static void infoProfile(int tokenCount, char **tokens)
{
DtpcVdb *vdb = getDtpcVdb();
Profile *vprofile;
PsmAddress elt;
PsmPartition wm = getIonwm();
unsigned int profileID;
if (tokenCount != 3)
{
SYNTAX_ERROR;
return;
}
profileID = atoi(tokens[2]);
for (elt = sm_list_first(wm, vdb->profiles); elt;
elt = sm_list_next(wm, elt))
{
vprofile = (Profile *) psp(wm, sm_list_data(wm, elt));
if (vprofile->profileID == profileID)
{
break;
}
}
if (elt == 0)
{
printText("Unknown profile.");
return;
}
printProfile(vprofile);
}
int stepWithAssembly (A& addressSpace, uint64_t pc, RemoteUnwindProfile* profile, R& registers) {
R newRegisters(registers);
RemoteProcInfo *procinfo = addressSpace.getRemoteProcInfo();
if (pc > profile->fEnd)
ABORT("stepWithAssembly called with pc not in RemoteUnwindProfile's bounds");
if (procinfo && (procinfo->getDebugLoggingLevel() & UNW_LOG_LEVEL_DEBUG))
printProfile (addressSpace, pc, profile, registers);
std::map<uint64_t, RemoteUnwindProfile::CFALocation>::iterator i = profile->cfa.lower_bound (pc);
if (i == profile->cfa.begin() && i == profile->cfa.end())
return UNW_EINVAL;
if (i == profile->cfa.end()) {
--i;
} else {
if (i != profile->cfa.begin() && i->first != pc)
--i;
}
uint64_t cfa = registers.getRegister (i->second.regno) + i->second.offset;
std::map<uint64_t, std::vector<RemoteUnwindProfile::SavedReg> >::iterator j;
for (j = profile->saved_registers.begin(); j != profile->saved_registers.end() && j->first <= pc; ++j) {
std::vector<RemoteUnwindProfile::SavedReg>::iterator k = j->second.begin();
for (; k != j->second.end(); ++k) {
RemoteUnwindProfile::SavedReg sr = *k;
if (sr.type == RemoteUnwindProfile::kGeneralPurposeRegister) {
uint64_t result;
int err = 0;
switch (sr.location) {
case RemoteUnwindProfile::kRegisterOffsetFromCFA:
result = addressSpace.getP(cfa + sr.value, err);
break;
case RemoteUnwindProfile::kRegisterIsCFA:
result = cfa;
break;
default:
ABORT("Unknown saved register location in stepWithAssembly.");
}
// If we failed to read remote memory, stop unwinding.
if (err)
return UNW_STEP_END;
newRegisters.setRegister (sr.regno, result);
}
}
}
newRegisters.setSP(cfa);
uint64_t ip = addressSpace.getP(cfa + profile->returnAddress.value);
if (ip == 0)
return UNW_STEP_END;
newRegisters.setIP(ip);
registers = newRegisters;
return UNW_STEP_SUCCESS;
}
static void listProfiles(int tokenCount, char **tokens)
{
PsmPartition wm = getIonwm();
PsmAddress elt;
Profile *vprofile;
if (tokenCount != 2)
{
SYNTAX_ERROR;
return;
}
for (elt = sm_list_first(wm, (getDtpcVdb())->profiles); elt;
elt = sm_list_next(wm, elt))
{
vprofile = (Profile *) psp(wm, sm_list_data(wm, elt));
printProfile(vprofile);
}
}
static
void printCountmatAndSites(Profile *countmat, int *sites, double *scorePerSite, Dataset *data)
{
updateCountmatFromSites(countmat, sites, data);
Profile *profile = initProfile(countmat->span, countmat->maxspan);
copyProfile(profile, countmat);
//normalize "profile"
for(int x = 0; x < countmat->span; x++) {
if( !profile->isgap[x]) {
double sum = 0.0;
for(int y = 0; y < NUMALPHAS; y++) {
sum += profile->mat[x][y];
}
for(int y = 0; y < NUMALPHAS; y++) {
profile->mat[x][y] /= sum;
}
}
}
/* print profile */
printf("Motif profile generated from sites:\n");
printProfile(stdout, profile);
printf("Flanking regions:\n");
printFlankingRegionProfile(stdout, sites, countmat->span, data);
/* NOW, PRINT CONSENSUS MOTIF */
printf("Motif span: %d\n", profile->span);
printf("Motif weight/width: %d\n", profile->cols);
printf("Consensus motif: ");
for(int x=0; x< profile->span; x++) {
if(!profile->isgap[x]) {
if(profile->mat[x][0] > 0.5)
printf("A");
else if(profile->mat[x][1] > 0.5)
printf("C");
else if(profile->mat[x][2] > 0.5)
printf("G");
else if(profile->mat[x][3] > 0.5)
printf("T");
else
printf("N");
}
else {
printf("_");
}
}
printf("\n");
int numsites = getNumSites(sites, data->numseqs);
printf("Number of predicted sites: %d (%.2lf%%)\n", numsites, (numsites * 100.0) / data->numseqs);
printf("\n");
if(profile->span != profile->cols) {
printGapPos(stdout, profile);
printf("\n");
}
printf("Sequence range is from 0 to (number of sequences - 1).\n");
printf("Motif sites are in range 1 to length or -1 to -length.\n");
for(int i=0; i< data->numseqs; i++) {
if(sites[i] >= 0) {
int pos = getConcat2DoubleStrandPos(data,i,sites[i]);
int revcomplPos = getConcat2DoubleStrandPos(data, i, getConcatPosOfOppStrand(data, i, sites[i], profile->span));
printf("Sequence %3d: motif site %6d (%6d)\n",i, pos, revcomplPos);
}
else {
printf("Sequence %3d: motif site %6s (%6s)\n",i, "none", "none");
}
}
printf("\n");
printf("Alignments and FASTA-headers:\n");
printAlignment(stdout, sites, profile->span, scorePerSite, data);
printf("\n");
if(numsites < data->numseqs) {
printf("FASTA-header of sequences with zero occurrences:\n");
printZeroOccurrencesSeqHeaders(stdout, sites, data);
printf("\n");
}
nilProfile(profile);
}
