/** Go prev while at < 0, mark end with STOP */
void find_stop(int& min_row, int& min_col) const {
while (track(min_row, min_col) != STOP) {
if (at(min_row, min_col) >= 0 ||
min_row == 0 || min_col == 0) {
track(min_row, min_col) = STOP;
break;
}
go_prev(min_row, min_col);
}
}
void MainPage::init_actions()
{
QWidget *spr1 = new QWidget();
spr1->setSizePolicy( QSizePolicy::Expanding , QSizePolicy::Minimum );
p->go_action = new QAction( SMasterIcons::icon(ICON_SIZE,"tools-media-optical-burn.png") , tr("Go") , this );
p->more_action = new QAction( SMasterIcons::icon(ICON_SIZE,"edit-rename.png") , tr("More") , this );
p->toolbar->addAction( p->more_action );
p->toolbar->addWidget( spr1 );
p->toolbar->addAction( p->go_action );
connect( p->go_action , SIGNAL(triggered()) , SLOT(go_prev()) );
connect( p->more_action , SIGNAL(triggered()) , SLOT(more_prev()) );
}
/** Strip out bad alignment tail.
Consider the following alignment:
\verbatim
TTCCGGTGCTGCGaggga
TTCCGGTGCTGCGcctct
\endverbatim
After tail stripping, it would be changed to
\verbatim
TTCCGGTGCTGCG
TTCCGGTGCTGCG
\endverbatim
*/
void cut_tail(int& first_last, int& second_last) const {
int& r_row = first_last;
int& r_col = second_last;
while (true) {
int prev_row = r_row;
int prev_col = r_col;
go_prev(prev_row, prev_col);
if (in(prev_row, prev_col) &&
at(prev_row, prev_col) < at(r_row, r_col)) {
r_row = prev_row;
r_col = prev_col;
} else {
break;
}
}
}
/** Write alignment as list of pairs of indices.
\param first_last Last aligned position in first sequence (input)
\param second_last Last aligned position in second sequence (input)
\param alignment Array of pairs of positions, -1 as gaps
*/
void export_alignment(int first_last, int second_last,
PairAlignment& alignment) const {
int row = first_last, col = second_last;
while (row != -1 || col != -1) {
int tr = track(row, col);
if (tr == STOP) {
tr = MATCH;
}
bool print_first = (tr == MATCH || tr == ROW_INC);
bool print_second = (tr == MATCH || tr == COL_INC);
int a_row = print_first ? row : -1;
int a_col = print_second ? col : -1;
alignment.push_back(std::make_pair(a_row, a_col));
if (track(row, col) == STOP) {
break;
}
go_prev(row, col);
ASSERT_TRUE(in(row, col));
}
std::reverse(alignment.begin(), alignment.end());
}
// ignores gap range
void track_local(int row, int col) const {
if (row == -1 || col == -1) {
return;
}
int min_row = row;
int min_col = col;
find_opt(min_row, min_col);
if (at(min_row, min_col) == 0) {
return;
}
// go right to col
for (int j = min_col; j <= col; j++) {
track(min_row, j) = COL_INC;
}
// go bottom to row
for (int i = min_row; i <= row; i++) {
track(i, col) = ROW_INC;
}
while (at(min_row, min_col) < 0) {
go_prev(min_row, min_col);
ASSERT_TRUE(in(min_row, min_col));
}
track_local(min_row, min_col);
}
void RootMount::goEvent( SProcessEvent * )
{
go_prev();
}
