void AminoacidData::CreateMatrixFromNCL(GarliReader &reader){
NxsCharactersBlock *charblock;
int num=0, numNuc = -1;
do{
charblock = reader.GetCharactersBlock(num);
if(charblock->GetDataType() == NxsCharactersBlock::protein){
if(numNuc < 0) numNuc = num;
else{
throw ErrorException("Multiple characters/data blocks containing protein data found in Nexus datafile!\n\tEither combine the blocks or comment one out.");
}
}
else outman.UserMessage("Ignoring non-protein characters block from Nexus datafile");
num++;
}while(num < reader.NumCharBlocks());
if(numNuc < 0) throw ErrorException("No characters/data blocks containing protein data found in Nexus datafile!");
charblock = reader.GetCharactersBlock(numNuc);
if(charblock->GetNumActiveChar() < charblock->GetNChar()){
outman.UserMessageNoCR("Excluded characters:\n\t");
for(int c=0;c<charblock->GetNCharTotal();c++)
if(charblock->IsExcluded(c)) outman.UserMessageNoCR("%d ", c+1);
outman.UserMessage("");
}
// vector<unsigned> reducedToOrigCharMap = charblock->GetOrigIndexVector();
NxsTaxaBlock *taxablock = reader.GetTaxaBlock();
int numOrigTaxa = charblock->GetNTax();
int numActiveTaxa = charblock->GetNumActiveTaxa();
int numOrigChar = charblock->GetNChar();
int numActiveChar = charblock->GetNumActiveChar();
//int num_chars = reducedToOrigCharMap.size();
//cout << num_chars << endl;
NewMatrix( numActiveTaxa, numActiveChar );
// read in the data, including taxon names
int i=0;
for( int origTaxIndex = 0; origTaxIndex < numOrigTaxa; origTaxIndex++ ) {
if(charblock->IsActiveTaxon(origTaxIndex)){
//internally, blanks in taxon names will be stored as underscores
NxsString tlabel = taxablock->GetTaxonLabel(origTaxIndex);
tlabel.BlanksToUnderscores();
SetTaxonLabel( i, tlabel.c_str());
int j = 0;
bool firstAmbig = true;
for( int origIndex = 0; origIndex < numOrigChar; origIndex++ ) {
if(charblock->IsActiveChar(origIndex)){
unsigned char datum = '\0';
if(charblock->IsGapState(origTaxIndex, origIndex) == true) datum = 20;
else if(charblock->IsMissingState(origTaxIndex, origIndex) == true) datum = 20;
else{
int nstates = charblock->GetNumStates(origTaxIndex, origIndex);
//assert(nstates == 1);
//need to deal with the possibility of multiple states represented in matrix
//just convert to full ambiguity
if(nstates == 1)
datum = CharToDatum(charblock->GetState(origTaxIndex, origIndex, 0));
else{
if(firstAmbig){
outman.UserMessageNoCR("Partially ambiguous characters of taxon %s converted to full ambiguity:\n\t", TaxonLabel(origTaxIndex));
firstAmbig = false;
}
outman.UserMessageNoCR("%d ", origIndex+1);
datum = CharToDatum('?');
}
}
SetMatrix( i, j++, datum );
}
}
if(firstAmbig == false) outman.UserMessage("");
i++;
}
}
}
void DataMatrix::CreateMatrixFromNCL(GarliReader &reader){
NxsCharactersBlock *charblock = reader.GetCharactersBlock();
// vector<unsigned> reducedToOrigCharMap = charblock->GetOrigIndexVector();
NxsTaxaBlock *taxablock = reader.GetTaxaBlock();
int numOrigTaxa = charblock->GetNTax();
int numActiveTaxa = charblock->GetNumActiveTaxa();
int numOrigChar = charblock->GetNChar();
int numActiveChar = charblock->GetNumActiveChar();
//int num_chars = reducedToOrigCharMap.size();
//cout << num_chars << endl;
NewMatrix( numActiveTaxa, numActiveChar );
// read in the data, including taxon names
int i=0;
if(modSpec.IsAminoAcid() == false){
for( int origTaxIndex = 0; origTaxIndex < numOrigTaxa; origTaxIndex++ ) {
if(charblock->IsActiveTaxon(origTaxIndex)){
SetTaxonLabel( i, taxablock->GetTaxonLabel(origTaxIndex).c_str());
int j = 0;
for( int origIndex = 0; origIndex < numOrigChar; origIndex++ ) {
if(charblock->IsActiveChar(origIndex)){
unsigned char datum = '\0';
if(charblock->IsGapState(origTaxIndex, origIndex) == true) datum = 15;
else if(charblock->IsMissingState(origTaxIndex, origIndex) == true) datum = 15;
else{
int nstates = charblock->GetNumStates(origTaxIndex, origIndex);
for(int s=0;s<nstates;s++){
datum += CharToBitwiseRepresentation(charblock->GetState(origTaxIndex, origIndex, s));
}
}
SetMatrix( i, j++, datum );
}
}
i++;
}
}
}
else{
for( int origTaxIndex = 0; origTaxIndex < numOrigTaxa; origTaxIndex++ ) {
if(charblock->IsActiveTaxon(origTaxIndex)){
SetTaxonLabel( i, taxablock->GetTaxonLabel(origTaxIndex).c_str());
int j = 0;
for( int origIndex = 0; origIndex < numOrigChar; origIndex++ ) {
if(charblock->IsActiveChar(origIndex)){
unsigned char datum = '\0';
if(charblock->IsGapState(origTaxIndex, origIndex) == true) datum = 20;
else if(charblock->IsMissingState(origTaxIndex, origIndex) == true) datum = 20;
else{
int nstates = charblock->GetNumStates(origTaxIndex, origIndex);
assert(nstates == 1);
datum = CharToAminoAcidNumber(charblock->GetState(origTaxIndex, origIndex, 0));
/* for(int s=0;s<nstates;s++){
datum += CharToBitwiseRepresentation(charblock->GetState(origTaxIndex, origIndex, s));
}
*/ }
SetMatrix( i, j++, datum );
}
}
i++;
}
}
}
}
void NucleotideData::CreateMatrixFromNCL(GarliReader &reader){
NxsCharactersBlock *charblock;
int num=0, numNuc = -1;
do{
charblock = reader.GetCharactersBlock(num);
if(charblock->GetDataType() == NxsCharactersBlock::nucleotide ||
charblock->GetDataType() == NxsCharactersBlock::dna ||
charblock->GetDataType() == NxsCharactersBlock::rna){
if(numNuc < 0) numNuc = num;
else{
throw ErrorException("Multiple characters/data blocks containing nucleotide data found in Nexus datafile!\n\tEither combine the blocks or comment one out.");
}
}
else outman.UserMessage("Ignoring non-nucleotide characters block from Nexus datafile");
num++;
}while(num < reader.NumCharBlocks());
if(numNuc < 0) throw ErrorException("No characters/data blocks containing nucleotide data found in Nexus datafile!");
charblock = reader.GetCharactersBlock(numNuc);
if(charblock->GetNumActiveChar() < charblock->GetNChar()){
outman.UserMessageNoCR("Excluded characters:\n\t");
for(int c=0;c<charblock->GetNCharTotal();c++)
if(charblock->IsExcluded(c)) outman.UserMessageNoCR("%d ", c+1);
outman.UserMessage("");
}
// vector<unsigned> reducedToOrigCharMap = charblock->GetOrigIndexVector();
NxsTaxaBlock *taxablock = reader.GetTaxaBlock();
int numOrigTaxa = charblock->GetNTax();
int numActiveTaxa = charblock->GetNumActiveTaxa();
int numOrigChar = charblock->GetNChar();
int numActiveChar = charblock->GetNumActiveChar();
//int num_chars = reducedToOrigCharMap.size();
//cout << num_chars << endl;
NewMatrix( numActiveTaxa, numActiveChar );
// read in the data, including taxon names
int i=0;
for( int origTaxIndex = 0; origTaxIndex < numOrigTaxa; origTaxIndex++ ) {
if(charblock->IsActiveTaxon(origTaxIndex)){
//internally, blanks in taxon names will be stored as underscores
NxsString tlabel = taxablock->GetTaxonLabel(origTaxIndex);
tlabel.BlanksToUnderscores();
SetTaxonLabel( i, tlabel.c_str());
int j = 0;
for( int origIndex = 0; origIndex < numOrigChar; origIndex++ ) {
if(charblock->IsActiveChar(origIndex)){
unsigned char datum = '\0';
if(charblock->IsGapState(origTaxIndex, origIndex) == true) datum = 15;
else if(charblock->IsMissingState(origTaxIndex, origIndex) == true) datum = 15;
else{
int nstates = charblock->GetNumStates(origTaxIndex, origIndex);
for(int s=0;s<nstates;s++){
datum += CharToBitwiseRepresentation(charblock->GetState(origTaxIndex, origIndex, s));
}
}
SetMatrix( i, j++, datum );
}
}
i++;
}
}
}