// Part C of Fig. 2 from DeSantis et al.
if((isalpha(newTemplateAlign[i]) != isalpha(tempAln[i]))){ //if there is a discrepancy between the regapped
// Part C of Fig. 2 from DeSantis et al.
if((isalpha(newTemplateAlign[i]) != isalpha(tempAln[i]))){ //if there is a discrepancy between the regapped
// Part D of Fig. 2 from DeSantis et al. // template sequence and the official template sequence
for(leftIndex=i-1;leftIndex>=0;leftIndex--){ // then we've got problems...
// Part D of Fig. 2 from DeSantis et al. // template sequence and the official template sequence
for(leftIndex=i-1;leftIndex>=0;leftIndex--){ // then we've got problems...
if(candAln.length() != tempAln.length()){ // if the regapped candidate sequence is longer than the official
removeExtraGaps(candAln, tempAln, newTemplateAlign);// template alignment then we need to do steps C-F in Fig.
} // 2 of Desantis et al.
if(candAln.length() != tempAln.length()){ // if the regapped candidate sequence is longer than the official
removeExtraGaps(candAln, tempAln, newTemplateAlign);// template alignment then we need to do steps C-F in Fig.
} // 2 of Desantis et al.