void Chain::turnover ()
{
stack<Part*> stack_part;
const int numparts = listOfParts.size ();
for (int i=0; i < numparts; i++)
{
Part* p = listOfParts[i];
stack_part.push (p);
if (p->getPartType () == "ForwardDNA")
p->setPartType ("ReverseDNA");
else if (p->getPartType () == "ReverseDNA")
p->setPartType ("ForwardDNA");
}
listOfParts.clear ();
for (int i=0; i < numparts; i++) {
listOfParts.push_back (stack_part.top ());
stack_part.pop ();
}
// reset unicode
unicode = genUnicode (0, listOfParts.size ()-1, true);
}
void Chain::__add_chain_prefix (
const string& prefix
)
{
for (int i=0; i<listOfParts.size (); i++) {
Part* p = listOfParts[i];
p->partLabel = prefix + p->partLabel;
}
genUnicode (0, listOfParts.size ()-1, true);
}
bool Chain::isCsymm ()
{
// is this chain a DNA chain?
this->setIsDNA ();
// is this chain a RNA chain?
this->setIsRNA ();
// yes
if (isDNA)
{
string fw_unicode = genUnicode (0, listOfParts.size ()-1, true);
string rev_unicode = genUnicode (0, listOfParts.size ()-1, false);
if (rev_unicode < fw_unicode) {turnover (); unicode = rev_unicode; return false;}
else if (rev_unicode > fw_unicode) {unicode = fw_unicode; return false;}
else {unicode = fw_unicode; return true;}
}
else
{
unicode = genUnicode (0, listOfParts.size ()-1, true);
return false;
}
}
bool Chain::match (
const Chain* c,
vector<cMatchType>& xyz
) const
{
//
// find parts of non-substituent type
//
vector<markType> ns_t;
vector<cMatchType> asmb;
bool start = true;
int numParts = c->listOfParts.size ();
for (int cnt =0; cnt < listOfParts.size (); cnt++)
{
Part* p = listOfParts[cnt];
string ctg = p->getPartCategory ();
if (ctg != "substituent")
{
if (start)
{
ns_t.push_back (make_pair (cnt, 0));
start = false;
}
}
else
{
ns_t.back ().second = cnt-1;
start = true;
}
}
if (ns_t.size () > 0)
{
vector< markType >* m_pos =
new vector< markType > [ns_t.size ()];
//
// for each non-substituent part, find its possible
// matching points in this chain
//
int permAll = 0;
for (int cnt =0; cnt < ns_t.size (); cnt++)
{
int start = ns_t[cnt].first;
int end = ns_t[cnt].second;
int diff = end-start;
Part* ps = listOfParts[start];
Part* pe = listOfParts[end];
string mkey = genUnicode (ps, pe);
for (string::size_type pos = 0;
(pos = unicode.find_first_of (mkey, pos))
!= string::npos; pos++)
{
int spos = count (unicode.begin (), unicode.begin ()+pos, ']');
int epos = spos + diff;
m_pos[cnt].push_back (make_pair (spos, epos));
}
if (m_pos[cnt].size () == 0)
{
delete [] m_pos;
return 0;
}
else permAll *= m_pos[cnt].size ();
}
//
// find possible matching combinations
//
for (int i =0; i < permAll; i++)
{
int lastp = -1;
cMatchType tmp;
int divide = i;
for (int j=0; j< ns_t.size (); j++)
{
markType p = m_pos[j][divide % m_pos[j].size ()];
if (p.first <= lastp)
{
tmp.clear ();
break;
}
else
{
lastp = p.second;
tmp.push_back (p);
}
divide /= m_pos[j].size ();
}
assert (tmp.size () == ns_t.size ());
if (!tmp.empty ()) asmb.push_back (tmp);
}
delete [] m_pos;
}
//
// insert substituent pieces into asmb
//
for (int cnt =0; cnt < asmb.size (); cnt++)
{
int lastf1, lastf2;
lastf1 = lastf2 = 0;
bool found = true;
//
// *it ==> pair<int,int>
//
vector<cMatchType> pm;
cMatchType::const_iterator it = asmb[cnt].begin ();
vector<cMatchType> tmp;
bool mok = substituent_m (
0, ns_t[0].first-1, 0, it->first-1, c, tmp
);
if (mok)
{
for (int i = 0; i < tmp.size (); i++)
pm.push_back (tmp[i]);
}
else continue;
//
for (int cnt2 =0; cnt2 < ns_t.size (); cnt2++, it++)
{
int start1 = ns_t[cnt2].first;
int end1 = ns_t[cnt2].second;
int start2 = it->first;
int end2 = it->second;
//
// add non-substituent type matching
//
for (int cnt3 =0; cnt3 < pm.size (); cnt3++)
{
for (int k =start2; k <= end2; k++)
pm[cnt3].push_back (make_pair (k,k));
}
//
// add substituent type matching
//
bool mok = substituent_m (
lastf1, start1-1, lastf2, start2-1, c, tmp
);
if (mok)
{
vector<cMatchType>::iterator iter = pm.begin ();
int k = -1;
int currsize = pm.size ();
while (++k < currsize)
{
cMatchType tmp1 = pm[k];
pm.erase (iter + k);
// tmp ==> vector<cMatchType>
for (int i =0; i < tmp.size (); i++)
{
cMatchType tmp2 = tmp1;
tmp2.insert (tmp2.end (), tmp[i].begin (), tmp[i].end ());
pm.push_back (tmp2);
}
}
}
else
{
found = false;
break;
}
//
// update
//
lastf1 = end1+1;
lastf2 = end2+1;
}
if (!found) continue;
else
{
for (int i =0; i < pm.size (); i++)
xyz.push_back (pm[cnt]);
}
}
if (xyz.empty ()) return false;
return true;
}
