NestedInteger deserialize(istringstream &in) {
int number;
if(in>>number) return NestedInteger(number); //如果开头是数字，那么一定是单个数的
in.clear();
in.get();
NestedInteger list;
while(in.peek() != ']')
{
list.add(deserialize(in));
if(in.peek()==',')
in.get();
}
in.get();
return list;
}
string get(istringstream & in)
{
while(true)
{
while(in.get()=='\"')
{
string result;
char buf;
while(true)
{
buf=in.get();
if(buf=='\"')
{
in.get();
return result;
}
result+=buf;
}
}
}
}
//********************************************************************************************************************
//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(istringstream& fastaString){
try {
m = MothurOut::getInstance();
initialize();
name = getSequenceName(fastaString);
if (!m->control_pressed) {
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
comment = getCommentString(fastaString);
int numAmbig = 0;
sequence = getSequenceString(fastaString, 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(); }
}