}
else{
-
if(tempAln[0] == '-'){
int pairwiseAlignmentLength = tempAln.length(); // we need to make sure that the candidate sequence alignment
for(int i=0;i<pairwiseAlignmentLength;i++){ // starts where the template sequence alignment starts, if it
}
}
}
-
int pairwiseAlignmentLength = tempAln.length();
if(tempAln[pairwiseAlignmentLength-1] == '-'){ // we need to make sure that the candidate sequence alignment
for(int i=pairwiseAlignmentLength-1; i>=0; i--){// ends where the template sequence alignment ends, if it runs
break;
}
}
-
-
+
for(rightIndex=i+1;rightIndex<longAlignmentLength-1;rightIndex++){
if(!isalpha(candAln[rightIndex])){
rightRoom = 1; //count how far it is to the nearest gap on the RIGHT side of the anomaly
errorOut(e, "Nast", "removeExtraGaps");
exit(1);
}
-
}
/**************************************************************************************************/
newTemplateAlign += tempAln[fullAlignIndex];// pairwise sequences
fullAlignIndex++;
}
-
+
string lastLoop = "";
while(pairwiseAlignIndex<pairwiseLength){