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Binary support #14

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18 changes: 16 additions & 2 deletions alignment.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -763,8 +763,22 @@ SeqType Alignment::detectSequenceType(StrVector &sequences) {
}
if (((double)num_nuc) / num_ungap > 0.9)
return SEQ_DNA;
if (((double)num_bin) / num_ungap > 0.9)
return SEQ_BINARY;
if (((double)num_bin) / num_ungap > 0.9) {
cout << "[BINARY-SEQUENCE-WARNING]" << endl;
cout << "Since the PLL library we are using only supports sequence of type DNA, the following process will treat the input as DNA (mapping 0 to A and 1 to G) and not break the property of resulting trees." << endl;
cout << "[BINARY-SEQUENCE-WARNING]" << endl;
cout << endl;

for (StrVector::iterator it = sequences.begin(); it != sequences.end(); it++) {
for (string::iterator i = it->begin(); i != it->end(); i++) {
if ((*i) == '0') *i = 'A';
if ((*i) == '1') *i = 'G';
if ((*i) == '-') *i = 'R';
}
}

return SEQ_DNA;
}
if (((double)num_alpha) / num_ungap > 0.9)
return SEQ_PROTEIN;
if (((double)(num_alpha+num_digit)) / num_ungap > 0.9)
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6 changes: 4 additions & 2 deletions phyloanalysis.cpp
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Expand Up @@ -2130,6 +2130,10 @@ void runPhyloAnalysis(Params &params) {
IQTree *tree;

/****************** read in alignment **********************/
if (strcmp(params.sequence_type, "BIN") == 0) {
params.sequence_type = "DNA";
}

if (params.partition_file) {
// Partition model analysis
if(params.partition_type){
Expand Down Expand Up @@ -2159,8 +2163,6 @@ void runPhyloAnalysis(Params &params) {
alignment = aln;
}
tree = new IQTree(alignment);


}

// if(params.maximum_parsimony && (params.gbo_replicates || params.sankoff_cost_file)){
Expand Down