/usr/share/hyphy/TemplateBatchFiles/dSdNTreeTools.ibf is in hyphy-common 2.2.6+dfsg-3build3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 | function ComputeScalingStencils (unused)
{
scalingStencils = {};
if (Columns(_Genetic_Code) != 64) {
fprintf (stdout, "\nError: _Genetic_Code is not properly defined\n");
}
else
{
nonStopCodonCount = 64;
for (k=0; k<64; k=k+1)
{
if (_Genetic_Code[k] == 10)
{
nonStopCodonCount = nonStopCodonCount - 1;
}
}
stencilMatrixNS = {nonStopCodonCount,nonStopCodonCount};
stencilMatrixS = {nonStopCodonCount,nonStopCodonCount};
hshift = 0;
for (h=0; h<64; h=h+1)
{
if (_Genetic_Code[h]==10)
{
hshift = hshift+1;
continue;
}
vshift = hshift;
for (v = h+1; v<64; v=v+1)
{
if (_Genetic_Code[v]==10)
{
vshift = vshift+1;
continue;
}
if (_Genetic_Code[h] == _Genetic_Code[v])
{
stencilMatrixS [h-hshift][v-vshift] = 1;
stencilMatrixS [v-vshift][h-hshift] = 1;
}
else
{
stencilMatrixNS [h-hshift][v-vshift] = 1;
stencilMatrixNS [v-vshift][h-hshift] = 1;
}
}
}
scalingStencils ["Syn"] = stencilMatrixS;
scalingStencils ["NonSyn"] = stencilMatrixNS;
}
return scalingStencils;
}
/*----------------------------------------------------------------------------------*/
function ReturnSandNSTrees (theStencil, treeID)
{
scaledTreeStrings = {};
BRANCH_LENGTH_STENCIL = theStencil["Syn"];
ExecuteCommands("scaledTreeStrings[\"Syn\"] = Format ("+treeID+", 1, 1);");
BRANCH_LENGTH_STENCIL = theStencil["NonSyn"];
ExecuteCommands("scaledTreeStrings[\"NonSyn\"] = Format ("+treeID+", 1, 1);");
BRANCH_LENGTH_STENCIL = 0;
return scaledTreeStrings;
}
/*----------------------------------------------------------------------------------*/
function ReturnVectorsOfCodonLengths (theStencil, treeID)
{
scaledVectors = {};
BRANCH_LENGTH_STENCIL = theStencil["Syn"];
ExecuteCommands("scaledVectors[\"Syn\"] = BranchLength ("+treeID+", -1);");
BRANCH_LENGTH_STENCIL = theStencil["NonSyn"];
ExecuteCommands("scaledVectors[\"NonSyn\"] = BranchLength ("+treeID+", -1);");
BRANCH_LENGTH_STENCIL = 0;
ExecuteCommands("scaledVectors[\"Total\"] = BranchLength ("+treeID+", -1);");
return scaledVectors;
}
/*----------------------------------------------------------------------------------*/
function ReturnCodonFormulas (theStencil, modelID)
{
scaledVectors = {};
BRANCH_LENGTH_STENCIL = theStencil["Syn"];
ExecuteCommands("GetString(_synFormula,`modelID`,-1);");
BRANCH_LENGTH_STENCIL = theStencil["NonSyn"];
ExecuteCommands("GetString(_nonSynFormula,`modelID`,-1);");
BRANCH_LENGTH_STENCIL = 0;
scaledVectors ["Syn"] = _synFormula;
scaledVectors ["NonSyn"] = _nonSynFormula;
return scaledVectors;
}
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