void ProgressBar::changed(ConstFieldMaskArg whichField,
UInt32 origin,
BitVector details)
{
Inherited::changed(whichField, origin, details);
//Do not respond to changes that have a Sync origin
if(origin & ChangedOrigin::Sync)
{
return;
}
if((whichField & SizeFieldMask))
{
setupProgressBar();
}
if(whichField & RangeModelFieldMask)
{
_ProgressStateChangedConnection.disconnect();
if(getRangeModel() != NULL)
{
_ProgressStateChangedConnection = getRangeModel()->connectStateChanged(boost::bind(&ProgressBar::handleProgressStateChanged, this, _1));
}
}
}
void ProgressBar::setupIndeterminateProgressBar(const Time& Elps)
{
_IndeterminateBarPosition += Elps * getIndeterminateBarMoveRate();
if(_IndeterminateBarPosition > 2.0)
{
_IndeterminateBarPosition -= 2.0f*osgFloor(_IndeterminateBarPosition/2.0f);
}
setupProgressBar();
}
void ProgressBar::handleProgressStateChanged(ChangeEventDetails* const e)
{
setupProgressBar();
}
void ProgressBar::endIndeterminate(void)
{
setIndeterminate(false);
_ProgressUpdateConnection.disconnect();
setupProgressBar();
}
bool FastaReader::readFile(QString fileName)
{
string file = fileName.toStdString();
//Make sure that we were requested to open a file
if(file.empty())
{
return false;
}
ui->print(file);
setupProgressBar();
//Parse the name of the chromosome from the file name and send it to glwidget to be stored
storeChrName(file);
//Clear out anything that may be left in the sequence string and set initial pad character
sequence.clear();
sequence = "";
sequence.reserve(5);
sequence = string(">");
//Clear out anything that may be in the ifstream then open the new file
wordfile.clear();
wordfile.open(file.c_str(), ifstream::in | ifstream::binary);
//See if we opened the file successfully
if(wordfile.fail())
{
ErrorBox msg("Could not read the file. Either Skittle doesn't have file permissions or the file does not exist.");
return false;
}
//Get how many characters are in the file
wordfile.seekg(0, ios::beg);
int begin = wordfile.tellg();
wordfile.seekg(0, ios::end);
int end = wordfile.tellg();
bytesInFile = end - begin;
//Discovered Reserve is different than malloc by creating a memory iterator
//The iterator takes old size, then virtually allocates a new vector to new size while at the same time copying start/end memory to this new location
//Then it destroys the old vector and walks through physical storage looking for a contiguous slot open, then dumps into the start and end location of new slot
sequence.reserve(bytesInFile);
//Start progress bar at 0
int progress = bytesInFile / 20;
progressBar->setValue(progress);
QApplication::processEvents();
//Return to the beginning of the file
wordfile.seekg(0, ios::beg);
//Skip the first line of the file as this is the chromosome name/info
wordfile.ignore(500, '\n');
//Read in the rest of the file
char current;
int i = 0;
cancelled = false;
do
{
//If the cancel button was pushed, go ahead and exit fasta reader
if(cancelled){
return false;
}
//Read the next character
wordfile >> current;
//If it is a letter, uppercase it
current = upperCase(current);
//if(current == 65 || current == 67 || current == 71 || current == 84 || current == 78) //A C G T N
if(current != '\n' && current != '\r')
{
sequence.push_back(current);
}
if(i != 0 && i % progress == 0)
{
progressBar->setValue(progressBar->value() + 5);
QApplication::processEvents();
}
i++;
}
while(!wordfile.eof() && !wordfile.fail() && !cancelled);
//Close up everything
progressBar->reset();
progressBar->close();
if(progressBar)
{
delete progressBar;
progressBar = NULL;
}
wordfile.close();
ui->print("Done loading file!");
emit newFileRead(seq());
return true;
}
