R PPForest<L>::maxScore(const Algebra<R,L> &alg, size_type i, size_type j) const
{
R down, over;
if(j==0)
return 0;
if(isLeave(i))
{
over=maxScore(alg,rb(i),j-1);
return alg.replace(label(i),0,label(i),over);
}
else
{
down=maxScore(alg,i+1,noc(i));
over=maxScore(alg,rb(i),j-1);
return alg.replace(label(i),down,label(i),over);
}
}
R PPForest<L>::maxScore(const RNA_Algebra<R,L> &alg, Uint i, Uint j) const
{
R down, over;
if(j==0)
return 0;
if(isLeave(i))
{
over=maxScore(alg,rb(i),j-1);
return alg.replace(label(i),0,label(i),over);
}
else
{
down=maxScore(alg,i+1+1,noc(i)-2);
over=maxScore(alg,rb(i),j-1);
return alg.replacepair(label(i+1),label(i+1),down,label(getRightmostBrotherIndex(i+1)),label(getRightmostBrotherIndex(i+1)),over);
}
}
void RNAProfileAlignment::getSeqAli(string &seq,Uint row, Uint i, Uint j) const
{
if(i==0 && j==getMaxLength(0))
seq="";
if(j==0)
return;
// basepair=internal node
if(isPair(i))
{
getSeqAli(seq,row,i+1,noc(i));
getSeqAli(seq,row,rb(i),j-1);
}
else
{
// base=leaf
seq+=m_lb[i].columnStr[row];
getSeqAli(seq,row,rb(i),j-1);
}
}
int sc_main(int argc, char ** argv){
sc_report_handler::set_actions("/IEEE_Std_1666/deprecated", SC_DO_NOTHING);
system("set SC_SIGNAL_WRITE_CHECK=\"DISABLE\"");
printHeader();
for (int i = 1; i< argc; i++)
{
string args = string(argv[i]);
if (args == "-f")
{
i++;
if (i<argc && argv[i][0] !='-')
ga_configPath = string(argv[i]);
else {
cout << "Argument to '-f' is missing" << endl;
return 0;
}
}
else if (args == "-e")
{
i++;
if (i<argc && argv[i][0] !='-')
ga_elfPath = string(argv[i]);
else {
cout << "Argument to '-e' is missing" << endl;
return 0;
}
}
else{
cout << args <<" Recognized option" << endl;
return 0;
}
}
char nirgamHomeTempStr[100];
g_nirgamHome = rwDirInLinuxStyl(string(getcwd(nirgamHomeTempStr, 100)));
g_configHome = getDirOfFile(ga_configPath);
if(loadConfig(ga_configPath) == false)
return 1;
if(checkConfig() == false)
return 1;
printConfig(cout);
tryDir(gc_resultHome);
g_clkPeriod = 1/gc_simFreq;
g_simPeriod = g_clkPeriod * gc_simNum;
g_clock = new sc_clock("NW_CLOCK",g_clkPeriod, SC_NS);
g_a = analyze(gc_topoFile, cout);
if(g_a == NULL){
cout << "Error occurred. Exit Simulation" << endl; return 1;
}
g_tileNum = g_a->nodeNum;
if (gc_simMode == 1)
initStandardMode();
else if (gc_simMode == 2)
initDebugMode();
else if (gc_simMode == 3)
initSelfcheckMode();
NoC noc("noc", g_a);
noc.switch_cntrl(*g_clock);
g_tracker = new Tracker();
g_tracker->addProbes(noc);
g_tracker->printRouteTables();
//////////////////////////////////////////////////////////////////////////
// soclib tile
#ifdef SL_TILE
if (gc_tileType == 1){
cerr << "SLNIRGAM is used for soclib IP" << endl;
return 1;
}
sc_start(sc_time(0, SC_NS));
g_resetN = false;
sc_start(sc_time(1, SC_NS));
g_resetN = true;
#else
if (gc_tileType == 2){
cerr << "NIRGAM is used for generic IP" << endl;
return 1;
}
#endif
//////////////////////////////////////////////////////////////////////////
if (gc_simMode == 1)
doStandardMode();
else if (gc_simMode == 2)
doDebugMode();
else if (gc_simMode == 3)
doSelfcheckMode();
if (gc_simMode == 1)
finaStandardMode();
else if (gc_simMode == 2)
finaDebugMode();
else if (gc_simMode == 3)
finaSelfcheckMode();
}
void RNAProfileAlignment::getStructureAlignmentFromCSF(string &s, deque<double> &pairprob, double t,size_type i, size_type j) const
{
size_type h;
double bestPairScore;
// list<Uint> leftPairList;
//list<Uint> rightPairList;
//Uint bestLeftIndex,bestRightIndex;
//Uint lastLeftIndex,lastRightIndex;
// QWATCH(i);
// QWATCH(j);
if(j==0)
return;
if(isPair(i))
{
// TRACE(DBG_GET_PROFILE_STRUCTURE,"Profile_RNA_Alignment_Forest::getStructureAlignmentFromCSF","basepair");
// WATCH(DBG_GET_PROFILE_STRUCTURE,"Profile_RNA_Alignment_Forest::getStructureAlignmentFromCSF",m_lb[i].p[ALPHA_BASEPAIR]);
bestPairScore=bestPairs(i);
// backtrack best pairs
if(bestPairScore == bestPairs(i+1) + bestPairs(getRightmostBrotherIndex(i+1)) || m_lb[i].p[ALPHA_PRO_BASEPAIR] < t)
{
// i pairs not
// cout << "unpaired" << endl;
getStructureAlignmentFromCSF(s,pairprob,t,i+1,noc(i));
// cout << "back to:" << endl;
// QWATCH(i);
// QWATCH(j);
}
else
{
// cout << "paired" << endl;
// i pairs
s += '(';
pairprob.push_back(m_lb[i].p[ALPHA_PRO_BASEPAIR]);
// left path - righthand best pairs
h=i+1;
while(h < size() && isPair(h))
{
// cout << "left" << endl;
// QWATCH(h);
assert((int)noc(h)-1>=0);
getStructureAlignmentFromCSF(s,pairprob,t,rb(h+1),noc(h)-1);
h=h+1;
}
assert((int)noc(i)-2>=0);
getStructureAlignmentFromCSF(s,pairprob,t,rb(i+1),noc(i)-2);
// cout << "back to:" << endl;
// QWATCH(i);
// QWATCH(j);
// right path - lefthand best pairs
h=getRightmostBrotherIndex(i+1);
while(h < size() && isPair(h))
{
// cout << "right" << endl;
// QWATCH(h);
assert((int)noc(h)-1>=0);
getStructureAlignmentFromCSF(s,pairprob,t,h+1,noc(h)-1);
//h=h+1;
h=getRightmostBrotherIndex(h+1);
}
s += ')';
pairprob.push_back(m_lb[i].p[ALPHA_PRO_BASEPAIR]);
}
}
else
{
s+= '.';
pairprob.push_back(m_lb[i].p[ALPHA_PRO_BASE]);
}
// right forest
getStructureAlignmentFromCSF(s,pairprob,t,rb(i),j-1);
}
