}
//********************************************************************************************************************
//this function will jump over commented out sequences, but if the last sequence in a file is commented out it makes a blank seq
+Sequence::Sequence(ifstream& fastaFile, string& extraInfo, bool getInfo){
+ try {
+ m = MothurOut::getInstance();
+ initialize();
+ fastaFile >> name;
+ extraInfo = "";
+
+ if (name.length() != 0) {
+
+ name = name.substr(1);
+
+ string sequence;
+
+ //read comments
+ while ((name[0] == '#') && fastaFile) {
+ while (!fastaFile.eof()) { char c = fastaFile.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ sequence = getCommentString(fastaFile);
+
+ if (fastaFile) {
+ fastaFile >> name;
+ name = name.substr(1);
+ }else {
+ name = "";
+ break;
+ }
+ }
+
+ //read info after sequence name
+ while (!fastaFile.eof()) {
+ char c = fastaFile.get();
+ if (c == 10 || c == 13){ break; }
+ extraInfo += c;
+ }
+
+ int numAmbig = 0;
+ sequence = getSequenceString(fastaFile, numAmbig);
+
+ setAligned(sequence);
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
+
+ if ((numAmbig / (float) numBases) > 0.25) { m->mothurOut("[WARNING]: We found more than 25% of the bases in sequence " + name + " to be ambiguous. Mothur is not setup to process protein sequences."); m->mothurOutEndLine(); }
+
+ }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");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+//this function will jump over commented out sequences, but if the last sequence in a file is commented out it makes a blank seq
Sequence::Sequence(ifstream& fastaFile, string JustUnaligned){
try {
m = MothurOut::getInstance();
int Sequence::getStartPos(){
if(startPos == -1){
for(int j = 0; j < alignmentLength; j++) {
- if(aligned[j] != '.'){
+ if((aligned[j] != '.')&&(aligned[j] != '-')){
startPos = j + 1;
break;
}
int Sequence::getEndPos(){
if(endPos == -1){
for(int j=alignmentLength-1;j>=0;j--){
- if(aligned[j] != '.'){
+ if((aligned[j] != '.')&&(aligned[j] != '-')){
endPos = j + 1;
break;
}