// Iteratively left-aligns the indels in the alignment until we have a stable
// realignment. Returns true on realignment success or non-realignment.
// Returns false if we exceed the maximum number of realignment iterations.
//
bool stablyLeftAlign(BAMALIGN& alignment, string referenceSequence, int maxiterations, bool debug) {
#ifdef VERBOSE_DEBUG
int mismatchesBefore = countMismatches(alignment, referenceSequence);
#endif
if (!leftAlign(alignment, referenceSequence, debug)) {
return true;
} else {
while (leftAlign(alignment, referenceSequence, debug) && --maxiterations > 0) {
LEFTALIGN_DEBUG("realigning ..." << endl);
}
#ifdef VERBOSE_DEBUG
int mismatchesAfter = countMismatches(alignment, referenceSequence);
if (mismatchesBefore != mismatchesAfter) {
cerr << alignment.QNAME << endl;
cerr << "ERROR: found " << mismatchesBefore << " mismatches before, but " << mismatchesAfter << " after left realignment!" << endl;
exit(1);
}
#endif
if (maxiterations <= 0) {
return false;
} else {
return true;
}
}
}
//! [4]
void MainWindow::createActions()
{
//! [5]
newAct = new QAction(tr("&New"), this);
newAct->setShortcuts(QKeySequence::New);
newAct->setStatusTip(tr("Create a new file"));
connect(newAct, SIGNAL(triggered()), this, SLOT(newFile()));
//! [4]
openAct = new QAction(tr("&Open..."), this);
openAct->setShortcuts(QKeySequence::Open);
openAct->setStatusTip(tr("Open an existing file"));
connect(openAct, SIGNAL(triggered()), this, SLOT(open()));
//! [5]
saveAct = new QAction(tr("&Save"), this);
saveAct->setShortcuts(QKeySequence::Save);
saveAct->setStatusTip(tr("Save the document to disk"));
connect(saveAct, SIGNAL(triggered()), this, SLOT(save()));
printAct = new QAction(tr("&Print..."), this);
printAct->setShortcuts(QKeySequence::Print);
printAct->setStatusTip(tr("Print the document"));
connect(printAct, SIGNAL(triggered()), this, SLOT(print()));
exitAct = new QAction(tr("E&xit"), this);
exitAct->setShortcuts(QKeySequence::Quit);
exitAct->setStatusTip(tr("Exit the application"));
connect(exitAct, SIGNAL(triggered()), this, SLOT(close()));
undoAct = new QAction(tr("&Undo"), this);
undoAct->setShortcuts(QKeySequence::Undo);
undoAct->setStatusTip(tr("Undo the last operation"));
connect(undoAct, SIGNAL(triggered()), this, SLOT(undo()));
redoAct = new QAction(tr("&Redo"), this);
redoAct->setShortcuts(QKeySequence::Redo);
redoAct->setStatusTip(tr("Redo the last operation"));
connect(redoAct, SIGNAL(triggered()), this, SLOT(redo()));
cutAct = new QAction(tr("Cu&t"), this);
cutAct->setShortcuts(QKeySequence::Cut);
cutAct->setStatusTip(tr("Cut the current selection's contents to the "
"clipboard"));
connect(cutAct, SIGNAL(triggered()), this, SLOT(cut()));
copyAct = new QAction(tr("&Copy"), this);
copyAct->setShortcuts(QKeySequence::Copy);
copyAct->setStatusTip(tr("Copy the current selection's contents to the "
"clipboard"));
connect(copyAct, SIGNAL(triggered()), this, SLOT(copy()));
pasteAct = new QAction(tr("&Paste"), this);
pasteAct->setShortcuts(QKeySequence::Paste);
pasteAct->setStatusTip(tr("Paste the clipboard's contents into the current "
"selection"));
connect(pasteAct, SIGNAL(triggered()), this, SLOT(paste()));
boldAct = new QAction(tr("&Bold"), this);
boldAct->setCheckable(true);
boldAct->setShortcut(QKeySequence::Bold);
boldAct->setStatusTip(tr("Make the text bold"));
connect(boldAct, SIGNAL(triggered()), this, SLOT(bold()));
QFont boldFont = boldAct->font();
boldFont.setBold(true);
boldAct->setFont(boldFont);
italicAct = new QAction(tr("&Italic"), this);
italicAct->setCheckable(true);
italicAct->setShortcut(QKeySequence::Italic);
italicAct->setStatusTip(tr("Make the text italic"));
connect(italicAct, SIGNAL(triggered()), this, SLOT(italic()));
QFont italicFont = italicAct->font();
italicFont.setItalic(true);
italicAct->setFont(italicFont);
setLineSpacingAct = new QAction(tr("Set &Line Spacing..."), this);
setLineSpacingAct->setStatusTip(tr("Change the gap between the lines of a "
"paragraph"));
connect(setLineSpacingAct, SIGNAL(triggered()), this, SLOT(setLineSpacing()));
setParagraphSpacingAct = new QAction(tr("Set &Paragraph Spacing..."), this);
setLineSpacingAct->setStatusTip(tr("Change the gap between paragraphs"));
connect(setParagraphSpacingAct, SIGNAL(triggered()),
this, SLOT(setParagraphSpacing()));
aboutAct = new QAction(tr("&About"), this);
aboutAct->setStatusTip(tr("Show the application's About box"));
connect(aboutAct, SIGNAL(triggered()), this, SLOT(about()));
aboutQtAct = new QAction(tr("About &Qt"), this);
aboutQtAct->setStatusTip(tr("Show the Qt library's About box"));
connect(aboutQtAct, SIGNAL(triggered()), qApp, SLOT(aboutQt()));
connect(aboutQtAct, SIGNAL(triggered()), this, SLOT(aboutQt()));
leftAlignAct = new QAction(tr("&Left Align"), this);
leftAlignAct->setCheckable(true);
leftAlignAct->setShortcut(tr("Ctrl+L"));
leftAlignAct->setStatusTip(tr("Left align the selected text"));
connect(leftAlignAct, SIGNAL(triggered()), this, SLOT(leftAlign()));
rightAlignAct = new QAction(tr("&Right Align"), this);
rightAlignAct->setCheckable(true);
rightAlignAct->setShortcut(tr("Ctrl+R"));
rightAlignAct->setStatusTip(tr("Right align the selected text"));
connect(rightAlignAct, SIGNAL(triggered()), this, SLOT(rightAlign()));
justifyAct = new QAction(tr("&Justify"), this);
justifyAct->setCheckable(true);
justifyAct->setShortcut(tr("Ctrl+J"));
justifyAct->setStatusTip(tr("Justify the selected text"));
connect(justifyAct, SIGNAL(triggered()), this, SLOT(justify()));
centerAct = new QAction(tr("&Center"), this);
centerAct->setCheckable(true);
centerAct->setShortcut(tr("Ctrl+E"));
centerAct->setStatusTip(tr("Center the selected text"));
connect(centerAct, SIGNAL(triggered()), this, SLOT(center()));
//! [6] //! [7]
alignmentGroup = new QActionGroup(this);
alignmentGroup->addAction(leftAlignAct);
alignmentGroup->addAction(rightAlignAct);
alignmentGroup->addAction(justifyAct);
alignmentGroup->addAction(centerAct);
leftAlignAct->setChecked(true);
//! [6]
}
