int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>& thisSeqs, string group){
try {
set<int> lengths;
alignSeqs.clear();
map<string, string>::iterator it;
bool error = false;
map<string, int> thisCount;
if (countfile != "") { thisCount = cparser->getCountTable(group); }
for (int i = 0; i < thisSeqs.size(); i++) {
if (m->control_pressed) { return 0; }
if (namefile != "") {
it = thisName.find(thisSeqs[i].getName());
//should never be true since parser checks for this
if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; }
else{
//get number of reps
int numReps = 1;
for(int j=0;j<(it->second).length();j++){
if((it->second)[j] == ','){ numReps++; }
}
seqPNode tempNode(numReps, thisSeqs[i], it->second);
alignSeqs.push_back(tempNode);
lengths.insert(thisSeqs[i].getAligned().length());
}
}else { //no names file, you are identical to yourself
int numRep = 1;
if (countfile != "") {
map<string, int>::iterator it2 = thisCount.find(thisSeqs[i].getName());
//should never be true since parser checks for this
if (it2 == thisCount.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); error = true; }
else { numRep = it2->second; }
}
seqPNode tempNode(numRep, thisSeqs[i], thisSeqs[i].getName());
alignSeqs.push_back(tempNode);
lengths.insert(thisSeqs[i].getAligned().length());
}
}
if (lengths.size() > 1) { error = true; m->mothurOut("[ERROR]: your sequences are not all the same length. pre.cluster requires sequences to be aligned."); m->mothurOutEndLine(); }
else if (lengths.size() == 1) { length = *(lengths.begin()); }
//sanity check
if (error) { m->control_pressed = true; }
thisSeqs.clear();
return alignSeqs.size();
}
catch(exception& e) {
m->errorOut(e, "PreClusterCommand", "loadSeqs");
exit(1);
}
}
int PreClusterCommand::readFASTA(){
try {
//ifstream inNames;
ifstream inFasta;
m->openInputFile(fastafile, inFasta);
set<int> lengths;
while (!inFasta.eof()) {
if (m->control_pressed) { inFasta.close(); return 0; }
Sequence seq(inFasta); m->gobble(inFasta);
if (seq.getName() != "") { //can get "" if commented line is at end of fasta file
if (namefile != "") {
itSize = sizes.find(seq.getName());
if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
else{
seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
alignSeqs.push_back(tempNode);
lengths.insert(seq.getAligned().length());
}
}else { //no names file, you are identical to yourself
int numRep = 1;
if (countfile != "") { numRep = ct.getNumSeqs(seq.getName()); }
seqPNode tempNode(numRep, seq, seq.getName());
alignSeqs.push_back(tempNode);
lengths.insert(seq.getAligned().length());
}
}
}
inFasta.close();
if (lengths.size() > 1) { method = "unaligned"; }
else if (lengths.size() == 1) { method = "aligned"; }
length = *(lengths.begin());
return alignSeqs.size();
}
catch(exception& e) {
m->errorOut(e, "PreClusterCommand", "readFASTA");
exit(1);
}
}
ListNode * merge(ListNode *lhs, ListNode *rhs) {
if (lhs == NULL && rhs == NULL) {
return NULL;
}else if (lhs == NULL) {
return rhs;
}else if (rhs == NULL) {
return lhs;
}
ListNode tempNode(0);
ListNode *p = &tempNode;
while (lhs && rhs) {
if (lhs->val < rhs->val) {
p->next = lhs;
lhs = lhs->next;
}else {
p->next = rhs;
rhs = rhs->next;
}
p = p->next;
}
if (lhs) {
p->next = lhs;
}
if (rhs) {
p->next = rhs;
}
return tempNode.next;
}
ListNode* reverseBetween(ListNode* head, int m, int n) {
if (head == NULL) {
return NULL;
}
ListNode tempNode(0);
tempNode.next = head;
ListNode *prev = &tempNode;
//move to m-1 elements
for (int i = 1; i < m; ++i) {
prev = prev->next;
}
ListNode *pm = prev->next;
//reverse m to n elements
for (int i = m; i < n; ++i) {
ListNode *pn = pm->next;
pm->next = pn->next;
pn->next = prev->next;
prev->next = pn;
}
return tempNode.next;
}