int
main(int /*argc*/, char** /*argv*/)
{
typedef gnash::geometry::SnappingRanges2d<int> Ranges;
typedef gnash::geometry::Range2d<int> Bounds;
string filename = string(TGTDIR) + string("/") + string(INPUT_FILENAME);
MovieTester tester(filename);
gnash::LogFile& dbglogfile = gnash::LogFile::getDefaultInstance();
dbglogfile.setVerbosity(1);
// Colors we'll use during the test
rgba red(255,0,0,255);
rgba white(255,255,255,255);
// Ranges we'll use during the test
Range2d<int> redRange1(100,300,160,360);
Range2d<int> redRange2(130,330,190,390);
Range2d<int> leftRange(20,300,80,390);
Range2d<int> rightRange(200,300,260,390);
Ranges invalidated;
MovieClip* root = tester.getRootMovie();
assert(root);
// FRAME 1 (start)
check_equals(root->get_frame_count(), 4);
check_equals(root->getPlayState(), MovieClip::PLAYSTATE_PLAY);
check_equals(root->get_current_frame(), 0);
check_equals(root->getDisplayList().size(), 1); // dejagnu clip
invalidated = tester.getInvalidatedRanges();
check( invalidated.contains(76, 4) ); // the "-xtrace enabled-" label...
tester.advance(); // FRAME 2, place DisplayObject
invalidated = tester.getInvalidatedRanges();
check_equals(root->getPlayState(), MovieClip::PLAYSTATE_PLAY);
check_equals(root->get_current_frame(), 1);
check_equals(root->getDisplayList().size(), 2); // dejagnu + red square
// check invalidated bounds contain the red square at (100,300 - 160,360)
check( invalidated.contains(redRange1) );
// check that we have a red square at (100,300 - 160,360)
check_pixel(104, 304, 2, red, 2); // UL
check_pixel(156, 304, 2, red, 2); // UR
check_pixel(156, 356, 2, red, 2); // LL
check_pixel(104, 356, 2, red, 2); // LR
// and nothing around it...
check_pixel( 96, 330, 2, white, 2); // Left
check_pixel(164, 330, 2, white, 2); // Right
check_pixel(130, 296, 2, white, 2); // Top
check_pixel(130, 364, 2, white, 2); // Bottom
tester.advance(); // FRAME 3, replace DisplayObject
invalidated = tester.getInvalidatedRanges();
check_equals(root->getPlayState(), MovieClip::PLAYSTATE_PLAY);
check_equals(root->get_current_frame(), 2);
check_equals(root->getDisplayList().size(), 2); // dejagnu + red square
// check invalidated bounds to contain:
// - the red square (moved)
// - the red square (original)
//
check( invalidated.contains(redRange1) );
check( invalidated.contains(redRange2) );
// but not the area on the right, nor on the left
check( ! invalidated.contains(rightRange) );
check( ! invalidated.contains(leftRange) );
// check that we have a red square at (130,330 - 190,390)
check_pixel(134, 334, 2, red, 2); // UL
check_pixel(186, 334, 2, red, 2); // UR
check_pixel(186, 386, 2, red, 2); // LL
check_pixel(134, 386, 2, red, 2); // LR
// and nothing around it...
check_pixel(126, 360, 2, white, 2); // Left
check_pixel(194, 360, 2, white, 2); // Right
check_pixel(160, 326, 2, white, 2); // Top
check_pixel(160, 394, 2, white, 2); // Bottom
tester.advance(); // FRAME 4, jump to frame 2 and stop
invalidated = tester.getInvalidatedRanges();
check_equals(root->getPlayState(), MovieClip::PLAYSTATE_STOP);
check_equals(root->get_current_frame(), 1);
check_equals(root->getDisplayList().size(), 2); // dejagnu + red square
// check invalidated bounds to contain:
// - the red square (moved)
// - the red square (original)
//
check( invalidated.contains(redRange1) );
check( invalidated.contains(redRange2) );
// but not the area on the right, nor on the left
xcheck( ! invalidated.contains(rightRange) );
xcheck( ! invalidated.contains(leftRange) );
// check that we have a red square at (100,300 - 160,360)
check_pixel(104, 304, 2, red, 2); // UL
check_pixel(156, 304, 2, red, 2); // UR
check_pixel(156, 356, 2, red, 2); // LL
check_pixel(104, 356, 2, red, 2); // LR
// and nothing around it...
check_pixel( 96, 330, 2, white, 2); // Left
check_pixel(164, 330, 2, white, 2); // Right
check_pixel(130, 296, 2, white, 2); // Top
check_pixel(130, 364, 2, white, 2); // Bottom
}
void DOMCharacterDataImpl::deleteData(const DOMNode *node, XMLSize_t offset, XMLSize_t count)
{
if (castToNodeImpl(node)->isReadOnly())
throw DOMException(DOMException::NO_MODIFICATION_ALLOWED_ERR, 0, GetDOMCharacterDataImplMemoryManager);
// Note: the C++ XMLCh * operation throws the correct DOMExceptions
// when parameter values are bad.
//
XMLSize_t len = this->fDataBuf->getLen();
if (offset > len)
throw DOMException(DOMException::INDEX_SIZE_ERR, 0, GetDOMCharacterDataImplMemoryManager);
// Cap the value of delLength to avoid trouble with overflows
// in the following length computations.
if (count > len)
count = len;
// If the length of data to be deleted would extend off the end
// of the string, cut it back to stop at the end of string.
if (offset + count >= len)
count = len - offset;
XMLSize_t newLen = len - count;
XMLCh* newString;
XMLCh temp[4096];
if (newLen >= 4095)
newString = (XMLCh*) XMLPlatformUtils::fgMemoryManager->allocate
(
(newLen+1) * sizeof(XMLCh)
);//new XMLCh[newLen+1];
else
newString = temp;
XMLString::copyNString(newString, fDataBuf->getRawBuffer(), offset);
XMLString::copyString(newString+offset, fDataBuf->getRawBuffer()+offset+count);
fDataBuf->set(newString);
if (newLen >= 4095)
XMLPlatformUtils::fgMemoryManager->deallocate(newString);//delete[] newString;
// We don't delete the old string (doesn't work), or alter
// the old string (may be shared)
// It just hangs around, possibly orphaned.
DOMDocumentImpl *doc = (DOMDocumentImpl *)node->getOwnerDocument();
if (doc != 0) {
Ranges* ranges = doc->getRanges();
if (ranges != 0) {
XMLSize_t sz = ranges->size();
if (sz != 0) {
for (XMLSize_t i =0; i<sz; i++) {
ranges->elementAt(i)->updateRangeForDeletedText( (DOMNode*)node, offset, count);
}
}
}
}
}
Parfactor*
readParfactor (YAP_Term pfTerm)
{
// read dist id
unsigned distId = YAP_IntOfTerm (YAP_ArgOfTerm (1, pfTerm));
// read the ranges
Ranges ranges;
YAP_Term rangeList = YAP_ArgOfTerm (3, pfTerm);
while (rangeList != YAP_TermNil()) {
unsigned range = (unsigned) YAP_IntOfTerm (YAP_HeadOfTerm (rangeList));
ranges.push_back (range);
rangeList = YAP_TailOfTerm (rangeList);
}
// read parametric random vars
ProbFormulas formulas;
unsigned count = 0;
unordered_map<YAP_Term, LogVar> lvMap;
YAP_Term pvList = YAP_ArgOfTerm (2, pfTerm);
while (pvList != YAP_TermNil()) {
YAP_Term formulaTerm = YAP_HeadOfTerm (pvList);
if (YAP_IsAtomTerm (formulaTerm)) {
string name ((char*) YAP_AtomName (YAP_AtomOfTerm (formulaTerm)));
Symbol functor = LiftedUtils::getSymbol (name);
formulas.push_back (ProbFormula (functor, ranges[count]));
} else {
LogVars logVars;
YAP_Functor yapFunctor = YAP_FunctorOfTerm (formulaTerm);
string name ((char*) YAP_AtomName (YAP_NameOfFunctor (yapFunctor)));
Symbol functor = LiftedUtils::getSymbol (name);
unsigned arity = (unsigned) YAP_ArityOfFunctor (yapFunctor);
for (unsigned i = 1; i <= arity; i++) {
YAP_Term ti = YAP_ArgOfTerm (i, formulaTerm);
unordered_map<YAP_Term, LogVar>::iterator it = lvMap.find (ti);
if (it != lvMap.end()) {
logVars.push_back (it->second);
} else {
unsigned newLv = lvMap.size();
lvMap[ti] = newLv;
logVars.push_back (newLv);
}
}
formulas.push_back (ProbFormula (functor, logVars, ranges[count]));
}
count ++;
pvList = YAP_TailOfTerm (pvList);
}
// read the parameters
const Params& params = readParameters (YAP_ArgOfTerm (4, pfTerm));
// read the constraint
Tuples tuples;
if (lvMap.size() >= 1) {
YAP_Term tupleList = YAP_ArgOfTerm (5, pfTerm);
while (tupleList != YAP_TermNil()) {
YAP_Term term = YAP_HeadOfTerm (tupleList);
assert (YAP_IsApplTerm (term));
YAP_Functor yapFunctor = YAP_FunctorOfTerm (term);
unsigned arity = (unsigned) YAP_ArityOfFunctor (yapFunctor);
assert (lvMap.size() == arity);
Tuple tuple (arity);
for (unsigned i = 1; i <= arity; i++) {
YAP_Term ti = YAP_ArgOfTerm (i, term);
if (YAP_IsAtomTerm (ti) == false) {
cerr << "error: constraint has free variables" << endl;
abort();
}
string name ((char*) YAP_AtomName (YAP_AtomOfTerm (ti)));
tuple[i - 1] = LiftedUtils::getSymbol (name);
}
tuples.push_back (tuple);
tupleList = YAP_TailOfTerm (tupleList);
}
}
return new Parfactor (formulas, params, tuples, distId);
}
DOMNode *XPathDocumentImpl::insertBefore(DOMNode *newChild, DOMNode *refChild)
{
// if the newChild is a documenttype node created from domimplementation, set the ownerDoc first
if ((newChild->getNodeType() == DOMNode::DOCUMENT_TYPE_NODE) && !newChild->getOwnerDocument())
((DOMDocumentTypeImpl*)newChild)->setOwnerDocument(this);
if(newChild==NULL)
throw DOMException(DOMException::HIERARCHY_REQUEST_ERR,0, getMemoryManager());
DOMNodeImpl *thisNodeImpl = castToNodeImpl(this);
if (thisNodeImpl->isReadOnly())
throw DOMException(DOMException::NO_MODIFICATION_ALLOWED_ERR, 0, getMemoryManager());
DOMNode* thisNode = castToNode(&fParent);
if (newChild->getOwnerDocument() != thisNode)
throw DOMException(DOMException::WRONG_DOCUMENT_ERR, 0, getMemoryManager());
// refChild must in fact be a child of this node (or 0)
if (refChild!=0 && refChild->getParentNode() != thisNode)
throw DOMException(DOMException::NOT_FOUND_ERR,0, getMemoryManager());
// if the new node has to be placed before itself, we don't have to do anything
// (even worse, we would crash if we continue, as we assume they are two distinct nodes)
if (refChild!=0 && newChild->isSameNode(refChild))
return newChild;
if (newChild->getNodeType() == DOMNode::DOCUMENT_FRAGMENT_NODE)
{
// SLOW BUT SAFE: We could insert the whole subtree without
// juggling so many next/previous pointers. (Wipe out the
// parent's child-list, patch the parent pointers, set the
// ends of the list.) But we know some subclasses have special-
// case behavior they add to insertBefore(), so we don't risk it.
// This approch also takes fewer bytecodes.
while(newChild->hasChildNodes()) // Move
insertBefore(newChild->getFirstChild(),refChild);
}
else
{
DOMNode *oldparent=newChild->getParentNode();
if(oldparent!=0)
oldparent->removeChild(newChild);
// Attach up
castToNodeImpl(newChild)->fOwnerNode = thisNode;
castToNodeImpl(newChild)->isOwned(true);
// Attach before and after
// Note: fFirstChild.previousSibling == lastChild!!
if (fParent.fFirstChild == 0) {
// this our first and only child
fParent.fFirstChild = newChild;
castToNodeImpl(newChild)->isFirstChild(true);
// castToChildImpl(newChild)->previousSibling = newChild;
DOMChildNode *newChild_ci = castToChildImpl(newChild);
newChild_ci->previousSibling = newChild;
} else {
if (refChild == 0) {
// this is an append
DOMNode *lastChild = castToChildImpl(fParent.fFirstChild)->previousSibling;
castToChildImpl(lastChild)->nextSibling = newChild;
castToChildImpl(newChild)->previousSibling = lastChild;
castToChildImpl(fParent.fFirstChild)->previousSibling = newChild;
} else {
// this is an insert
if (refChild == fParent.fFirstChild) {
// at the head of the list
castToNodeImpl(fParent.fFirstChild)->isFirstChild(false);
castToChildImpl(newChild)->nextSibling = fParent.fFirstChild;
castToChildImpl(newChild)->previousSibling = castToChildImpl(fParent.fFirstChild)->previousSibling;
castToChildImpl(fParent.fFirstChild)->previousSibling = newChild;
fParent.fFirstChild = newChild;
castToNodeImpl(newChild)->isFirstChild(true);
} else {
// somewhere in the middle
DOMNode *prev = castToChildImpl(refChild)->previousSibling;
castToChildImpl(newChild)->nextSibling = refChild;
castToChildImpl(prev)->nextSibling = newChild;
castToChildImpl(refChild)->previousSibling = newChild;
castToChildImpl(newChild)->previousSibling = prev;
}
}
}
}
changed();
Ranges* ranges = getRanges();
if ( ranges != 0) {
XMLSize_t sz = ranges->size();
if (sz != 0) {
for (XMLSize_t i =0; i<sz; i++) {
ranges->elementAt(i)->updateRangeForInsertedNode(newChild);
}
}
}
// If insert succeeded, cache the kid appropriately
if(newChild->getNodeType() == DOMNode::ELEMENT_NODE)
fMyDocElement=(DOMElement *)newChild;
else if(newChild->getNodeType() == DOMNode::DOCUMENT_TYPE_NODE)
fMyDocType=(DOMDocumentType *)newChild;
return newChild;
}
DOMNode *DOMParentNode::insertBefore(DOMNode *newChild, DOMNode *refChild) {
DOMNodeImpl *thisNodeImpl = castToNodeImpl(this);
if (thisNodeImpl->isReadOnly())
throw DOMException(DOMException::NO_MODIFICATION_ALLOWED_ERR, 0, GetDOMParentNodeMemoryManager);
if (newChild->getOwnerDocument() != fOwnerDocument)
throw DOMException(DOMException::WRONG_DOCUMENT_ERR, 0, GetDOMParentNodeMemoryManager);
// Prevent cycles in the tree
//only need to do this if the node has children
if(newChild->hasChildNodes()) {
bool treeSafe=true;
for(DOMNode *a=castToNode(this)->getParentNode();
treeSafe && a!=0;
a=a->getParentNode())
treeSafe=(newChild!=a);
if(!treeSafe)
throw DOMException(DOMException::HIERARCHY_REQUEST_ERR,0, GetDOMParentNodeMemoryManager);
}
// refChild must in fact be a child of this node (or 0)
if (refChild!=0 && refChild->getParentNode() != castToNode(this))
throw DOMException(DOMException::NOT_FOUND_ERR,0, GetDOMParentNodeMemoryManager);
// if the new node has to be placed before itself, we don't have to do anything
// (even worse, we would crash if we continue, as we assume they are two distinct nodes)
if (refChild!=0 && newChild->isSameNode(refChild))
return newChild;
if (newChild->getNodeType() == DOMNode::DOCUMENT_FRAGMENT_NODE)
{
// SLOW BUT SAFE: We could insert the whole subtree without
// juggling so many next/previous pointers. (Wipe out the
// parent's child-list, patch the parent pointers, set the
// ends of the list.) But we know some subclasses have special-
// case behavior they add to insertBefore(), so we don't risk it.
// This approch also takes fewer bytecodes.
// NOTE: If one of the children is not a legal child of this
// node, throw HIERARCHY_REQUEST_ERR before _any_ of the children
// have been transferred. (Alternative behaviors would be to
// reparent up to the first failure point or reparent all those
// which are acceptable to the target node, neither of which is
// as robust. PR-DOM-0818 isn't entirely clear on which it
// recommends?????
// No need to check kids for right-document; if they weren't,
// they wouldn't be kids of that DocFrag.
for(DOMNode *kid=newChild->getFirstChild(); // Prescan
kid!=0;
kid=kid->getNextSibling())
{
if (!DOMDocumentImpl::isKidOK(castToNode(this), kid))
throw DOMException(DOMException::HIERARCHY_REQUEST_ERR,0, GetDOMParentNodeMemoryManager);
}
while(newChild->hasChildNodes()) // Move
insertBefore(newChild->getFirstChild(),refChild);
}
else if (!DOMDocumentImpl::isKidOK(castToNode(this), newChild))
throw DOMException(DOMException::HIERARCHY_REQUEST_ERR,0, GetDOMParentNodeMemoryManager);
else
{
DOMNode *oldparent=newChild->getParentNode();
if(oldparent!=0)
oldparent->removeChild(newChild);
// Attach up
castToNodeImpl(newChild)->fOwnerNode = castToNode(this);
castToNodeImpl(newChild)->isOwned(true);
// Attach before and after
// Note: fFirstChild.previousSibling == lastChild!!
if (fFirstChild == 0) {
// this our first and only child
fFirstChild = newChild;
castToNodeImpl(newChild)->isFirstChild(true);
// castToChildImpl(newChild)->previousSibling = newChild;
DOMChildNode *newChild_ci = castToChildImpl(newChild);
newChild_ci->previousSibling = newChild;
} else {
if (refChild == 0) {
// this is an append
DOMNode *lastChild = castToChildImpl(fFirstChild)->previousSibling;
castToChildImpl(lastChild)->nextSibling = newChild;
castToChildImpl(newChild)->previousSibling = lastChild;
castToChildImpl(fFirstChild)->previousSibling = newChild;
} else {
// this is an insert
if (refChild == fFirstChild) {
// at the head of the list
castToNodeImpl(fFirstChild)->isFirstChild(false);
castToChildImpl(newChild)->nextSibling = fFirstChild;
castToChildImpl(newChild)->previousSibling = castToChildImpl(fFirstChild)->previousSibling;
castToChildImpl(fFirstChild)->previousSibling = newChild;
fFirstChild = newChild;
castToNodeImpl(newChild)->isFirstChild(true);
} else {
// somewhere in the middle
DOMNode *prev = castToChildImpl(refChild)->previousSibling;
castToChildImpl(newChild)->nextSibling = refChild;
castToChildImpl(prev)->nextSibling = newChild;
castToChildImpl(refChild)->previousSibling = newChild;
castToChildImpl(newChild)->previousSibling = prev;
}
}
}
}
changed();
if (this->getOwnerDocument() != 0) {
Ranges* ranges = ((DOMDocumentImpl *)this->getOwnerDocument())->getRanges();
if ( ranges != 0) {
XMLSize_t sz = ranges->size();
if (sz != 0) {
for (XMLSize_t i =0; i<sz; i++) {
ranges->elementAt(i)->updateRangeForInsertedNode(newChild);
}
}
}
}
return newChild;
}
DOMNode *DOMParentNode::removeChild(DOMNode *oldChild)
{
if (castToNodeImpl(this)->isReadOnly())
throw DOMException(
DOMException::NO_MODIFICATION_ALLOWED_ERR, 0, GetDOMParentNodeMemoryManager);
if (oldChild == 0 || oldChild->getParentNode() != castToNode(this))
throw DOMException(DOMException::NOT_FOUND_ERR, 0, GetDOMParentNodeMemoryManager);
if (this->getOwnerDocument() != 0 ) {
//notify iterators
NodeIterators* nodeIterators = ((DOMDocumentImpl *)this->getOwnerDocument())->getNodeIterators();
if (nodeIterators != 0) {
XMLSize_t sz = nodeIterators->size();
if (sz != 0) {
for (XMLSize_t i =0; i<sz; i++) {
if (nodeIterators->elementAt(i) != 0)
nodeIterators->elementAt(i)->removeNode(oldChild);
}
}
}
//fix other ranges for change before deleting the node
Ranges* ranges = ((DOMDocumentImpl *)this->getOwnerDocument())->getRanges();
if (ranges != 0) {
XMLSize_t sz = ranges->size();
if (sz != 0) {
for (XMLSize_t i =0; i<sz; i++) {
if (ranges->elementAt(i) != 0)
ranges->elementAt(i)->updateRangeForDeletedNode(oldChild);
}
}
}
}
// Patch linked list around oldChild
// Note: lastChild == fFirstChild->previousSibling
if (oldChild == fFirstChild) {
// removing first child
castToNodeImpl(oldChild)->isFirstChild(false);
fFirstChild = castToChildImpl(oldChild)->nextSibling;
if (fFirstChild != 0) {
castToNodeImpl(fFirstChild)->isFirstChild(true);
castToChildImpl(fFirstChild)->previousSibling = castToChildImpl(oldChild)->previousSibling;
}
} else {
DOMNode *prev = castToChildImpl(oldChild)->previousSibling;
DOMNode *next = castToChildImpl(oldChild)->nextSibling;
castToChildImpl(prev)->nextSibling = next;
if (next == 0) {
// removing last child
castToChildImpl(fFirstChild)->previousSibling = prev;
} else {
// removing some other child in the middle
castToChildImpl(next)->previousSibling = prev;
}
}
// Remove oldChild's references to tree
castToNodeImpl(oldChild)->fOwnerNode = fOwnerDocument;
castToNodeImpl(oldChild)->isOwned(false);
castToChildImpl(oldChild)->nextSibling = 0;
castToChildImpl(oldChild)->previousSibling = 0;
changed();
return oldChild;
}
virtual void SetUp()
{
unsigned int num_constraints = 3;
unsigned int num_joints = 7;
true_constraints.resize(num_constraints, num_joints);
false_constraints.resize(num_constraints, num_joints);
std::vector<double> task_values;
Ranges true_cmd, false_cmd;
true_cmd.resize(num_constraints);
false_cmd.resize(num_constraints);
for(unsigned int i=0; i<num_constraints; i++)
{
true_cmd.pos_lo(i) = -1.0;
true_cmd.pos_hi(i) = 2.5;
task_values.push_back(0.25);
false_cmd.pos_lo(i) = -1.0;
false_cmd.pos_hi(i) = 2.5;
}
true_constraints.setTaskValues(task_values);
task_values[0] = (0.0);
task_values[1] = (-2.0);
task_values[2] = (5.5);
false_constraints.setTaskValues(task_values);
true_constraints.setCommands(true_cmd);
false_constraints.setCommands(false_cmd);
Feature pan, bottle;
pan.name = "pan";
pan.pos = KDL::Vector(0.0, 0.0, 0.0);
pan.dir = KDL::Vector(0.0, 0.0, 1.0);
pan.contact_dir = KDL::Vector(1.0, 0.0, 0.0);
bottle.name = "bottle";
bottle.pos = KDL::Vector(0.0, 0.0, 0.0);
bottle.dir = KDL::Vector(0.0, 0.0, 1.0);
bottle.contact_dir = KDL::Vector(1.0, 0.0, 0.0);
Constraint c1, c2, c3;
c1.name = "height of bottle over pan";
c1.setFunction("height");
c1.tool_feature = bottle;
c1.object_feature = pan;
c2.name = "distance of bottle over pan";
c2.setFunction("distance");
c2.tool_feature = bottle;
c2.object_feature = pan;
c3.name = "bottle upright";
c3.setFunction("perpendicular");
c3.tool_feature = bottle;
c3.object_feature = pan;
constraints.resize(3, num_joints);
std::vector<Constraint> constraint_vector;
constraint_vector.push_back(c1);
constraint_vector.push_back(c2);
constraint_vector.push_back(c3);
constraints.setConstraints(constraint_vector);
constraints.setObjectPose(KDL::Frame(KDL::Rotation::RotZ(M_PI/2.0), KDL::Vector(1.0, 1.0, 0.75)));
Ranges cmd;
cmd.resize(3);
// height
cmd.weight(0) = 1.0;
cmd.pos_lo(0) = 0.1;
cmd.pos_hi(0) = 2.0;
// distance
cmd.weight(1) = 1.0;
cmd.pos_lo(1) = 0.0;
cmd.pos_hi(1) = 0.1;
// upright
cmd.weight(2) = 1.0;
cmd.pos_lo(2) = 0.95;
cmd.pos_hi(2) = 1.2;
constraints.setCommands(cmd);
}
void EnPhrasalVerb(const Phrase &source, int revision, ostream &out)
{
Ranges ranges;
// find ranges to label
for (int start = 0; start < source.size(); ++start) {
size_t end = std::numeric_limits<size_t>::max();
if (IsA(source, start, 0, 0, "ask asked asking")) {
end = Found(source, start, 0, "out");
}
else if (IsA(source, start, 0, 0, "back backed backing")) {
end = Found(source, start, 0, "up");
}
else if (IsA(source, start, 0, 0, "blow blown blew")) {
end = Found(source, start, 0, "up");
}
else if (IsA(source, start, 0, 0, "break broke broken")) {
end = Found(source, start, 0, "down up in");
}
else if (IsA(source, start, 0, 0, "bring brought bringing")) {
end = Found(source, start, 0, "down up in");
}
else if (IsA(source, start, 0, 0, "call called calling")) {
end = Found(source, start, 0, "back up off");
}
else if (IsA(source, start, 0, 0, "check checked checking")) {
end = Found(source, start, 0, "out in");
}
else if (IsA(source, start, 0, 0, "cheer cheered cheering")) {
end = Found(source, start, 0, "up");
}
else if (IsA(source, start, 0, 0, "clean cleaned cleaning")) {
end = Found(source, start, 0, "up");
}
else if (IsA(source, start, 0, 0, "cross crossed crossing")) {
end = Found(source, start, 0, "out");
}
else if (IsA(source, start, 0, 0, "cut cutting")) {
end = Found(source, start, 0, "down off out");
}
else if (IsA(source, start, 0, 0, "do did done")) {
end = Found(source, start, 0, "over up");
}
else if (IsA(source, start, 0, 0, "drop dropped dropping")) {
end = Found(source, start, 0, "off");
}
else if (IsA(source, start, 0, 0, "figure figured figuring")) {
end = Found(source, start, 0, "out");
}
else if (IsA(source, start, 0, 0, "fill filled filling")) {
end = Found(source, start, 0, "in out up");
}
else if (IsA(source, start, 0, 0, "find found finding")) {
end = Found(source, start, 0, "out");
}
else if (IsA(source, start, 0, 0, "get got getting gotten")) {
end = Found(source, start, 0, "across over back");
}
else if (IsA(source, start, 0, 0, "give given gave giving")) {
end = Found(source, start, 0, "away back out up");
}
else if (IsA(source, start, 0, 0, "hand handed handing")) {
end = Found(source, start, 0, "down in over");
}
else if (IsA(source, start, 0, 0, "hold held holding")) {
end = Found(source, start, 0, "back up");
}
else if (IsA(source, start, 0, 0, "keep kept keeping")) {
end = Found(source, start, 0, "from up");
}
else if (IsA(source, start, 0, 0, "let letting")) {
end = Found(source, start, 0, "down in");
}
else if (IsA(source, start, 0, 0, "look looked looking")) {
end = Found(source, start, 0, "over up");
}
else if (IsA(source, start, 0, 0, "make made making")) {
end = Found(source, start, 0, "up");
}
else if (IsA(source, start, 0, 0, "mix mixed mixing")) {
end = Found(source, start, 0, "up");
}
else if (IsA(source, start, 0, 0, "pass passed passing")) {
end = Found(source, start, 0, "out up");
}
else if (IsA(source, start, 0, 0, "pay payed paying")) {
end = Found(source, start, 0, "back");
}
else if (IsA(source, start, 0, 0, "pick picked picking")) {
end = Found(source, start, 0, "out");
}
else if (IsA(source, start, 0, 0, "point pointed pointing")) {
end = Found(source, start, 0, "out");
}
else if (IsA(source, start, 0, 0, "put putting")) {
end = Found(source, start, 0, "down off out together on");
}
else if (IsA(source, start, 0, 0, "send sending")) {
end = Found(source, start, 0, "back");
}
else if (IsA(source, start, 0, 0, "set setting")) {
end = Found(source, start, 0, "up");
}
else if (IsA(source, start, 0, 0, "sort sorted sorting")) {
end = Found(source, start, 0, "out");
}
else if (IsA(source, start, 0, 0, "switch switched switching")) {
end = Found(source, start, 0, "off on");
}
else if (IsA(source, start, 0, 0, "take took taking")) {
end = Found(source, start, 0, "apart back off out");
}
else if (IsA(source, start, 0, 0, "tear torn tearing")) {
end = Found(source, start, 0, "up");
}
else if (IsA(source, start, 0, 0, "think thought thinking")) {
end = Found(source, start, 0, "over");
}
else if (IsA(source, start, 0, 0, "thrown threw thrown throwing")) {
end = Found(source, start, 0, "away");
}
else if (IsA(source, start, 0, 0, "turn turned turning")) {
end = Found(source, start, 0, "down off on");
}
else if (IsA(source, start, 0, 0, "try tried trying")) {
end = Found(source, start, 0, "on out");
}
else if (IsA(source, start, 0, 0, "use used using")) {
end = Found(source, start, 0, "up");
}
else if (IsA(source, start, 0, 0, "warm warmed warming")) {
end = Found(source, start, 0, "up");
}
else if (IsA(source, start, 0, 0, "work worked working")) {
end = Found(source, start, 0, "out");
}
// found range to label
if (end != std::numeric_limits<size_t>::max() &&
end > start + 1) {
bool add = true;
if (revision == 1 && Exist(source,
start + 1,
end - 1,
1,
"VB VBD VBG VBN VBP VBZ")) {
// there's a verb in between
add = false;
}
if (add) {
Range range(start + 1, end - 1, "reorder-label");
ranges.push_back(range);
}
}
}
OutputWithLabels(source, ranges, out);
}
void write_int(Properties &properties, int nbits, int val) {
assert(properties.size() == range.size());
FinalCompoundSymbolChances<BitChance,bits> &chances = find_leaf(properties);
coder.write_int(chances, nbits, val);
}
int read_int(Properties &properties, int nbits) {
assert(properties.size() == range.size());
FinalCompoundSymbolChances<BitChance,bits> &chances = find_leaf(properties);
return coder.read_int(chances, nbits);
}
void write_int(Properties &properties, int min, int max, int val) {
if (min == max) { assert(val==min); return; }
assert(properties.size() == range.size());
FinalCompoundSymbolChances<BitChance,bits> &chances = find_leaf(properties);
coder.write_int(chances, min, max, val);
}
int read_int(Properties &properties, int min, int max) {
if (min == max) { return min; }
assert(properties.size() == range.size());
FinalCompoundSymbolChances<BitChance,bits> &chances = find_leaf(properties);
return coder.read_int(chances, min, max);
}
int main(int argc, char* argv[]) {
#ifdef USE_GOOGLE_PROFILER
char *profileFileName = getenv("CPUPROFILE");
if (profileFileName != NULL) {
ProfilerStart(profileFileName);
}
else {
ProfilerStart("google_profile.txt");
}
#endif
// Register inputs and outputs.
string samFileName, refFileName, outFileName;
CommandLineParser clp;
clp.RegisterStringOption("file.sam", &samFileName,
"Input SAM file.");
clp.RegisterStringOption("reference.fasta", &refFileName,
"Reference used to generate reads.");
clp.RegisterStringOption("out.sam", &outFileName,
"Output SAM file.");
clp.RegisterPreviousFlagsAsHidden();
// Register filter criteria options.
int minAlnLength = 50;
float minPctSimilarity = 70, minPctAccuracy = 70;
string hitPolicyStr = "randombest";
bool useScoreCutoff = false;
int scoreCutoff = INF_INT;
int scoreSignInt = -1;
RegisterFilterOptions(clp, minAlnLength, minPctSimilarity,
minPctAccuracy, hitPolicyStr, useScoreCutoff,
scoreSignInt, scoreCutoff);
int seed = 1;
clp.RegisterIntOption("seed", &seed,
"(1) Seed for random number generator.\n"
"If seed is 0, then use current time as seed.",
CommandLineParser::Integer);
string holeNumberStr;
Ranges holeNumberRanges;
clp.RegisterStringOption("holeNumbers", &holeNumberStr,
"A string of comma-delimited hole number ranges to output hits, "
"such as '1,2,10-12'. "
"This requires hit titles to be in SMRT read title format.");
bool parseSmrtTitle = false;
clp.RegisterFlagOption("smrtTitle", &parseSmrtTitle,
"Use this option when filtering alignments generated by "
"programs other than blasr, e.g. bwa-sw or gmap. "
" Parse read coordinates from the SMRT read title. "
"The title is in the format /name/hole/coordinates, where"
" coordinates are in the format \\d+_\\d+, and represent "
"the interval of the read that was aligned.");
/* This experimental option can be useful for metagenomics, in which case
* there are hundreds of sequences in the target, of which many titles are
* long and may contain white spaces (e.g., ' ', '\t').
* In order to save disc space and avoid the (possibly) none unique mapping
* between full and short reference names, one may call blasr with
* -titleTable option to represent all target sequences in the output
* by their indices in the title table.*/
string titleTableName = "";
clp.RegisterStringOption("titleTable", &titleTableName,
"Use this experimental option when filtering alignments generated by "
"blasr with -titleTable titleTableName, in which case "
"reference titles in SAM are represented by their "
"indices (e.g., 0, 1, 2, ...) in the title table.");
string adapterGffFileName = "";
clp.RegisterStringOption("filterAdapterOnly", &adapterGffFileName,
"Use this option to remove reads which can only map to adapters "
"specified in the GFF file.");
bool verbose = false;
clp.RegisterFlagOption("v", &verbose, "Be verbose.");
clp.SetExamples(
"Because SAM has optional tags that have different meanings"
" in different programs, careful usage is required in order "
"to have proper output. The \"xs\" tag in bwa-sw is used to "
"show the suboptimal score, but in PacBio SAM (blasr) it is "
"defined as the start in the query sequence of the alignment.\n"
"When \"-smrtTitle\" is specified, the xs tag is ignored, but "
"when it is not specified, the coordinates given by the xs and "
"xe tags are used to define the interval of a read that is "
"aligned. The CIGAR string is relative to this interval.");
clp.ParseCommandLine(argc, argv);
// Set random number seed.
if (seed == 0) {
srand(time(NULL));
} else {
srand(seed);
}
scoreSign = (scoreSignInt == -1)?ScoreSign::NEGATIVE:ScoreSign::POSITIVE;
Score s(static_cast<float>(scoreCutoff), scoreSign);
FilterCriteria filterCriteria(minAlnLength, minPctSimilarity,
minPctAccuracy, true, s);
filterCriteria.Verbose(verbose);
HitPolicy hitPolicy(hitPolicyStr, scoreSign);
string errMsg;
if (not filterCriteria.MakeSane(errMsg)) {
cout << errMsg << endl;
exit(1);
}
// Parse hole number ranges.
if (holeNumberStr.size() != 0) {
if (not holeNumberRanges.setRanges(holeNumberStr)) {
cout << "Could not parse hole number ranges: "
<< holeNumberStr << "." << endl;
exit(1);
}
}
// Open output file.
ostream * outFilePtr = &cout;
ofstream outFileStrm;
if (outFileName != "") {
CrucialOpen(outFileName, outFileStrm, std::ios::out);
outFilePtr = &outFileStrm;
}
GFFFile adapterGffFile;
if (adapterGffFileName != "")
adapterGffFile.ReadAll(adapterGffFileName);
SAMReader<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> samReader;
FASTAReader fastaReader;
//
// Initialize samReader and fastaReader.
//
samReader.Initialize(samFileName);
fastaReader.Initialize(refFileName);
//
// Configure the file log.
//
string command;
CommandLineParser::CommandLineToString(argc, argv, command);
string log = "Filter sam hits.";
string program = "samFilter";
string versionString = VERSION;
AppendPerforceChangelist(PERFORCE_VERSION_STRING, versionString);
//
// Read necessary input.
//
vector<FASTASequence> references;
fastaReader.ReadAllSequences(references);
// If the SAM file is generated by blasr with -titleTable,
// then references in the SAM are represented by
// their corresponding indices in the title table.
// In that case, we need to convert reference titles in fasta file
// to their corresponding indices in the title table, such that
// references in both SAM and fasta files are represented
// by title table indices and therefore can match.
if (titleTableName != "") {
ConvertTitlesToTitleTableIndices(references, titleTableName);
}
AlignmentSet<SAMFullReferenceSequence, SAMReadGroup, SAMAlignment> alignmentSet;
vector<string> allHeaders = samReader.ReadHeader(alignmentSet);
// Process SAM Header.
string commandLineString;
clp.CommandLineToString(argc, argv, commandLineString);
allHeaders.push_back("@PG\tID:SAMFILTER\tVN:" + versionString + \
"\tCL:" + program + " " + commandLineString);
for (int i = 0; i < allHeaders.size(); i++) {
outFileStrm << allHeaders[i] << endl;
}
//
// The order of references in vector<FASTASequence> references and
// AlignmentSet<, , >alignmentSet.references can be different.
// Rearrange alignmentSet.references such that they are ordered in
// exactly the same way as vector<FASTASequence> references.
//
alignmentSet.RearrangeReferences(references);
// Map reference name obtained from SAM file to indices
map<string, int> refNameToIndex;
for (int i = 0; i < references.size(); i++) {
string refName = alignmentSet.references[i].GetSequenceName();
refNameToIndex[refName] = i;
}
//
// Store the alignments.
//
SAMAlignment samAlignment;
int alignIndex = 0;
//
// For 150K, each chip produces about 300M sequences
// (not including quality values and etc.).
// Let's assume that the sam file and reference data can
// fit in the memory.
// Need to scale for larger sequal data in the future.
//
vector<SAMAlignment> allSAMAlignments;
while (samReader.GetNextAlignment(samAlignment)) {
if (samAlignment.rName == "*") {
continue;
}
if (parseSmrtTitle and holeNumberStr.size() != 0) {
string movieName;
int thisHoleNumber;
if (not ParsePBIReadName(samAlignment.qName,
movieName,
thisHoleNumber)) {
cout << "ERROR, could not parse SMRT title: "
<< samAlignment.qName << "." << endl;
exit(1);
}
if (not holeNumberRanges.contains(UInt(thisHoleNumber))) {
if (verbose)
cout << thisHoleNumber << " is not in range." << endl;
continue;
}
}
if (samAlignment.cigar.find('P') != string::npos) {
cout << "WARNING. Could not process SAM record with 'P' in "
<< "its cigar string." << endl;
continue;
}
vector<AlignmentCandidate<> > convertedAlignments;
SAMAlignmentsToCandidates(samAlignment,
references, refNameToIndex,
convertedAlignments, parseSmrtTitle, false);
if (convertedAlignments.size() > 1) {
cout << "WARNING. Ignore multiple segments." << endl;
continue;
}
for (int i = 0; i < 1; i++) {
AlignmentCandidate<> & alignment = convertedAlignments[i];
//score func does not matter
DistanceMatrixScoreFunction<DNASequence, DNASequence> distFunc;
ComputeAlignmentStats(alignment, alignment.qAlignedSeq.seq,
alignment.tAlignedSeq.seq, distFunc);
// Check whether this alignment can only map to adapters in
// the adapter GFF file.
if (adapterGffFileName != "" and
CheckAdapterOnly(adapterGffFile, alignment, refNameToIndex)) {
if (verbose)
cout << alignment.qName << " filter adapter only."
<< endl;
continue;
}
// Assign score to samAlignment.
samAlignment.score = samAlignment.as;
if (not filterCriteria.Satisfy(static_cast<AlignmentCandidate<> *>(&alignment))) {
continue;
}
allSAMAlignments.push_back( samAlignment );
alignment.FreeSubsequences();
}
++alignIndex;
}
// Sort all SAM alignments by qName, score and target position.
sort(allSAMAlignments.begin(), allSAMAlignments.end(),
byQNameScoreTStart);
unsigned int groupBegin = 0;
unsigned int groupEnd = -1;
vector<SAMAlignment> filteredSAMAlignments;
while(groupBegin < allSAMAlignments.size()) {
// Get the next group of SAM alignments which have the same qName
// from allSAMAlignments[groupBegin ... groupEnd)
GetNextSAMAlignmentGroup(allSAMAlignments, groupBegin, groupEnd);
vector<unsigned int> hitIndices = ApplyHitPolicy(
hitPolicy, allSAMAlignments, groupBegin, groupEnd);
for(unsigned int i = 0; i < hitIndices.size(); i++) {
filteredSAMAlignments.push_back(allSAMAlignments[hitIndices[i]]);
}
groupBegin = groupEnd;
}
// Sort all SAM alignments by reference name and query name
sort(filteredSAMAlignments.begin(), filteredSAMAlignments.end(),
byRNameQName);
for(unsigned int i = 0; i < filteredSAMAlignments.size(); i++) {
filteredSAMAlignments[i].PrintSAMAlignment(outFileStrm);
}
if (outFileName != "") {
outFileStrm.close();
}
#ifdef USE_GOOGLE_PROFILER
ProfilerStop();
#endif
return 0;
}
