}
}
- while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
sequence = getSequenceString(fastaString);
setAligned(sequence);
//setUnaligned removes any gap characters for us
setUnaligned(sequence);
}else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
-
+
}
catch(exception& e) {
m->errorOut(e, "Sequence", "Sequence");
}
}
- while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
sequence = getSequenceString(fastaString);
//setUnaligned removes any gap characters for us
setUnaligned(sequence);
}else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
+
}
catch(exception& e) {
m->errorOut(e, "Sequence", "Sequence");
}
//read real sequence
- while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
sequence = getSequenceString(fastaFile);
-
+
setAligned(sequence);
//setUnaligned removes any gap characters for us
setUnaligned(sequence);
}else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
-
+
}
catch(exception& e) {
m->errorOut(e, "Sequence", "Sequence");
}
//read real sequence
- while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
sequence = getSequenceString(fastaFile);
//setUnaligned removes any gap characters for us
setUnaligned(sequence);
}else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
-
+
}
catch(exception& e) {
m->errorOut(e, "Sequence", "Sequence");
while(fastaFile){
letter=fastaFile.get();
if((letter == '\r') || (letter == '\n')){
- gobble(fastaFile); //in case its a \r\n situation
+ m->gobble(fastaFile); //in case its a \r\n situation
break;
}
}
while(fastaFile){
letter=fastaFile.get();
if((letter == '\r') || (letter == '\n')){
- gobble(fastaFile); //in case its a \r\n situation
+ m->gobble(fastaFile); //in case its a \r\n situation
break;
}
}
//********************************************************************************************************************
+void Sequence::removeAmbigBases(){
+
+ for(int j=0;j<alignmentLength;j++){
+ if(aligned[j] != 'A' && aligned[j] != 'T' && aligned[j] != 'G' && aligned[j] != 'C'){
+ aligned[j] = '-';
+ }
+ }
+ setUnaligned(aligned);
+}
+
+//********************************************************************************************************************
+
int Sequence::getLongHomoPolymer(){
if(longHomoPolymer == -1){
longHomoPolymer = 1;