- fileHandle >> firstName >> secondName >> distance; // get the row and column names and distance
-
- if(nameMap->count(firstName)==0){
- cerr << "AError: Sequence '" << firstName << "' was not found in the names file, please correct\n";
- }
- if(nameMap->count(secondName)==0){
- cerr << "AError: Sequence '" << secondName << "' was not found in the names file, please correct\n";
- }
-
- if (distance == -1) { distance = 1000000; }
-
- if(distance < cutoff && nameMap->get(firstName) != nameMap->get(secondName)){
- if(nameMap->get(firstName) > nameMap->get(secondName)){
- PCell value(nameMap->get(firstName), nameMap->get(secondName), distance);
-
- if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
- refRow = nameMap->get(firstName);
- refCol = nameMap->get(secondName);
- D->addCell(value);
- }
- else if(refRow == nameMap->get(firstName) && refCol == nameMap->get(secondName)){
- lt = 0;
- }
- else{
- D->addCell(value);
- }
- }
- else if(nameMap->get(firstName) < nameMap->get(secondName)){
- PCell value(nameMap->get(secondName), nameMap->get(firstName), distance);
-
- if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...
- refRow = nameMap->get(firstName);
- refCol = nameMap->get(secondName);
- D->addCell(value);
- }
- else if(refRow == nameMap->get(secondName) && refCol == nameMap->get(firstName)){
- lt = 0;
- }
- else{
- D->addCell(value);
- }
- }
- reading->update(nameMap->get(firstName) * nseqs);
- }
- gobble(fileHandle);
+ if(itA == nameMap->end()){
+ cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n";
+ }
+ if(itB == nameMap->end()){
+ cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n";