}
}
- 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");
m = MothurOut::getInstance();
initialize();
fastaFile >> name;
-
+
if (name.length() != 0) {
name = name.substr(1);
}
//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;
}
}
else { return aligned; }
}
+//********************************************************************************************************************
+
+string Sequence::getInlineSeq(){
+ return name + '\t' + aligned;
+}
+
+
//********************************************************************************************************************
string Sequence::getPairwise(){
//********************************************************************************************************************
+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;
//********************************************************************************************************************
int Sequence::getStartPos(){
- if(endPos == -1){
+ if(startPos == -1){
for(int j = 0; j < alignmentLength; j++) {
if(aligned[j] != '.'){
startPos = j + 1;
//********************************************************************************************************************
+void Sequence::padToPos(int start){
+
+ for(int j = startPos-1; j < start-1; j++) {
+ aligned[j] = '.';
+ }
+ startPos = start;
+
+}
+
+//********************************************************************************************************************
+
int Sequence::getEndPos(){
if(endPos == -1){
for(int j=alignmentLength-1;j>=0;j--){
//********************************************************************************************************************
+void Sequence::padFromPos(int end){
+
+ for(int j = end; j < endPos; j++) {
+ aligned[j] = '.';
+ }
+ endPos = end;
+
+}
+
+//********************************************************************************************************************
+
bool Sequence::getIsAligned(){
return isAligned;
}
aligned = temp;
}
-/**************************************************************************************************/
+
+//********************************************************************************************************************
+
+void Sequence::trim(int length){
+
+ if(numBases > length){
+ unaligned = unaligned.substr(0,length);
+ numBases = length;
+ }
+
+}
+
+///**************************************************************************************************/