void doJob(const std::string& inputMaf, const std::string& outDir,
std::vector<ParamPair> simplParams, std::vector<int> minBlockSizes)
{
const int MIN_ALIGNMENT = 1;
const int MAX_ALIGNMENT_GAP = 0;
const auto EMPTY_GROUP = BlockGroups();
BlockGroups blockGroups = EMPTY_GROUP;
PermVec currentBlocks;
//sort blocks in reverse order (will use it as stack)
std::sort(minBlockSizes.begin(), minBlockSizes.end(), std::greater<int>());
makeDirectory(outDir);
//read maf alignment and join adjacent columns
std::cerr << "\tParsing MAF file\n";
PermVec mafBlocks = mafToPermutations(inputMaf, MIN_ALIGNMENT);
compressPaths(mafBlocks, MAX_ALIGNMENT_GAP, currentBlocks, blockGroups);
//iterative simplification
for (const ParamPair& ppair : simplParams)
{
if (minBlockSizes.empty()) break;
//output blocks of certain size
while (!minBlockSizes.empty() && minBlockSizes.back() < ppair.minBlock)
{
std::string blockDir = outDir + "/" +
std::to_string(minBlockSizes.back());
outputBlocks(blockDir, currentBlocks, blockGroups,
minBlockSizes.back());
minBlockSizes.pop_back();
}
std::cerr << "\tSimplification with " << ppair.minBlock << " "
<< ppair.maxGap << std::endl;
PermVec inputBlocks = filterBySize(currentBlocks, EMPTY_GROUP,
ppair.minBlock, true);
PermVec outBlocks;
blockGroups.clear();
processGraph(inputBlocks, ppair.maxGap, outBlocks, blockGroups);
currentBlocks = outBlocks;
}
//if any left
for (int minBlock : minBlockSizes)
{
std::string blockDir = outDir + "/" + std::to_string(minBlock);
outputBlocks(blockDir, currentBlocks, blockGroups, minBlock);
}
}
void outputBlocks(const std::string& outDir, PermVec& blocks,
BlockGroups& groups, int blockSize)
{
makeDirectory(outDir);
std::string permsFile = outDir + "/genomes_permutations.txt";
std::string coordsFile = outDir + "/blocks_coords.txt";
std::string statsFile = outDir + "/coverage_report.txt";
PermVec outPerms = filterBySize(blocks, groups, blockSize, true);
renumerate(outPerms);
outputPermutation(outPerms, permsFile);
outputCoords(outPerms, coordsFile);
outputStatistics(outPerms, statsFile);
}
bool FilterDialog::validateInputs()
{
if(!validateSizeInputs())
return false;
if(!validateRegexInput())
return false;
if(!validatePathInput())
return false;
if(sizeRangeGroupBox->isChecked())
emit filterBySize( minFileSizeLineEdit->value(), maxFileSizeLineEdit->value() );
if(typesGroupBox->isChecked())
/* fire */ signalTypesSelection();
if(pathGroupBox->isChecked())
emit filterByPath(folderPathLineEdit->text());
if(regexGroupBox->isChecked())
emit filterByRegex( QRegExp(regexLineEdit->text()) );
return true;
}
ActionsButtonPanel::ActionsButtonPanel(QWidget *parent)
: QWidget(parent)
{
//createDefaultExtensions();
QVBoxLayout *mainLayout = new QVBoxLayout(this);
filter_pushButton = new QPushButton("&Filter", this);
sort_pushButton = new QPushButton("&Sort", this);
reset_pushButton = new QPushButton("&Reset", this);
markings_pushButton = new QPushButton("Markings", this);
autoSelection_pushButton = new QPushButton("&Auto Selection", this);
commit_pushButton = new QPushButton("&Commit", this);
auto_pushButton = new QPushButton("A&uto", this);
filterDialog = new FilterDialog(this);
sort_pushButton->setCheckable(true);
markings_pushButton->setCheckable(true);
autoSelection_pushButton->setCheckable(true);
QFrame* line = new QFrame(this);
line->setFrameShape(QFrame::HLine);
QFrame* line2 = new QFrame(this);
line2->setFrameShape(QFrame::HLine);
QFrame* line3 = new QFrame(this);
line3->setFrameShape(QFrame::HLine);
mainLayout->addWidget(commit_pushButton);
mainLayout->addWidget(line);
mainLayout->addWidget(filter_pushButton);
mainLayout->addWidget(sort_pushButton);
mainLayout->addWidget(reset_pushButton);
mainLayout->addWidget(line2);
mainLayout->addWidget(autoSelection_pushButton);
mainLayout->addWidget(markings_pushButton);
mainLayout->addWidget(line3);
mainLayout->addWidget(auto_pushButton);
mainLayout->addStretch();
auto_pushButton->setEnabled(false);
sortContextMenu.addAction("&Descending Order of File size", this, SLOT(sortByDescendingFileSize()));
sortContextMenu.addAction("&Ascending Order of File size", this, SLOT(sortByAscendingFileSize()));
autoSelectionContextMenu.addAction("Select Group Keeps", this, SIGNAL(selectGroupKeeps()));
autoSelectionContextMenu.addAction("Select Group Deletes", this, SIGNAL(selectGroupDeletes()));
autoSelectionContextMenu.addAction("Select Next Group Keeps", this, SIGNAL(selectNextGroupKeeps()));
autoSelectionContextMenu.addAction("Select Next Group Deletes", this, SIGNAL(selectNextGroupDeletes()));
autoSelectionContextMenu.addAction("Auto Select Next &Possibilities", this, SIGNAL(autoSelectDeletePossibilities()))
;// ->setEnabled(false);
autoSelectionContextMenu.addAction("Auto Select Highest &Keeps", this, SIGNAL(autoSelectNextKeeps()));
autoSelectionContextMenu.addAction("Auto Select Highest &Deletes", this, SIGNAL(autoSelectNextDeletes()));
markingsContextMenu.addAction("Unmark &All", this, SIGNAL(unmarkAll()));
markingsContextMenu.addAction("Unmark All &Keeps", this, SIGNAL(unmarkAllKeeps()));
markingsContextMenu.addAction("Unmark all &Deletes", this, SIGNAL(unmarkAllDeletes()));
connect(reset_pushButton, SIGNAL(clicked()), this, SIGNAL(resetRequested()));
connect(commit_pushButton, SIGNAL(clicked()), this, SIGNAL(commitRequested()));
connect(filter_pushButton, SIGNAL(clicked()), this, SLOT(filterContextMenuClicked()));
connect(sort_pushButton, SIGNAL(clicked()), this, SLOT(processSortRequest()));
connect(autoSelection_pushButton, SIGNAL(clicked()), this, SLOT(processAutoSelectionClicked()));
connect(markings_pushButton, SIGNAL(clicked()), this, SLOT(processMarkingsClicked()));
connect(auto_pushButton, SIGNAL(clicked()), this, SIGNAL(autoCleanDeletes()));
connect(&sortContextMenu, SIGNAL(aboutToHide()), this, SLOT(sortContextMenuAboutToHide()));
connect(&autoSelectionContextMenu, SIGNAL(aboutToHide()), this,
SLOT(autoSelectionContextMenuAboutToHide()));
connect(&markingsContextMenu, SIGNAL(aboutToHide()), this,
SLOT(markingsContextMenuAboutToHide()));
connect(&filterContextMenu, SIGNAL(aboutToHide()), this,
SLOT(filterContextMenuAboutToHide()));
connect(filterDialog, SIGNAL(aboutToHide()), this, SLOT(filterContextMenuAboutToHide()));
connect(filterDialog, SIGNAL(filterByExtension(QStringList)), this, SIGNAL(filterByExtension(QStringList)));
connect(filterDialog, SIGNAL(filterByPath(QString)), this, SIGNAL(filterByPath(QString)));
connect(filterDialog, SIGNAL(filterByRegex(QRegExp)), this, SIGNAL(filterByRegex(QRegExp)));
connect(filterDialog, SIGNAL(filterBySize(ulong,ulong)), this, SIGNAL(filterBySize(ulong,ulong)));
}
