 84 | } |
|---|
| 85 | |
|---|
| 86 | // Perecent group identity of a pair of sequences. |
|---|
| 87 | // Positions with one or both gapped are ignored. |
|---|
| 88 | double MSA::GetPctGroupIdentityPair(unsigned uSeqIndex1, |
|---|
| 89 | unsigned uSeqIndex2) const |
|---|
| 90 | { |
|---|
| 91 | extern unsigned ResidueGroup[]; |
|---|
| 92 | |
|---|
| 93 | const unsigned uColCount = GetColCount(); |
|---|
| 94 | unsigned uPosCount = 0; |
|---|
| 95 | unsigned uSameCount = 0; |
|---|
| 96 | for (unsigned uColIndex = 0; uColIndex < uColCount; ++uColIndex) |
|---|
| 97 | { |
|---|
| 98 | if (IsGap(uSeqIndex1, uColIndex)) |
|---|
| 99 | continue; |
|---|
| 100 | if (IsGap(uSeqIndex2, uColIndex)) |
|---|
| 101 | continue; |
|---|
| 102 | if (IsWildcard(uSeqIndex1, uColIndex)) |
|---|
| 103 | continue; |
|---|
| 104 | if (IsWildcard(uSeqIndex2, uColIndex)) |
|---|
| 105 | continue; |
|---|
| 106 | |
|---|
| 107 | const unsigned uLetter1 = GetLetter(uSeqIndex1, uColIndex); |
|---|
| 108 | const unsigned uLetter2 = GetLetter(uSeqIndex2, uColIndex); |
|---|
| 109 | const unsigned uGroup1 = ResidueGroup[uLetter1]; |
|---|
| 110 | const unsigned uGroup2 = ResidueGroup[uLetter2]; |
|---|
| 111 | if (uGroup1 == uGroup2) |
|---|
| 112 | ++uSameCount; |
|---|
| 113 | ++uPosCount; |
|---|
| 114 | } |
|---|
| 115 | if (0 == uPosCount) |
|---|
| 116 | return 0; |
|---|
| 117 | return (double) uSameCount / (double) uPosCount; |
|---|
| 118 | } |
|---|
