bool ContextBase::handle_i()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -i option given, but no input file specified. *****";
return false;
}
addInputFile(_argv[_i+1]);
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextIntersect::handle_abam()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -abam option given, but no query BAM file specified. *****";
return false;
}
addInputFile(_argv[_i+1]);
_queryFileIdx = getNumInputFiles() -1;
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
return true;
}
bool ContextGroupBy::isValidState()
{
// The user was required to have entered one or more columns
if (_keyListOps->getColumns().empty()) {
_errorMsg = "***** ERROR: -opCols parameter requires a value.";
return false;
}
//default to stdin
if (getNumInputFiles() == 0) {
addInputFile("-");
}
//default grouping is cols 1,2,3
if (_groupStr.empty()) _groupStr = "1,2,3";
return ContextBase::isValidState();
}
bool ContextIntersect::handle_b()
{
if (_argc <= _i+1) {
_errorMsg = "\n***** ERROR: -b option given, but no database file specified. *****";
return false;
}
do {
addInputFile(_argv[_i+1]);
int fileId = getNumInputFiles() -1;
_dbFileIdxs.push_back(fileId);
_fileIdsToDbIdxs[fileId] = _dbFileIdxs.size() -1;
markUsed(_i - _skipFirstArgs);
_i++;
markUsed(_i - _skipFirstArgs);
} while (_argc > _i+1 && _argv[_i+1][0] != '-');
return true;
}
bool ContextMerge::isValidState()
{
// Special: The merge program does not have default
//column operations, so if none were entered, disable column ops.
if (_keyListOps->getColumns().empty() && _keyListOps->getOperations().empty()) {
setColumnOpsMethods(false);
delete _keyListOps;
_keyListOps = NULL;
}
//default to stdin
if (getNumInputFiles() == 0) {
addInputFile("-");
}
if (!ContextBase::isValidState()) {
return false;
}
//
// Tests for stranded merge
//
if (_desiredStrand != FileRecordMergeMgr::ANY_STRAND) { // requested stranded merge
// make sure file has strand.
if (!getFile(0)->recordsHaveStrand()) {
_errorMsg = "\n***** ERROR: stranded merge requested, but input file records do not have strand. *****";
return false;
}
//make sure file is not VCF.
if (getFile(0)->getFileType() == FileRecordTypeChecker::VCF_FILE_TYPE) {
_errorMsg = "\n***** ERROR: stranded merge not supported for VCF files. *****";
return false;
}
}
return true;
}
void oms::Mosaic::setupOrthoThumbnail(const std::string& filename,
const std::string& entryId,
const std::string& srsCode,
ossim_uint32 resolution,
const std::string& histogramAutoStretchModeType)
{
thePrivateData->clear();
std::string id = addInputFile(filename, entryId);
if(id.empty())
{
return;
}
if(srsCode.empty())
{
ossimRefPtr<ossimImageGeometry> geom = thePrivateData->theImageChainList[0]->theHandler->getImageGeometry();
if(geom.valid())
{
if(!dynamic_cast<ossimMapProjection*>(geom->getProjection()))
{
ossimIrect rect = thePrivateData->theImageChainList[0]->theHandler->getBoundingRect();
if(!rect.hasNans())
{
ossimGpt midPoint;
geom->localToWorld(rect.midPoint(), midPoint);
ossimMapProjection* mapProj = new ossimEquDistCylProjection();
mapProj->setMetersPerPixel(geom->getMetersPerPixel());
mapProj->setOrigin(midPoint);
thePrivateData->theViewGeometry = new ossimImageGeometry(0, mapProj);
}
}
else
{
thePrivateData->theViewGeometry = (ossimImageGeometry*)geom->dup();
}
}
}
else
{
ossimRefPtr<ossimProjection> proj = ossimProjectionFactoryRegistry::instance()->createProjection(srsCode);
thePrivateData->theViewGeometry = new ossimImageGeometry(0, proj.get());
}
if(!thePrivateData->theViewGeometry.valid())
{
return;
}
thePrivateData->theImageChainList[0]->theBandSelector = new ossimBandSelector;
thePrivateData->theImageChainList[0]->theBandSelector->connectMyInputTo(0, thePrivateData->theImageChainList[0]->theHandler.get());
thePrivateData->theImageChainList[0]->theHistogramRemapper = new ossimHistogramRemapper;
thePrivateData->theImageChainList[0]->theHistogramRemapper->connectMyInputTo(0, thePrivateData->theImageChainList[0]->theBandSelector.get());
if(!histogramAutoStretchModeType.empty())
{
if(thePrivateData->theImageChainList[0]->theHistogramRemapper->openHistogram(thePrivateData->theImageChainList[0]->theHandler->createDefaultHistogramFilename()))
{
thePrivateData->theImageChainList[0]->theHistogramRemapper->setStretchModeAsString(histogramAutoStretchModeType);
}
}
thePrivateData->theImageChainList[0]->theReprojection = new ossimImageRenderer;
thePrivateData->theImageChainList[0]->theReprojection->setView(thePrivateData->theViewGeometry.get());
thePrivateData->theImageChainList[0]->theReprojection->connectMyInputTo(0, thePrivateData->theImageChainList[0]->theHistogramRemapper.get());
ossimIrect bounds = thePrivateData->theImageChainList[0]->theReprojection->getBoundingRect();
ossim_uint32 maxRes = ossim::max(bounds.width(), bounds.height());
if(maxRes > resolution)
{
double scale = 0.0;
if(resolution > 1)
{
scale = (double)maxRes/(double)(resolution-1);
}
else
{
scale = (double)maxRes/(double)(resolution);
}
ossimMapProjection* mapProj = dynamic_cast<ossimMapProjection*>(thePrivateData->theViewGeometry->getProjection());
if(mapProj)
{
mapProj->applyScale(ossimDpt(scale,scale), true);
thePrivateData->theImageChainList[0]->theReprojection->setView(thePrivateData->theViewGeometry.get());
}
else
{
return;
}
}
thePrivateData->theMosaic->connectMyInputTo(thePrivateData->theImageChainList[0]->theReprojection.get());
bounds = thePrivateData->theMosaic->getBoundingRect();
}
void NTupleEventReader::addInputFileWithoutCheck(const char * fileName) {
// numberOfFiles += input->Add(fileName);
addInputFile(fileName);
}
