}
else{
list = new ListVector(nameMap->getListVector());
- if(nameMap->count(name)==0){ cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
+ if(nameMap->count(name)==0){ mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
}
char d;
}
Progress* reading;
-
+
if(square == 0){
reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2);
int index = 0;
-
+
for(int i=1;i<nseqs;i++){
fileHandle >> name;
matrixNames.push_back(name);
}
else{
- if(nameMap->count(name)==0){ cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
+ if(nameMap->count(name)==0){ mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
for(int j=0;j<i;j++){
fileHandle >> distance;
}
else{
- if(nameMap->count(name)==0){ cout << "Error: Sequence '" << name << "' was not found in the names file, please correct" << endl; }
+ if(nameMap->count(name)==0){ mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); mothurOutEndLine(); }
for(int j=0;j<nseqs;j++){
fileHandle >> distance;
list->setLabel("0");
fileHandle.close();
- if(nameMap != NULL){
+ /* if(nameMap != NULL){
for(int i=0;i<matrixNames.size();i++){
nameMap->erase(matrixNames[i]);
}
if(nameMap->size() > 0){
//should probably tell them what is missing if we missed something
- cout << "missed something" << '\t' << nameMap->size() << endl;
+ mothurOut("missed something\t" + toString(nameMap->size())); mothurOutEndLine();
}
- }
+ } */
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadPhylipMatrix class Function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "ReadPhylipMatrix", "read");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the ReadPhylipMatrix class function read. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-}
+ }
/***********************************************************************/
ReadPhylipMatrix::~ReadPhylipMatrix(){
- delete D;
- delete list;
+ // delete D;
+ // delete list;
}