initialize();
fastaString >> name;
- name = name.substr(1);
- string sequence;
-
- //read comments
- while ((name[0] == '#') && fastaString) {
- while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
- sequence = getCommentString(fastaString);
-
- if (fastaString) {
- fastaString >> name;
- name = name.substr(1);
- }else {
- name = "";
- break;
- }
- }
- while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ if (name.length() != 0) {
+
+ name = name.substr(1);
+ string sequence;
- sequence = getSequenceString(fastaString);
- setAligned(sequence);
- //setUnaligned removes any gap characters for us
- setUnaligned(sequence);
+ //read comments
+ while ((name[0] == '#') && fastaString) {
+ while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ sequence = getCommentString(fastaString);
+
+ if (fastaString) {
+ fastaString >> name;
+ name = name.substr(1);
+ }else {
+ name = "";
+ break;
+ }
+ }
+
+ 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");
initialize();
fastaString >> name;
- name = name.substr(1);
- string sequence;
-
- //read comments
- while ((name[0] == '#') && fastaString) {
- while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
- sequence = getCommentString(fastaString);
-
- if (fastaString) {
- fastaString >> name;
- name = name.substr(1);
- }else {
- name = "";
- break;
- }
- }
- while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ if (name.length() != 0) {
- sequence = getSequenceString(fastaString);
+ name = name.substr(1);
+ string sequence;
- //setUnaligned removes any gap characters for us
- setUnaligned(sequence);
+ //read comments
+ while ((name[0] == '#') && fastaString) {
+ while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+ sequence = getCommentString(fastaString);
+
+ if (fastaString) {
+ fastaString >> name;
+ name = name.substr(1);
+ }else {
+ name = "";
+ break;
+ }
+ }
+
+ 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");
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 = MothurOut::getInstance();
initialize();
fastaFile >> name;
- 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 (name.length() != 0) {
+ name = name.substr(1);
+ string sequence;
- if (fastaFile) {
- fastaFile >> name;
- name = name.substr(1);
- }else {
- name = "";
- break;
+ //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 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
-
- sequence = getSequenceString(fastaFile);
-
- //setUnaligned removes any gap characters for us
- setUnaligned(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
+
+ 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");