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Set alternate alphabet to exclude lowercase by default #10

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Set alternate alphabet to exclude lowercase by default #10

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af2e363
Remove alphabet dependency
joshuaroll Aug 18, 2020
9c9ff6f
Update plm.c
joshuaroll Aug 18, 2020
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12 changes: 3 additions & 9 deletions src/plm.c
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Original file line number Diff line number Diff line change
Expand Up @@ -373,14 +373,8 @@ alignment_t *MSARead(char *alignFile, options_t *options) {
for (int i = 0; i < ali->nSites; i++) siteValid[i] = 1;
if (ali->target >= 0) {
for (int i = 0; i < ali->nSites; i++) {
/* For proteins, remove lower case and gap columns */
if ((ali->alphabet == codesAA)
&& (seq(ali->target, i) < 0))
siteValid[i] = 0;
/* Discard gaps */
if ((ali->alphabet == codesAA)
|| (options->estimatorMAP == INFER_MAP_PLM_GAPREDUCE))
if (seq(ali->target, i) == 0) siteValid[i] = 0;
if (seq(ali->target, i) <= 0) siteValid[i] = 0;
}
nValidSites = 0;
for (int i = 0; i < ali->nSites; i++)
Expand Down Expand Up @@ -527,7 +521,7 @@ letter_t MSAReadCode(char c, char *alphabet, int nCodes) {
letter_t i = 0;

/* Protein-specific treatment of '.' */
if (alphabet == codesAA) if (c == '.') c = '-';
if (c == '.') c = '-'; // Assumes '.' are gaps in alphabet

/* Store lowercase characters as down-shifted by nCodes */
while ((i < nCodes - 1) && toupper(c) != alphabet[i]) i++;
Expand Down Expand Up @@ -1146,4 +1140,4 @@ void OutputCouplingScores(char *couplingsFile, const numeric_t *x,
fprintf(stderr, "Error writing coupling scores\n");
exit(1);
}
}
}