int main(int argc, char* argv[])
{
//options
// -i inputfile -a annotationfiles -f forcestrand
bool showHelp = false;
string infile;
vector<string> annofiles;
bool forcestrand = false;
// Show help when has no options
if(argc <= 1)
{
Help();
return 0;
}
// Parsing options
for(int i = 1; i < argc; i++)
{
int parameterLength = (int)strlen(argv[i]);
if((PARAMETER_CHECK("-h", 2, parameterLength)) || (PARAMETER_CHECK("--help", 5, parameterLength)))
showHelp=true;
else if ((PARAMETER_CHECK("-i", 2, parameterLength)) || (PARAMETER_CHECK("--input", 7, parameterLength)))
{
if ((++i) < argc)
infile=argv[i];
}
else if ((PARAMETER_CHECK("-a", 2, parameterLength)) || (PARAMETER_CHECK("--annotations", 13, parameterLength)))
{
if ((++i) < argc)
{
StringUtils::tokenize(string(argv[i]),annofiles,",");
}
}
else if ((PARAMETER_CHECK("-s", 2, parameterLength)) || (PARAMETER_CHECK("--forcestrand", 13, parameterLength)))
forcestrand = true;
else
{
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
}
}
// Show help if no proper auguments.
if (showHelp)
{
Help();
return 0;
}
// definition
int annocount=annofiles.size(); // File count
vector<BedMap> bedmaps(annocount); // BedMap
vector<double> annos(annocount+1,0); // Count reads for each kind of annotaions. The last one counts the remained reads.
LINE_ELEMS elems; // Column reader buffer
Hits hits;
ColumnReader beds(infile);
// Load annotations into BedMaps
for(int i=0;i<annocount;i++)
BedUtils::loadBedFileToMap(bedmaps[i],annofiles[i]);
// Annotation
beds.open();
while(beds.getNext(elems)!=LINE_INVALID)
{
Bed tbed(elems);
cout << tbed;
bool intersectflag=true;
for(int i=0;i<annocount;i++)
{
if(intersectflag)
{
BedUtils::intersectBed(tbed,bedmaps[i],hits,forcestrand);
if(hits.size())
{
annos[i]+=tbed.score;
cout << "\t" << tbed.score;
intersectflag=false; // if found hits, suppress intersection for the following annotations.
}
else
cout << "\t0";
hits.clear();
}
else
cout << "\t0";
}
if(intersectflag) // No overlas with annotations.
{
cout << "\t" << tbed.score << endl;
annos[annocount]+=tbed.score;
}
else
cout << "\t0" << endl;
}
for(int i=0;i<annocount;i++)
cerr << annofiles[i] << "\t" << annos[i] << endl;
cerr << "Remained\t" << annos[annocount] << endl;
return 0;
}
bool
Picker::pick( float x, float y, Hits& results ) const
{
float local_x, local_y = 0.0;
const osg::Camera* camera = _view->getCameraContainingPosition(x, y, local_x, local_y);
if ( !camera )
camera = _view->getCamera();
osg::ref_ptr<osgEarth::PrimitiveIntersector> picker;
double buffer_x = _buffer, buffer_y = _buffer;
if ( camera->getViewport() )
{
double aspectRatio = camera->getViewport()->width()/camera->getViewport()->height();
buffer_x *= aspectRatio;
buffer_y /= aspectRatio;
}
osg::Matrix windowMatrix;
if ( _root.valid() )
{
osg::Matrix modelMatrix;
if (camera->getViewport())
{
windowMatrix = camera->getViewport()->computeWindowMatrix();
modelMatrix.preMult( windowMatrix );
}
modelMatrix.preMult( camera->getProjectionMatrix() );
modelMatrix.preMult( camera->getViewMatrix() );
osg::NodePath prunedNodePath( _path.begin(), _path.end()-1 );
modelMatrix.preMult( osg::computeWorldToLocal(prunedNodePath) );
osg::Matrix modelInverse;
modelInverse.invert(modelMatrix);
osg::Vec3d startLocal(local_x, local_y, 0.0);
osg::Vec3d startModel = startLocal * modelInverse;
osg::Vec3d endLocal(local_x, local_y, 1.0);
osg::Vec3d endModel = endLocal * modelInverse;
osg::Vec3d bufferLocal(local_x + buffer_x, local_y + buffer_y, 0.0);
osg::Vec3d bufferModel = bufferLocal * modelInverse;
double buffer = osg::maximum((bufferModel - startModel).length(), 5.0); //TODO: Setting a minimum of 4.0 may need revisited
OE_DEBUG
<< "local_x:" << local_x << ", local_y:" << local_y
<< ", buffer_x:" << buffer_x << ", buffer_y:" << buffer_y
<< ", bm.x:" << bufferModel.x() << ", bm.y:" << bufferModel.y()
<< ", bm.z:" << bufferModel.z()
<< ", BUFFER: " << buffer
<< std::endl;
picker = new osgEarth::PrimitiveIntersector(osgUtil::Intersector::MODEL, startModel, endModel, buffer);
}
else
{
picker = new osgEarth::PrimitiveIntersector(camera->getViewport() ? osgUtil::Intersector::WINDOW : osgUtil::Intersector::PROJECTION, local_x, local_y, _buffer);
}
picker->setIntersectionLimit( (osgUtil::Intersector::IntersectionLimit)_limit );
osgUtil::IntersectionVisitor iv(picker.get());
//picker->setIntersectionLimit( osgUtil::Intersector::LIMIT_ONE_PER_DRAWABLE );
// in MODEL mode, we need to window and proj matrixes in order to support some of the
// features in osgEarth (like Annotation::OrthoNode).
if ( _root.valid() )
{
iv.pushWindowMatrix( new osg::RefMatrix(windowMatrix) );
iv.pushProjectionMatrix( new osg::RefMatrix(camera->getProjectionMatrix()) );
iv.pushViewMatrix( new osg::RefMatrix(camera->getViewMatrix()) );
}
iv.setTraversalMask( _travMask );
if ( _root.valid() )
_path.back()->accept(iv);
else
const_cast<osg::Camera*>(camera)->accept(iv);
if (picker->containsIntersections())
{
results = picker->getIntersections();
return true;
}
else
{
results.clear();
return false;
}
}
bool
Picker::pick( float x, float y, Hits& results ) const
{
float local_x, local_y = 0.0;
const osg::Camera* camera = _view->getCameraContainingPosition(x, y, local_x, local_y);
if ( !camera )
camera = _view->getCamera();
osg::ref_ptr<osgUtil::PolytopeIntersector> picker;
double buffer_x = _buffer, buffer_y = _buffer;
if ( camera->getViewport() )
{
double aspectRatio = camera->getViewport()->width()/camera->getViewport()->height();
buffer_x *= aspectRatio;
buffer_y /= aspectRatio;
}
double zNear = 0.00001;
double zFar = 1.0;
double xMin = local_x - buffer_x;
double xMax = local_x + buffer_x;
double yMin = local_y - buffer_y;
double yMax = local_y + buffer_y;
osg::Polytope winPT;
winPT.add(osg::Plane( 1.0, 0.0, 0.0, -xMin));
winPT.add(osg::Plane(-1.0, 0.0 ,0.0, xMax));
winPT.add(osg::Plane( 0.0, 1.0, 0.0, -yMin));
winPT.add(osg::Plane( 0.0,-1.0, 0.0, yMax));
winPT.add(osg::Plane( 0.0, 0.0, 1.0, zNear));
osg::Matrix windowMatrix;
if ( _root.valid() )
{
osg::Matrix matrix;
if (camera->getViewport())
{
windowMatrix = camera->getViewport()->computeWindowMatrix();
matrix.preMult( windowMatrix );
zNear = 0.0;
zFar = 1.0;
}
matrix.preMult( camera->getProjectionMatrix() );
matrix.preMult( camera->getViewMatrix() );
osg::NodePath prunedNodePath( _path.begin(), _path.end()-1 );
matrix.preMult( osg::computeWorldToLocal(prunedNodePath) );
osg::Polytope transformedPT;
transformedPT.setAndTransformProvidingInverse( winPT, matrix );
picker = new osgUtil::PolytopeIntersector(osgUtil::Intersector::MODEL, transformedPT);
}
else
{
osgUtil::Intersector::CoordinateFrame cf = camera->getViewport() ? osgUtil::Intersector::WINDOW : osgUtil::Intersector::PROJECTION;
picker = new osgUtil::PolytopeIntersector(cf, winPT);
}
//picker->setIntersectionLimit( (osgUtil::Intersector::IntersectionLimit)_limit );
osgUtil::IntersectionVisitor iv(picker.get());
// in MODEL mode, we need to window and proj matrixes in order to support some of the
// features in osgEarth (like Annotation::OrthoNode).
if ( _root.valid() )
{
iv.pushWindowMatrix( new osg::RefMatrix(windowMatrix) );
iv.pushProjectionMatrix( new osg::RefMatrix(camera->getProjectionMatrix()) );
iv.pushViewMatrix( new osg::RefMatrix(camera->getViewMatrix()) );
}
iv.setTraversalMask( _travMask );
if ( _root.valid() )
_path.back()->accept(iv);
else
const_cast<osg::Camera*>(camera)->accept(iv);
if (picker->containsIntersections())
{
results = picker->getIntersections();
return true;
}
else
{
results.clear();
return false;
}
}