/usr/share/hyphy/UserAddins/AAContent is in hyphy-common 2.2.7+dfsg-1.
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 | characterOrderIn = "ACDEFGHIKLMNPQRSTVWY";
SetDialogPrompt ("Protein data file:");
DataSet ds1 = ReadDataFile (PROMPT_FOR_FILE);
while (1)
{
fprintf (stdout, "1-based site to map (-1 to stop:):");
fscanf (stdin, "Number", siteToMap);
if (siteToMap < 0)
{
break;
}
mapSite (siteToMap);
}
function mapSite (aSite)
{
DataSetFilter f1 = CreateFilter (ds1, 1, siteIndex == (aSite-1));
HarvestFrequencies (freqs,f1,1,1,1);
freqs = freqs * f1.species;
rankedMatrix = {20,3}["freqs[_MATRIX_ELEMENT_ROW_]*(_MATRIX_ELEMENT_COLUMN_==0)+(_MATRIX_ELEMENT_COLUMN_==1)*_MATRIX_ELEMENT_ROW_"];
for (k=0; k<20; k=k+1)
{
rankedMatrix[k][2] = rankedMatrix[k][1]/40+rankedMatrix[k][0];
}
rankedMatrix = rankedMatrix%2;
fprintf (stdout, "$");
for (k=19; k>=0; k=k-1)
{
if (rankedMatrix[k][0]<1)
{
break;
}
fprintf (stdout, characterOrderIn[rankedMatrix[k][1]], "_{", rankedMatrix[k][0]$1, "}");
}
fprintf (stdout, "$\n");
return 0;
}
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