void DynSuffixArray::Delete(unsigned index, unsigned num2del)
{
int ltmp = m_L->at(m_ISA->at(index));
int true_pos = LastFirstFunc(m_ISA->at(index)); // track cycle shift (newIndex - 1)
for(size_t q = 0; q < num2del; ++q) {
int row = m_ISA->at(index); // gives the position of index in SA and m_F
//std::cerr << "row = " << row << std::endl;
//std::cerr << "SA[r]/index = " << m_SA->at(row) << "/" << index << std::endl;
true_pos -= (row <= true_pos ? 1 : 0); // track changes
m_L->erase(m_L->begin() + row);
m_F->erase(m_F->begin() + row);
m_ISA->erase(m_ISA->begin() + index); // order is important
for (vuint_t::iterator itr = m_ISA->begin(); itr != m_ISA->end(); ++itr) {
if((int)*itr > row) --(*itr);
}
m_SA->erase(m_SA->begin() + row);
for (vuint_t::iterator itr = m_SA->begin(); itr != m_SA->end(); ++itr) {
if(*itr > index) --(*itr);
}
}
m_L->at(m_ISA->at(index))= ltmp;
Reorder(LastFirstFunc(m_ISA->at(index)), true_pos);
//PrintAuxArrays();
}
void ReorderOddEven(int *pData, unsigned int length)
{
if (pData == NULL || length == 0)
return;
Reorder(pData, length, isEven);
}
/* Converts a multiple alignment (possibly with gaps) to a bunch of
* aligned single-letter seqeunces. Also reorders aligned residues.
*/
SequenceAlignment *GetSequenceAlignment(MultipleAlignment *ma) {
SequenceAlignment *out = (SequenceAlignment *) malloc(sizeof(SequenceAlignment));
int chain, block, chain2;
int *indices = (int*) calloc(ma->numChains, sizeof(int));
out->numSeqs = ma->numChains;
out->seqs = (Sequence**) malloc(sizeof(Sequence*) * ma->numChains);
for (chain=0; chain<ma->numChains; chain++) {
out->seqs[chain] = CreateSequence(ma->chains[chain]->pdb->idString);
}
for (block=0; block < ma->numBlocks; block++) {
int first = ma->blocks[block].first;
int last = ma->blocks[block].last;
for (chain=0; chain<ma->numChains; chain++) {
int find = first;
int index;
while (find <= last && !ma->residues[chain].res[find].exists) find++;
if (find > last) break;
index = ma->residues[chain].res[find].index;
while (indices[chain] < index) {
for (chain2=0; chain2<ma->numChains; chain2++) {
if (chain2 != chain) {
AddCharacter(out->seqs[chain2], '-');
}
else {
AddCharacter(out->seqs[chain2], ma->chains[chain2]->res[indices[chain2]++].residue);
}
}
}
}
while (first <= last) {
for (chain=0; chain<ma->numChains; chain++) {
if (ma->residues[chain].res[first].exists) {
AddCharacter(out->seqs[chain], ma->chains[chain]->res[indices[chain]++].residue);
}
else {
AddCharacter(out->seqs[chain], '-');
}
}
first++;
}
}
for (chain=0; chain<ma->numChains; chain++) {
while (indices[chain] < ma->chains[chain]->length) {
for (chain2=0; chain2<ma->numChains; chain2++) {
if (chain2 != chain) {
AddCharacter(out->seqs[chain2], '-');
}
else {
AddCharacter(out->seqs[chain2], ma->chains[chain2]->res[indices[chain2]++].residue);
}
}
}
}
free(indices);
Reorder(out);
return out;
}
void cDialogManager::DestroyDialog (cDialog* pDialog) {
if (!pDialog) return;
mlDialogs.remove(pDialog);
std::list<cWidget*> mycopy(pDialog->mlRootWidget); // use a copy of the list to avoid breakting iterator by automatic unregistering
for (std::list<cWidget*>::iterator itor=mycopy.begin();itor!=mycopy.end();++itor)
pDialog->DestroyWidget(*itor); // this might trigger callbacks, must be outside dialog destructor
delete pDialog;
Reorder();
}
int FAMGMultiGrid::Deconstruct()
{
int i;
#ifdef FAMG_REORDERCOLUMN
if(Reorder()) RETURN(1);
#endif
for(i = n-1; i >= 0; i--) if(grid[i] != NULL) grid[i]->Deconstruct(i);
FAMGReleaseHeap(FAMG_FROM_TOP); // mark in construct
n = 1;
return 0;
}
void reorderList(ListNode* head) {
if( !head || !head->next )
{
return;
}
ListNode* mid = FindMid( head );
ListNode* second_head = mid->next;
mid->next = NULL;
second_head = ReverseLL(second_head);
head = Reorder( head, second_head );
}
void DynSuffixArray::Insert(vuint_t* newSent, unsigned newIndex)
{
// for sentences
//stages 1, 2, 4 stay same from 1char case
//(use last word of new text in step 2 and save Ltmp until last insert?)
//stage 3...all words of new sentence are inserted backwards
// stage 2: k=ISA[newIndex], tmp= L[k], L[k] = newChar
//PrintAuxArrays();
CHECK(newIndex <= m_SA->size());
int k(-1), kprime(-1);
k = (newIndex < m_SA->size() ? m_ISA->at(newIndex) : m_ISA->at(0)); // k is now index of the cycle that starts at newindex
int true_pos = LastFirstFunc(k); // track cycle shift (newIndex - 1)
int Ltmp = m_L->at(k);
m_L->at(k) = newSent->at(newSent->size()-1); // cycle k now ends with correct word
for(int j = newSent->size()-1; j > -1; --j) {
kprime = LastFirstFunc(k); // find cycle that starts with (newindex - 1)
//kprime += ((m_L[k] == Ltmp) && (k > isa[k]) ? 1 : 0); // yada yada
// only terminal char can be 0 so add new vocab at end
kprime = (kprime > 0 ? kprime : m_SA->size());
true_pos += (kprime <= true_pos ? 1 : 0); // track changes
// insert everything
m_F->insert(m_F->begin() + kprime, newSent->at(j));
int theLWord = (j == 0 ? Ltmp : newSent->at(j-1));
m_L->insert(m_L->begin() + kprime, theLWord);
for (vuint_t::iterator itr = m_SA->begin(); itr != m_SA->end(); ++itr) {
if(*itr >= newIndex) ++(*itr);
}
m_SA->insert(m_SA->begin() + kprime, newIndex);
for (vuint_t::iterator itr = m_ISA->begin(); itr != m_ISA->end(); ++itr) {
if((int)*itr >= kprime) ++(*itr);
}
m_ISA->insert(m_ISA->begin() + newIndex, kprime);
k = kprime;
//PrintAuxArrays();
}
// Begin stage 4
Reorder(true_pos, LastFirstFunc(kprime)); // actual position vs computed position of cycle (newIndex-1)
}
void cDialogManager::SendToBack (cDialog* pDialog) {
mlDialogs.remove(pDialog);
mlDialogs.push_front(pDialog);
Reorder();
}
void cDialogManager::BringToFront (cDialog* pDialog) {
mlDialogs.remove(pDialog);
mlDialogs.push_back(pDialog);
Reorder();
}
void
ALOperator::BuildALOperator()
{
TEUCHOS_ASSERT(blockedMapping_ != Teuchos::null);
// Get an Epetra_CrsMatrix.
const Teuchos::RCP<const Epetra_CrsMatrix> crsContent
= Teuchos::rcp_dynamic_cast<const Epetra_CrsMatrix>(fullContent_);
// Ask the strategy to build the Thyra operator for you.
if(blockedOperator_ == Teuchos::null)
{
blockedOperator_
= blockedMapping_->buildBlockedThyraOp(crsContent, label_);
}
else
{
const Teuchos::RCP<Thyra::BlockedLinearOpBase<double> > blkOp
= Teuchos::rcp_dynamic_cast<Thyra::BlockedLinearOpBase<double> >
(blockedOperator_, true);
blockedMapping_->rebuildBlockedThyraOp(crsContent, blkOp);
}
// Extract blocks.
const Teuchos::RCP<Thyra::BlockedLinearOpBase<double> > blkOp
= Teuchos::rcp_dynamic_cast<Thyra::BlockedLinearOpBase<double> >
(blockedOperator_, true);
numBlockRows_ = blkOp->productRange()->numBlocks();
Teuchos::RCP<const Thyra::LinearOpBase<double> > blockedOpBlocks[4][4];
for(int i = 0; i <= dim_; i++)
{
for(int j = 0; j <= dim_; j++)
{
blockedOpBlocks[i][j] = blkOp->getBlock(i, j);
}
}
// Pressure mass matrix.
if(pressureMassMatrix_ != Teuchos::null)
{
invPressureMassMatrix_ = getInvDiagonalOp(pressureMassMatrix_);
}
// We need the size of the sub-block to build the identity matrix.
else
{
std::cout << "Pressure mass matrix is null. Use identity." << std::endl;
pressureMassMatrix_
= Thyra::identity<double>(blockedOpBlocks[dim_][0]->range());
invPressureMassMatrix_
= Thyra::identity<double>(blockedOpBlocks[dim_][0]->range());
}
// Build the AL operator.
Teuchos::RCP<Thyra::DefaultBlockedLinearOp<double> > alOperator_
= Thyra::defaultBlockedLinearOp<double>();
alOperator_->beginBlockFill(dim_ + 1, dim_ + 1);
// Set blocks for the velocity parts and gradient.
for(int i = 0; i < dim_; i++)
{
for(int j = 0; j < dim_; j++)
{
// build the blocks and place it the right location
alOperator_->setBlock(i, j,
Thyra::add(blockedOpBlocks[i][j],
Thyra::scale(gamma_,
Thyra::multiply(blockedOpBlocks[i][dim_],
invPressureMassMatrix_, blockedOpBlocks[dim_][j]))));
} // end for j
} // end for i
// Last row. Divergence and (possible) stabilization matrix.
for(int j = 0; j <= dim_; j++)
{
alOperator_->setBlock(dim_, j, blockedOpBlocks[dim_][j]);
}
// Last column. Gradient.
for(int i = 0; i < dim_; i++)
{
alOperator_->setBlock(i, dim_,
Thyra::add(blockedOpBlocks[i][dim_],
Thyra::scale(gamma_,
Thyra::multiply(blockedOpBlocks[i][dim_],
invPressureMassMatrix_,blockedOpBlocks[dim_][dim_]))));
}
alOperator_->endBlockFill();
// Set whatever is returned.
SetOperator(alOperator_, false);
// Set operator for augmenting the right-hand side.
Teuchos::RCP<Thyra::DefaultBlockedLinearOp<double> > alOpRhs_
= Thyra::defaultBlockedLinearOp<double>();
alOpRhs_->beginBlockFill(dim_ + 1, dim_ + 1);
// Identity matrices on the main diagonal.
for(int i = 0; i < dim_; i++)
{
// build the blocks and place it the right location
alOpRhs_->setBlock(i, i,
Thyra::identity<double>(blockedOpBlocks[0][0]->range()));
} // end for i
alOpRhs_->setBlock(dim_, dim_,
Thyra::identity<double>(blockedOpBlocks[dim_][dim_]->range()));
// Last column.
for(int i = 0; i < dim_; i++)
{
alOpRhs_->setBlock(i, dim_,
Thyra::scale(gamma_,
Thyra::multiply(blockedOpBlocks[i][dim_], invPressureMassMatrix_)));
}
alOpRhs_->endBlockFill();
alOperatorRhs_ = alOpRhs_;
// reorder if necessary
if(reorderManager_ != Teuchos::null)
Reorder(*reorderManager_);
}
EXPORT_C void CHuiLayout::MoveVisualToBack(CHuiVisual& aVisual, TInt aLayoutTransitionTime)
{
Reorder(aVisual, 0, aLayoutTransitionTime);
}
EXPORT_C void CHuiLayout::MoveVisualToFront(CHuiVisual& aVisual, TInt aLayoutTransitionTime)
{
Reorder(aVisual, Count() - 1, aLayoutTransitionTime);
}
int main(int argc, char* argv[])
{
programname = copystring(Basename(argv[0]));
argc--, argv++;
while (argc && argv[0][0] == '-') {
while (*++*argv)
switch(**argv) {
case 'p':
pflag++;
break;
case 'e':
eflag++;
epsfwidth = WidthInPoints(*argv + 1);
goto nextarg;
case 'd':
dflag++;
goto nextarg;
case 'i':
switch( *(*argv + 1) ) {
case '-':
iflag = -1;
case '+':
default:
iflag = 1;
}
goto nextarg;
case 'g':
gflag++;
goto nextarg;
case 'y':
yflag++;
goto nextarg;
case 'b':
bflag++;
goto nextarg;
case 's':
sflag++;
goto nextarg;
case 'm':
mflag++;
TWENTY = atoi(*argv + 1);
if (TWENTY > DEFAULT_TWENTY)
Usage(*argv-1);
goto nextarg;
case 't':
tflag++;
THRESHOLD_PERCENT = (floatish) atof(*argv + 1);
if (THRESHOLD_PERCENT < 0 || THRESHOLD_PERCENT > 5)
Usage(*argv-1);
goto nextarg;
case 'c':
cflag++;
goto nextarg;
case '?':
default:
Usage(*argv-1);
}
nextarg: ;
argc--, argv++;
}
hpfile = "stdin";
psfile = "stdout";
hpfp = stdin;
psfp = stdout;
filter = argc < 1;
if (!filter) {
pathName = copystring(argv[0]);
DropSuffix(pathName, ".hp");
baseName = copystring(Basename(pathName));
hpfp = Fp(pathName, &hpfile, ".hp", "r");
// I changed these two lines to use 'pathName' instead of
// 'baseName'. This means that the .ps and .aux files get put in
// the same directory as the .hp file. This solved Valgrind bugt
// #117686. --njn
// psfp = Fp(baseName, &psfile, ".ps", "w");
psfp = Fp(pathName, &psfile, ".ps", "w");
// if (pflag) auxfp = Fp(baseName, &auxfile, ".aux", "r");
if (pflag) auxfp = Fp(pathName, &auxfile, ".aux", "r");
}
GetHpFile(hpfp);
if (!filter && pflag) GetAuxFile(auxfp);
TraceElement(); /* Orders on total, Removes trace elements (tflag) */
if (dflag) Deviation(); /* ReOrders on deviation */
if (iflag) Identorder(iflag); /* ReOrders on identifier */
if (pflag) Reorder(); /* ReOrders on aux file */
if (TWENTY) TopTwenty(); /* Selects top twenty (mflag) */
Dimensions();
areabelow = AreaBelow();
Scale();
PutPsFile();
if (!filter) {
auxfp = Fp(baseName, &auxfile, ".aux", "w");
PutAuxFile(auxfp);
}
return(0);
}
int main(int argc, char *argv[])
{
programname = copystring(Basename(argv[0]));
argc--, argv++;
while (argc && argv[0][0] == '-') {
while (*++*argv)
switch(**argv) {
case 'p':
pflag++;
break;
case 'e':
eflag++;
epsfwidth = WidthInPoints(*argv + 1);
goto nextarg;
case 'd':
dflag++;
goto nextarg;
case 'i':
switch( *(*argv + 1) ) {
case '-':
iflag = -1;
break;
case '+':
default:
iflag = 1;
}
goto nextarg;
case 'g':
gflag++;
goto nextarg;
case 'y':
yflag++;
goto nextarg;
case 'b':
bflag++;
goto nextarg;
case 's':
sflag++;
goto nextarg;
case 'm':
mflag++;
TWENTY = atoi(*argv + 1);
// only 20 keys fit on a page
if (TWENTY > DEFAULT_TWENTY)
multipageflag++;
goto nextarg;
case 'M':
multipageflag++;
goto nextarg;
case 't':
tflag++;
THRESHOLD_PERCENT = (floatish) atof(*argv + 1);
if (THRESHOLD_PERCENT < 0 || THRESHOLD_PERCENT > 5)
Usage(*argv-1);
goto nextarg;
case 'c':
cflag++;
goto nextarg;
case '?':
default:
Usage(*argv-1);
}
nextarg: ;
argc--, argv++;
}
hpfile = "stdin";
psfile = "stdout";
hpfp = stdin;
psfp = stdout;
filter = argc < 1;
if (!filter) {
pathName = copystring(argv[0]);
DropSuffix(pathName, ".hp");
#if defined(_WIN32)
DropSuffix(pathName, ".exe");
#endif
baseName = copystring(Basename(pathName));
hpfp = Fp(pathName, &hpfile, ".hp", "r");
psfp = Fp(baseName, &psfile, ".ps", "w");
if (pflag) auxfp = Fp(baseName, &auxfile, ".aux", "r");
}
GetHpFile(hpfp);
if (!filter && pflag) GetAuxFile(auxfp);
TraceElement(); /* Orders on total, Removes trace elements (tflag) */
if (dflag) Deviation(); /* ReOrders on deviation */
if (iflag) Identorder(iflag); /* ReOrders on identifier */
if (pflag) Reorder(); /* ReOrders on aux file */
/* Selects top bands (mflag) - can be more than 20 now */
if (TWENTY != 0) TopTwenty();
Dimensions();
areabelow = AreaBelow();
Scale();
PutPsFile();
if (!filter) {
auxfp = Fp(baseName, &auxfile, ".aux", "w");
PutAuxFile(auxfp);
}
return(0);
}
void PackageList::SaveBin(Profile* profile,BOStream&file)
{
if (!profile->route)
profile->wpsused=0;
int numraids=0;
if (profile->raidnumentries)
{
while (profile->raidnumentries[numraids].squadliststart!=Profile::RNEC_LISTVALISLASTREC)
numraids++;
numraids=profile->raidnumentries[numraids].raidnum;
}
file<<CSprintf(line1out,
profile->attackmethod,profile->packagestatus,profile->squadlist.Max(),numraids,profile->flags,
profile->packagetakeoff,Reorder(profile->packagetarget[0]),profile->doglegloc,
profile->primarytargetETA,profile->playerETAdelta );
int targets[10];
int subtargets[10];
{
for (int i=1;i<10;i++)
{
targets[i]=Reorder(profile->packagetarget[i].SGT);
subtargets[i]=profile->packagetarget[i].band+profile->packagetarget[i].bandoff;
}
}
file<<CSprintf(line2out,
targets[1],subtargets[1], targets[2],subtargets[2],
targets[3],subtargets[3], targets[4],subtargets[4],
targets[5],subtargets[5], targets[6],subtargets[6],
targets[7],subtargets[7], targets[8],subtargets[8],
targets[9],subtargets[9]);
//DeadCode JIM 20Oct00 int loopcount=0; //increase for any fixed fields....
int maxsq=profile->squadlist;
{
for (int i=0;i<maxsq;i++)
{
Profile::Squad squadbuff=profile->squadlist[i]; //JIM 29Oct00
if (profile->packagestatus!=Profile::PS_COMPLETE)
squadbuff.instance=ReorderNoCheck(squadbuff.instance);
else
squadbuff.instance=UID_NULL;
file<<"Sq: ";
ULong* squadptr=(ULong*)&squadbuff;
assert (sizeof(Profile::Squad)%4==0);
for (int countdown=sizeof(Profile::Squad)/4;countdown;countdown--)
{
ULong p0=*squadptr++,
p1=p0/90,
p2=p1/90,
p3=p2/90,
p4=p3/90;
char packstr[6];
packstr[0]=p0%90+34;
packstr[1]=p1%90+34;
packstr[2]=p2%90+34;
packstr[3]=p3%90+34;
packstr[4]=p4%90+34;
packstr[5]=0;
file<<packstr;
}
file<<'\n';
//DeadCode CRAIG 30Oct100 Profile::Squad& squad=profile->squadlist[i];
//DeadCode CRAIG 30Oct100 if (profile->packagestatus!=Profile::PS_COMPLETE)
//DeadCode CRAIG 30Oct100 file<<CSprintf(linesqout,
//DeadCode CRAIG 30Oct100 ReorderNoCheck(squad.instance), +squad.squadnum, +squad.formtype, squad.diaryentry, squad.numbers, squad.fightperiods,
//DeadCode CRAIG 30Oct100 +squad.targetindex, squad.takeofftime, squad.lastwptime,
//DeadCode CRAIG 30Oct100 +squad.method, +squad.submethod, +squad.status, squad.fuelleft
//DeadCode CRAIG 30Oct100
//DeadCode CRAIG 30Oct100 );
//DeadCode CRAIG 30Oct100 else
//DeadCode CRAIG 30Oct100 file<<CSprintf(linesqout,
//DeadCode CRAIG 30Oct100 0, +squad.squadnum, +squad.formtype, squad.diaryentry, squad.numbers,
//DeadCode CRAIG 30Oct100 +squad.targetindex, squad.takeofftime, squad.lastwptime,
//DeadCode CRAIG 30Oct100 +squad.method, +squad.submethod, +squad.status, squad.fuelleft
//DeadCode CRAIG 30Oct100
//DeadCode CRAIG 30Oct100 );
//DeadCode CRAIG 30Oct100
}
}
if (maxsq==1)
{
file<<CSprintf(lollyout,profile->squadlist.AcBitsFirstSquad());
}
{
for (int i=0;i<numraids;i++)
{
file<<"Rd: ";
ULong* raidptr=(ULong*)&profile->raidnumentries[i]; //JIM 29Oct00
assert (sizeof(Profile::RaidNumEntry)%4==0);
for (int countdown=sizeof(Profile::RaidNumEntry)/4;countdown;countdown--)
{
ULong p0=*raidptr++,
p1=p0/90,
p2=p1/90,
p3=p2/90,
p4=p3/90;
char packstr[6];
packstr[0]=p0%90+34;
packstr[1]=p1%90+34;
packstr[2]=p2%90+34;
packstr[3]=p3%90+34;
packstr[4]=p4%90+34;
packstr[5]=0;
file<<packstr;
}
file<<'\n';
//DeadCode CRAIG 30Oct100 file<<CSprintf(linerout,
//DeadCode C profile->raidnumentries[i].raidnum, profile->raidnumentries[i].squadliststart,profile->raidnumentries[i].detector,profile->raidnumentries[i].alertlevel,profile->raidnumentries[i].detectlatency,profile->raidnumentries[i].firstsquaddiaryentry,
//DeadCode CRAIG 30Oct100 profile->raidnumentries[i].prevpositions[0].X,profile->raidnumentries[i].prevpositions[0].Y,profile->raidnumentries[i].prevpositions[0].Z,
//DeadCode CRAIG 30Oct100 profile->raidnumentries[i].prevpositions[1].X,profile->raidnumentries[i].prevpositions[1].Y,profile->raidnumentries[i].prevpositions[1].Z,
//DeadCode CRAIG 30Oct100 profile->raidnumentries[i].prevpositions[2].X,profile->raidnumentries[i].prevpositions[2].Y,profile->raidnumentries[i].prevpositions[2].Z,
//DeadCode CRAIG 30Oct100 profile->raidnumentries[i].prevpositions[3].X,profile->raidnumentries[i].prevpositions[3].Y,profile->raidnumentries[i].prevpositions[3].Z);
}
}
file<<C 26 <<C 0;
if (profile->wpsused)
{
file <<C T_bfsave <<C T_linklist <<C maxsq;
{
Profile::Squad& squad=profile->squadlist[0];
//AirGroup
// T_inform:
// T_inwing:
// T_duty:
// T_form:
// T_pos:
// T_route: only leader
// T_itemA:
// T_leader: - new in this position!
file<<C T_airgrp <<C T_linklist <<C 7;
SaveRouteBin(profile->route,file);
profile->SaveAirItemBin(&squad,profile->route,file);
}
for (int i=1;i<maxsq;i++)
{
Profile::Squad& squad=profile->squadlist[i];
//AirGroup
// T_inform:
// T_inwing:
// T_duty:
// T_form:
// T_pos:
// T_route: only leader
// T_itemA:
// T_leader: - new in this position!
info_airgrp *a=*Persons2::ConvertPtrUID(squad.instance);
if (a->leader.Evaluate()==ENABLE_COMPLEX_VAL || ReorderZero(UniqueID(a->leader.Evaluate())))
{
file<<C T_airgrp <<C T_linklist <<C 7;
file<<C T_leader;
if (a->leader.Evaluate()!=ENABLE_COMPLEX_VAL)
Expr::putint(ReorderZero(UniqueID(a->leader.Evaluate())),file);
else
Expr::putint(0,file); //NEED TO WORK ON THIS!!!!!
}
else
file<<C T_airgrp <<C T_linklist <<C 6;
profile->SaveAirItemBin(&squad,profile->route,file);
}
}
}
void ReorderOddEven(int A[], int N) {
Reorder(A, N, devideBy3);
}
