/**
* @method HandleNextPass [int:protected]
* @param token [NexusToken&] the token we are using for reading the data file
* @param offset [int&] the offset (see below)
*
* Called from within HandleMatrix, this function is used to deal with interleaved
* matrices. It is called once for each pass through the taxa.
*
* <P>The local variable jmax records the number of columns read in the current
* interleaved page and is used to determine the offset used for j in subsequent
* pages.
*/
int DistancesBlock::HandleNextPass( NexusToken& token, int& offset )
{
int i, j, k, jmax = 0, done = 0;
int i_first = 0;
if( triangle == lower )
i_first = offset;
int i_last = ntax;
for( i = i_first; i < i_last; i++ )
{
// Deal with taxon label if provided
//
if( labels && ( !newtaxa || offset>0 ) )
{
do {
token.SetLabileFlagBit( NexusToken::newlineIsToken );
token.GetNextToken();
} while( token.AtEOL() );
try {
k = taxa.FindTaxon( token.GetToken() );
if( taxonPos[i]==-1 )
taxonPos[i] = k;
else if( taxonPos[i] != k ) {
errormsg = "Taxon labeled ";
errormsg += token.GetToken();
errormsg += " is out of order compared to previous interleave pages";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
catch (std::out_of_range) {
errormsg = "Could not find ";
errormsg += token.GetToken();
errormsg += " among taxa previously defined";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
else if( labels && newtaxa ) {
do {
token.SetLabileFlagBit( NexusToken::newlineIsToken );
token.GetNextToken();
} while( token.AtEOL() );
taxa.AddTaxonLabel( token.GetToken() );
taxonPos[i] = i;
}
// Now deal with the row of distance values
//
int true_j = 0;
for( j = 0; j < ntax; j++ )
{
if( i == ntax-1 && j == ntax-1 ) {
done = 1;
}
if( i == ntax-1 && true_j == ntax-1 ) {
done = 1;
break;
}
if( i == ntax-1 && !diagonal && triangle==upper ) {
done = 1;
break;
}
if( !diagonal && triangle==lower && j == ntax-offset-1) {
done = 1;
break;
}
token.SetLabileFlagBit( NexusToken::newlineIsToken );
token.GetNextToken();
if( token.AtEOL() ) {
if( j > jmax ) {
jmax = j;
if( !diagonal && triangle == upper && i >= offset )
jmax++;
if( interleave && triangle == upper )
i_last = jmax + offset;
}
break;
}
true_j = j+offset;
if( triangle==upper && i > offset )
true_j += ( i - offset );
if( !diagonal && triangle==upper && i >= offset )
true_j++;
if( true_j == ntax ) {
errormsg = "Too many distances specified in row just read in";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
std::string t = token.GetToken();
if( token.GetTokenLength() == 1 && t[0] == missing )
SetMissing( i, true_j );
else
SetDistance( i, true_j, atof( t.c_str() ) );
}
}
offset += jmax;
if( done )
return 1;
else
return 0;
}
/**
* @method HandleFormatCommand [void:protected]
* @param token [NexusToken&] the token used to read from in
* @throws XNexus
*
* Called when FORMAT command needs to be parsed from within the
* DISTANCES block. Deals with everything after the token FORMAT
* up to and including the semicolon that terminates the FORMAT
* command.
*/
void DistancesBlock::HandleFormatCommand( NexusToken& token )
{
for(;;)
{
token.GetNextToken();
// token should either be ';' or the name of a subcommand
//
if( token.Equals(";") ) {
break;
}
else if( token.Equals("TRIANGLE") ) {
// this should be the equals sign
token.GetNextToken();
if( !token.Equals("=") ) {
errormsg = "Expecting '=' but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
// this should be LOWER, UPPER, or BOTH
token.GetNextToken();
if( token.Equals("LOWER") )
triangle = lower;
else if( token.Equals("UPPER") )
triangle = upper;
else if( token.Equals("BOTH") )
triangle = both;
else {
errormsg = "Expecting UPPER, LOWER, or BOTH but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
else if( token.Equals("DIAGONAL") ) {
diagonal = 1;
}
else if( token.Equals("NODIAGONAL") ) {
diagonal = 0;
}
else if( token.Equals("LABELS") ) {
labels = 1;
}
else if( token.Equals("NOLABELS") ) {
labels = 0;
}
else if( token.Equals("INTERLEAVE") ) {
interleave = 1;
}
else if( token.Equals("NOINTERLEAVE") ) {
interleave = 0;
}
else if( token.Equals("MISSING") ) {
// this should be the equals sign
token.GetNextToken();
if( !token.Equals("=") ) {
errormsg = "Expecting '=' but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
// this should be the missing data symbol
token.GetNextToken();
if( token.GetTokenLength() != 1 ) {
errormsg = "Missing data symbol specified (";
errormsg += token.GetToken();
errormsg += ") is invalid (must be a single character)";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
missing = token.GetToken()[0];
}
else {
errormsg = "Token specified (";
errormsg += token.GetToken();
errormsg += ") is an invalid subcommand for the FORMAT command";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
}
