| 1 | #include "muscle.h" |
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| 2 | #include "tree.h" |
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| 3 | #include "textfile.h" |
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| 4 | |
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| 5 | unsigned Tree::GetAnyNonLeafNode() const |
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| 6 | { |
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| 7 | for (unsigned uNodeIndex = 0; uNodeIndex < m_uNodeCount; ++uNodeIndex) |
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| 8 | if (!IsLeaf(uNodeIndex)) |
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| 9 | return uNodeIndex; |
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| 10 | return NULL_NEIGHBOR; |
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| 11 | } |
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| 12 | |
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| 13 | void Tree::ToFile(TextFile &File) const |
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| 14 | { |
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| 15 | if (IsRooted()) |
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| 16 | { |
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| 17 | ToFileNodeRooted(File, m_uRootNodeIndex); |
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| 18 | File.PutString(";\n"); |
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| 19 | return; |
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| 20 | } |
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| 21 | |
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| 22 | // Unrooted. |
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| 23 | unsigned uNodeIndex = GetAnyNonLeafNode(); |
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| 24 | |
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| 25 | File.PutString("(\n"); |
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| 26 | ToFileNodeUnrooted(File, m_uNeighbor1[uNodeIndex], uNodeIndex); |
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| 27 | File.PutString(",\n"); |
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| 28 | ToFileNodeUnrooted(File, m_uNeighbor2[uNodeIndex], uNodeIndex); |
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| 29 | File.PutString(",\n"); |
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| 30 | ToFileNodeUnrooted(File, m_uNeighbor3[uNodeIndex], uNodeIndex); |
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| 31 | File.PutString(");\n"); |
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| 32 | } |
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| 33 | |
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| 34 | void Tree::ToFileNodeUnrooted(TextFile &File, unsigned uNodeIndex, unsigned uParent) const |
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| 35 | { |
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| 36 | assert(!IsRooted()); |
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| 37 | |
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| 38 | bool bGroup = !IsLeaf(uNodeIndex); |
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| 39 | if (bGroup) |
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| 40 | File.PutString("(\n"); |
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| 41 | |
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| 42 | if (IsLeaf(uNodeIndex)) |
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| 43 | File.PutString(GetName(uNodeIndex)); |
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| 44 | else |
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| 45 | { |
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| 46 | ToFileNodeUnrooted(File, GetFirstNeighbor(uNodeIndex, uParent), uNodeIndex); |
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| 47 | File.PutString(",\n"); |
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| 48 | ToFileNodeUnrooted(File, GetSecondNeighbor(uNodeIndex, uParent), uNodeIndex); |
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| 49 | } |
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| 50 | |
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| 51 | if (bGroup) |
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| 52 | File.PutString(")"); |
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| 53 | |
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| 54 | if (HasEdgeLength(uNodeIndex, uParent)) |
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| 55 | File.PutFormat(":%g", GetEdgeLength(uNodeIndex, uParent)); |
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| 56 | File.PutString("\n"); |
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| 57 | } |
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| 58 | |
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| 59 | void Tree::ToFileNodeRooted(TextFile &File, unsigned uNodeIndex) const |
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| 60 | { |
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| 61 | assert(IsRooted()); |
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| 62 | |
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| 63 | bool bGroup = !IsLeaf(uNodeIndex) || IsRoot(uNodeIndex); |
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| 64 | if (bGroup) |
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| 65 | File.PutString("(\n"); |
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| 66 | |
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| 67 | if (IsLeaf(uNodeIndex)) |
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| 68 | File.PutString(GetName(uNodeIndex)); |
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| 69 | else |
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| 70 | { |
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| 71 | ToFileNodeRooted(File, GetLeft(uNodeIndex)); |
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| 72 | File.PutString(",\n"); |
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| 73 | ToFileNodeRooted(File, GetRight(uNodeIndex)); |
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| 74 | } |
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| 75 | |
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| 76 | if (bGroup) |
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| 77 | File.PutString(")"); |
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| 78 | |
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| 79 | if (!IsRoot(uNodeIndex)) |
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| 80 | { |
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| 81 | unsigned uParent = GetParent(uNodeIndex); |
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| 82 | if (HasEdgeLength(uNodeIndex, uParent)) |
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| 83 | File.PutFormat(":%g", GetEdgeLength(uNodeIndex, uParent)); |
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| 84 | } |
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| 85 | File.PutString("\n"); |
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| 86 | } |
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