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PaparaMainWidget.cpp
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PaparaMainWidget.cpp
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/*
* Copyright (C) 2009-2012 Simon A. Berger
*
* This file is part of visual_papara.
*
* visual_papara is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* visual_papara is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with visual_papara. If not, see <http://www.gnu.org/licenses/>.
*/
#include "papara.h"
#include "blast_partassign.h"
#include "PaparaMainWidget.h"
#include "ui_PaparaMainWidget.h"
#include <QFileDialog>
#include <QProgressDialog>
#include <QThread>
#include <QLabel>
#include <QTableView>
#include <QScrollBar>
#include <QMessageBox>
#include <QGraphicsView>
#include <QGraphicsScene>
#include "ivymike/time.h"
#include "build_versions.h"
#if 1
Q_DECLARE_METATYPE(QSharedPointer<papara_state>)
Q_DECLARE_METATYPE(QSharedPointer<papara::scoring_results> )
Q_DECLARE_METATYPE(QSharedPointer<output_alignment_store> )
#endif
PaparaLogSink_QPlainTextEdit::PaparaLogSink_QPlainTextEdit( QPlainTextEdit *qpte )
{
QObject::connect( this, SIGNAL(post_text(QString)), qpte, SLOT(insertPlainText(const QString &)), Qt::QueuedConnection );
QObject::connect( this, SIGNAL(post_text(QString)), qpte, SLOT(centerCursor()), Qt::QueuedConnection );
}
void PaparaLogSink_QPlainTextEdit::post ( char overflow, char* start, char* end )
{
size_t size = std::distance ( start, end );
// std::cout << "append: " << char(of) << " " << std::distance(first,last) << "\n";
assert ( size < 100000 );
QByteArray ba ( start, size );
QString s;
s.append ( ba );
if ( overflow > 0 ) {
const char b[2] = {char ( overflow ), '\0'};
s.append ( b );
}
//qpte_->appendPlainText(s);
emit post_text ( s );
}
class output_alignment_store : public papara::output_alignment {
public:
virtual ~output_alignment_store() { std::cerr << "<<<<<<<<<<<<<< output_alignment_store" << std::endl; }
virtual void push_back( const std::string &name, const out_seq &seq, seq_type t ) {
if( t == output_alignment::type_qs ) {
qs_.push_back(seqs_.size());
} else {
refs_.push_back(seqs_.size());
}
names_.push_back(name);
seqs_.push_back(seq);
}
virtual void set_max_name_length( size_t len ) {}
virtual void set_size( size_t num_rows, size_t num_cols ) {}
const out_seq &qs_at( size_t idx ) const {
return seqs_.at(qs_.at(idx));
}
const std::string &qs_name_at( size_t idx ) const {
return names_.at(qs_.at(idx));
}
size_t num_qs() const {
return qs_.size();
}
out_seq ref_at(int idx) const {
return seqs_.at(refs_.at(idx));
}
size_t num_ref() const {
return refs_.size();
}
const std::string &ref_name_at( size_t idx ) const {
return names_.at(refs_.at(idx));
}
void write_phylip( const char *filename ) {
papara::output_alignment_phylip oa(filename);
size_t max_name_len = 0;
for( std::vector< std::string >::iterator it = names_.begin(), last = names_.end(); it != last; ++it ) {
max_name_len = std::max( max_name_len, it->size() );
}
max_name_len += 1;
oa.set_max_name_length(max_name_len);
oa.set_size( names_.size(), seqs_.at(0).size() );
for( std::vector< size_t >::iterator it = refs_.begin(), last = refs_.end(); it != last; ++it ) {
oa.push_back( names_.at(*it), seqs_.at(*it), output_alignment::type_ref );
}
for( std::vector< size_t >::iterator it = qs_.begin(), last = qs_.end(); it != last; ++it ) {
oa.push_back( names_.at(*it), seqs_.at(*it), output_alignment::type_qs );
}
}
private:
std::vector <std::string> names_;
std::vector <out_seq> seqs_;
std::vector <size_t> refs_;
std::vector <size_t> qs_;
// std::vector <seq_type> refs_;
// std::vector <seq_type> qs_;
//
};
class alignment_grid_model : public TextGridModel {
public:
alignment_grid_model( QSharedPointer<output_alignment_store> oas, bool use_ref, bool protein ) : oas_(oas), use_ref_(use_ref),
protein_(protein)
{}
virtual QSize size() {
if( use_ref_ ) {
return QSize( oas_->ref_at(0).size(), oas_->num_ref() );
} else {
return QSize( oas_->qs_at(0).size(), oas_->num_qs() );
}
}
virtual QChar data( size_t x, size_t y ) {
try {
return data_int(x,y);
} catch( std::out_of_range ) {
return 'X';
}
}
inline QChar data_int( size_t x, size_t y ) {
char ret;
// std::cout << x << " " << y << " " << use_ref_ << "\n";
if( use_ref_ ) {
/*if( y >= oas_->num_ref() ) {
std::cerr << "meeep y: " << y << "\n";
return 'Y';
}
if( x >= oas_->ref_at(y).size() ) {
std::cerr << "meeep x: " << x << "\n";
return 'X';
}*/
ret = (char)oas_->ref_at(y).at(x);
} else {
// if( y >= oas_->num_qs() ) {
// std::cerr << "qs meeep y: " << y << "\n";
//
// return 'W';
// }
//
//
// if( x >= oas_->qs_at(y).size() ) {
// std::cerr << "qs meeep x: " << x << "\n";
// return 'Z';
//
// }
ret = (char)oas_->qs_at(y).at(x);
}
return ret;
}
virtual QColor color( size_t x, size_t y ) {
char c;
try {
if( use_ref_ ) {
c = (char)oas_->ref_at(y).at(x);
} else {
c = (char)oas_->qs_at(y).at(x);
}
} catch( std::out_of_range x ) {
return QColor( 255, 0, 255 );
}
if( !protein_ ) {
// nucleotice color mapping
switch( c ) {
case 'A':
return QColor( 255, 0, 0 );
case 'C':
return QColor( 0, 255, 0 );
case 'G':
return QColor( 0, 0, 255 );
case 'T':
return QColor( 255, 200, 0 );
default:
return Qt::white;
}
} else {
// protein color mapping
switch( c ) {
case 'A':
case 'I':
case 'L':
case 'M':
case 'F':
case 'W':
case 'V':
return Qt::blue;
case 'R':
case 'K':
return Qt::red;
case 'N':
return Qt::green;
case 'C':
return Qt::blue;
case 'Q':
return Qt::green;
case 'E':
return Qt::magenta;
case 'D':
return Qt::magenta;
case 'G':
return QColor(255,200,0);
case 'H':
case 'Y':
return Qt::cyan;
case 'P':
return Qt::yellow;
case 'S':
case 'T':
return Qt::green;
default:
return Qt::white;
}
}
}
private:
QSharedPointer<output_alignment_store> oas_;
bool use_ref_;
bool protein_;
};
class papara_state {
public:
virtual ~papara_state() {}
virtual void set_scoring_parameters( const papara::papara_score_parameters &sp ) = 0;
virtual void do_preprocessing() = 0;
virtual papara::scoring_results *do_scoring_only() const = 0;
virtual output_alignment_store *do_scoring( const papara::scoring_results &res, bool ref_gaps ) const = 0;
// virtual void align_single(size_t qs_idx) = 0;
virtual papara::papara_score_parameters scoring_parameters() = 0;
virtual sptr::shared_ptr<ivy_mike::tree_parser_ms::lnode> tree() const = 0;
};
template<typename seq_tag>
class papara_state_impl : public papara_state {
public:
papara_state_impl( QPlainTextEdit *qpte_dont_use_me, const std::string &tree_name, const std::string &ref_name, const std::string &qs_name, const std::string &pg_blast, const std::string &pg_partitions )
: sbq_(qpte_dont_use_me),
log_file_( "contraption_log.txt"),
log_file_tee_(log_file_),
log_window_sink_(&sbq_),
// ost_( &sbq_ ),
//ldev( ost_, log_file_ ),
//lout_guard( papara::lout, ldev ),
qs_(qs_name),
refs_(tree_name.c_str(), ref_name.c_str(), &qs_ ),
scoring_parameters_(papara::papara_score_parameters::default_scores())
{
if( !pg_blast.empty() && !pg_partitions.empty() ) {
std::ifstream blast_is( pg_blast.c_str() );
if( !blast_is.good() ) {
throw std::runtime_error( "can not open blast hits file" );
}
std::ifstream part_is( pg_partitions.c_str() );
if( !part_is.good() ) {
throw std::runtime_error( "can not open partition file" );
}
part_assignment_.reset( new partassign::part_assignment( blast_is, part_is ));
}
// qpte->appendPlainText( "xxx");
//qpte->appendPlainText( "yyy\n");
// papara::lout << "bla bla bla" << std::endl;
}
virtual void set_scoring_parameters( const papara::papara_score_parameters &sp ) {
scoring_parameters_ = sp;
}
virtual void do_preprocessing() {
papara::lout << "qs preprocess" << std::endl;
qs_.preprocess();
papara::lout << "num qs: " << qs_.size() << "\n";
papara::lout << "ref preprocess" << std::endl;
refs_.remove_full_gaps();
refs_.build_ref_vecs();
papara::lout << "done." << std::endl;
if( !part_assignment_.isNull() ) {
//qs.init_partition_assignments( *part_assign );
std::vector<std::pair<size_t,size_t> > qs_bounds = partassign::resolve_qs_bounds( refs_, qs_, *part_assignment_ );
qs_.set_per_qs_bounds( qs_bounds );
}
// std::ofstream os( "queries.txt" );
//
// qs_.write( os );
//
}
virtual papara::scoring_results *do_scoring_only() const {
ivy_mike::perf_timer t1;
const size_t num_threads = QThread::idealThreadCount();
const size_t num_candidates = 1;
// papara::papara_score_parameters sp = papara::papara_score_parameters::default_scores();
papara::scoring_results *res = new papara::scoring_results(qs_.size(), papara::scoring_results::candidates(num_candidates));
scoring_parameters_.print(std::cerr);
papara::driver<pvec_pgap,seq_tag>::calc_scores(num_threads, refs_, qs_, res, scoring_parameters_ );
//QMessageBox::critical(0, "return", "bla" );
t1.add_int();
t1.print( );//papara::lout );
return res;
}
virtual output_alignment_store *do_scoring( const papara::scoring_results &res, bool ref_gaps ) const {
ivy_mike::perf_timer t1;
QScopedPointer<output_alignment_store> oas(new output_alignment_store);
//papara::papara_score_parameters sp = papara::papara_score_parameters::default_scores();
papara::lout << "aligning best scoring QS" << std::endl;
scoring_parameters_.print(std::cerr);
papara::driver<pvec_pgap,seq_tag>::align_best_scores_oa( oas.data(), qs_, refs_, res, size_t(0), ref_gaps, scoring_parameters_ );
t1.add_int();
t1.print();//papara::lout);
return oas.take();
}
virtual ~papara_state_impl() { std::cout << "~papara_state_impl\n"; }
// const papara::references<pvec_pgap,papara::tag_dna> &refs() const {
// return refs_;
// }
// void align_single(size_t qs_idx);
virtual papara::papara_score_parameters scoring_parameters() {
return scoring_parameters_;
}
sptr::shared_ptr<ivy_mike::tree_parser_ms::lnode> tree() const {
return refs_.tree();
}
private:
//streambuf_to_q_plain_text_edit sbq_;
PaparaLogSink_QPlainTextEdit sbq_;
std::ofstream log_file_;
papara::add_log_tee log_file_tee_;
papara::add_log_sink log_window_sink_;
// std::ostream ost_;
// papara::log_device ldev;
// papara::log_stream_guard lout_guard;
papara_state_impl();
papara::queries<seq_tag> qs_;
papara::references<pvec_pgap,seq_tag> refs_;
papara::papara_score_parameters scoring_parameters_;
QScopedPointer<partassign::part_assignment> part_assignment_;
};
// converting from QString to const char* is ridiculusly complicated. so store string as std::string when conversion is necessary
static std::string de_q_string( QString qs ) {
std::string s = qs.toStdString();
return s;
}
static bool is_readable( std::string filename ) {
std::ifstream is( filename.c_str() );
return is.good();
}
PaparaMainWidget::PaparaMainWidget(QString treeName, QString refName, QString queryName, bool is_protein, QString pgBlastName, QString pgPartitionsName, QWidget* parent) :
QWidget(parent),
ui(new Ui::MainWidget),
progress_dialog_(0),
bg_thread_(new QThread()),
tg_ref_(0),
tg_qs_(0),
is_protein_(is_protein),
log_size_(0)
// table_model_(0),
// qs_table_model_(0),
// ref_table_model_(0,true)
{
qRegisterMetaType<QSharedPointer<papara_state> >();
qRegisterMetaType<QSharedPointer<papara::scoring_results> >();
qRegisterMetaType<QSharedPointer<output_alignment_store> >();
ui->setupUi(this);
ui->frButtons->setVisible(false);
ui->pbRun->setPalette(QPalette( Qt::red ));
papara::papara_score_parameters sp = papara::papara_score_parameters::default_scores();
ui->sbOpen->setValue( sp.gap_open );
ui->sbExt->setValue( sp.gap_extend );
ui->sbMatch->setValue( sp.match );
ui->sbCgap->setValue( sp.match_cgap );
// ui->pte_log->setVisible(false);
// sv_ref_ = new QScrollArea(ui->w_ref);
// sv_qs_ = new QScrollArea(ui->w_qs);
//
// sv_ref_->show();
// sv_qs_->show();
// // ui->w_ref->setSizePolicy( QSizePolicy::Expanding, QSizePolicy::Expanding );
// sv_qs_->setSizePolicy( QSizePolicy::Expanding, QSizePolicy::Expanding );
// sv_ref_->setSizePolicy( QSizePolicy::Expanding, QSizePolicy::Expanding );
//
sv_ref_ = new QScrollArea();
sv_qs_ = new QScrollArea();
ui->splitter->insertWidget(0, sv_ref_);
ui->splitter->insertWidget(1, sv_qs_);
connect(sv_ref_->horizontalScrollBar(), SIGNAL(valueChanged(int)), sv_qs_->horizontalScrollBar(), SLOT(setValue(int)));
connect(sv_qs_->horizontalScrollBar(), SIGNAL(valueChanged(int)), sv_ref_->horizontalScrollBar(), SLOT(setValue(int)));
// ui->tv_alignment->setModel( &table_model_ );
// #ifndef WIN32
// if( false ) {
// tree_filename_ = "/home/sim/src_exelixis/contraption/small.tree";
// ref_filename_ = "/home/sim/src_exelixis/contraption/small.phy";
// qs_filename_ = "/home/sim/src_exelixis/contraption/small_qs.fa";
// } else if(false) {
// tree_filename_ = "/home/sim/src_exelixis/contraption/test_1604/RAxML_bestTree.ref_orig";
// ref_filename_ = "/home/sim/src_exelixis/contraption/test_1604/orig.phy.1";
// qs_filename_ = "/home/sim/src_exelixis/contraption/test_1604/qs.fa.20";
// } else if( false ){
// tree_filename_ = "/space/projects/2012_robert_454/RAxML_bestTree.cora_Sanger_reference_alignment.tre";
// ref_filename_ = "/space/projects/2012_robert_454/cora_Sanger_reference_alignment.phy";
// qs_filename_ = "/space/projects/2012_robert_454/cluster_52_72_cora_inversa_squamiformis_DIC_148_149.fas";
// } else {
// tree_filename_ = "/space/projects/2012_robert_454/RAxML_bestTree.cora_Sanger_reference_alignment.tre";
// ref_filename_ = "/space/projects/2012_robert_454/cora_Sanger_reference_alignment.phy";
// qs_filename_ = "/space/projects/2012_robert_454/cluster_52_72_cora_inversa_squamiformis_DIC_148_149.fas";
// }
// #else
// tree_filename_ = "C:/2012_robert_454/RAxML_bestTree.cora_Sanger_reference_alignment.tre";
// ref_filename_ = "C:/2012_robert_454/cora_Sanger_reference_alignment.phy";
// qs_filename_ = "C:/2012_robert_454/cluster_52_72_cora_inversa_squamiformis_DIC_148_149.fas";
// #endif
//
tree_filename_ = de_q_string( treeName );
ref_filename_ = de_q_string( refName );
qs_filename_ = de_q_string( queryName );
pg_blast_name_ = de_q_string( pgBlastName );
pg_partitions_name_ = de_q_string( pgPartitionsName );
check_filenames();
bg_thread_->start();
}
PaparaMainWidget::~PaparaMainWidget()
{
bg_thread_->quit();
bg_thread_->wait( 1000 );
if( !bg_thread_->isFinished() ) {
QMessageBox::critical(this, "Job Running", "A background job is still running. The Program needs to perform unclean termination, which might look like a crash (e.g., core dump, show scary warning dialogs or cause the end of the world.) ..." );
// give it one more chance in case it has shut down cleanly in the meantime
if( !bg_thread_->isFinished() ) {
abort();
}
//bg_thread_->terminate();
}
delete ui;
}
void PaparaMainWidget::showLog( bool v ) {
// return;
if( !v ) {
QList<int> old_sizes = ui->splitter->sizes();
assert( old_sizes.size() == 3 );
std::cout << "sizes: " << old_sizes[0] << " " << old_sizes[1] << " " << old_sizes[2] << "\n";
log_size_ = old_sizes[2];
old_sizes[2] = 0;
ui->splitter->setSizes(old_sizes);
} else {
QList<int> old_sizes = ui->splitter->sizes();
assert( old_sizes.size() == 3 );
std::cout << "sizes: " << old_sizes[0] << " " << old_sizes[1] << " " << old_sizes[2] << "\n";
// old_sizes[2] = 0;
old_sizes[2] = log_size_;
ui->splitter->setSizes(old_sizes);
}
}
void PaparaMainWidget::post_show_stuff() {
showLog(false);
if( is_readable( tree_filename_ ) && is_readable( ref_filename_ ) && is_readable( qs_filename_ ) ) {
on_pbLoad_clicked();
} else {
QMessageBox::critical(this, "Input Files not readable", "One or more of the input files are not readble.", QMessageBox::Abort );
QApplication::exit();
//throw std::runtime_error( "bailing out\n" );
}
}
void PaparaMainWidget::on_pb_tree_clicked()
{
//QFileDialog::exec
std::cout << "tree\n";
tree_filename_ = de_q_string(QFileDialog::getOpenFileName(this));
ui->pte_log->appendPlainText(tree_filename_.c_str());
check_filenames();
}
void PaparaMainWidget::on_pb_ref_clicked()
{
std::cout << "ref\n";
ref_filename_ = de_q_string(QFileDialog::getOpenFileName(this));
ui->pte_log->appendPlainText(ref_filename_.c_str());
check_filenames();
}
void PaparaMainWidget::on_pb_qs_clicked()
{
std::cout << "qs\n";
qs_filename_ = de_q_string(QFileDialog::getOpenFileName(this));
ui->pte_log->appendPlainText(qs_filename_.c_str());
check_filenames();
}
void PaparaMainWidget::on_pbLoad_clicked()
{
if( tree_filename_.empty() || ref_filename_.empty() || qs_filename_.empty() ) {
ui->pte_log->appendPlainText( "file missing\n");
return;
}
// ui->pte_log->setVisible( true );
showLog(true);
progress_dialog_ = new QProgressDialog( "Initializing papara static data", "cancel (not really)", 0, 1 );
// QProgressDialog *pd = new QProgressDialog( "Initializing papara static data", "cancel (not really)", 0, 1 );
// pd->show();
papara_.clear();
setEnabled(false);
// QThread *thread = new QThread;
state_worker_.reset( new StateWorker( ui->pte_log, tree_filename_, ref_filename_, qs_filename_, is_protein_, pg_blast_name_, pg_partitions_name_ ));
//obj is a pointer to a QObject that will trigger the work to start. It could just be this
assert( bg_thread_->isRunning() );
state_worker_->moveToThread(bg_thread_.data());
// thread->start();
connect(state_worker_.data(), SIGNAL(done( QSharedPointer<papara_state>, QString)), this, SLOT(on_state_ready(QSharedPointer<papara_state>, QString)));
QMetaObject::invokeMethod(state_worker_.data(), "doWork", Qt::QueuedConnection);
//obj will need to emit startWork() to get the work going.
}
void PaparaMainWidget::on_pbRun_clicked() {
//setEnabled(false);
//ui->pte_log->setVisible(true);
showLog(true);
int sopen = ui->sbOpen->value();
int sext = ui->sbExt->value();
int smatch = ui->sbMatch->value();
int scgap = ui->sbCgap->value();
if( sopen > 0 || sext > 0 || smatch < 1 || scgap > 0 ) {
QMessageBox::StandardButton b = QMessageBox::warning( this, "Weird Scoring Scheme", "The scoring scheme you selected seems weird\nThe results may be even weirder. Continue?", QMessageBox::Ok|QMessageBox::Cancel );
if( b != QMessageBox::Ok ) {
return; // bail out
}
}
// std::cout << "x: " << smatch + scgap << "\n";
if( smatch + scgap >= 0 ) {
QMessageBox::StandardButton b = QMessageBox::warning( this, "Scoring Scheme Trouble", "The scoring scheme you selected does not work with the current version of PaPaRa because match+match_cgap < 0. This is no fundamental restriction of the algorithm but necessary for a specific kind of performance optimization.\nPlease chose a smaller match score or a smaller match cgap score.\n\nIf you think that this is not acceptable, please write me at [email protected]", QMessageBox::Cancel );
return; // bail out
}
ui->frButtons->setEnabled(false);
ui->frRun->setEnabled(false);
progress_dialog_ = new QProgressDialog( "Doing the papara", "cancel (not really)", 0, 1 );
progress_dialog_->setMinimumDuration(0);
papara::papara_score_parameters op = papara_->scoring_parameters();
papara::papara_score_parameters np(sopen, sext, smatch, scgap );
// check if the scoring scheme was changed and clear scoring_results if necessary
if( !scoring_result_.isNull() && op != np ) {
// QMessageBox::StandardButton b = QMessageBox::warning( this, "Weird Scoring Scheme", "clear results", QMessageBox::Ok );
scoring_result_.clear();
}
papara_->set_scoring_parameters( np );
// QThread *thread = new QThread;
scoring_worker_.reset( new ScoringWorker( ui->pte_log, papara_, scoring_result_, ui->cbRefGaps->isChecked() ));
//obj is a pointer to a QObject that will trigger the work to start. It could just be this
scoring_worker_->moveToThread(bg_thread_.data());
// thread->start();
connect(scoring_worker_.data(), SIGNAL(done( QSharedPointer<output_alignment_store>, QSharedPointer<papara::scoring_results>, QString)), this, SLOT(on_scoring_done(QSharedPointer<output_alignment_store>, QSharedPointer<papara::scoring_results>, QString)));
QMetaObject::invokeMethod(scoring_worker_.data(), "doWork", Qt::QueuedConnection);
//obj will need to emit startWork() to get the work going.
}
void PaparaMainWidget::on_state_ready(QSharedPointer< papara_state > state, QString msg) {
if( progress_dialog_ != 0 ) {
delete progress_dialog_;
}
std::cout << "state_ready: " << state.data() << "\n";
if( state.isNull() ) {
QMessageBox::critical(this,"Internal Error", msg );
QApplication::exit();
//abort();
}
papara_ = state;
// table_model_.set_papara_state( state );
/* ui->tv_alignment->setModel(&table_model_);
ui->tv_alignment->horizontalHeader()->hide();
ui->tv_alignment->verticalHeader()->hide();
*/
// ui->tv_alignment->resizeColumnsToContents();
// ui->tv_alignment->resizeRowsToContents();
// resize_rows_columns(ui->tv_alignment, 12, 12 );
setEnabled(true);
ui->pte_log->appendPlainText("papara static state initialized\n");
ui->frRun->setEnabled(true);
//ui->pte_log->setVisible(false);
showLog(false);
if( false ) {
QScrollArea *qs = new QScrollArea();
PhyloTreeView *ptv = new PhyloTreeView(papara_->tree());
QGraphicsView *gv = new QGraphicsView( ptv->initGraphicsScene(0) );
qs->setWidget(gv);
qs->setVisible(true);
}
}
void PaparaMainWidget::resize_rows_columns( QTableView *tv, int row_size, int column_size ) {
const int num_rows = tv->model()->rowCount();
const int num_cols = tv->model()->columnCount();
for( int i = 0; i < num_rows; ++i ) {
tv->setRowHeight(i, row_size);
}
for( int i = 0; i < num_cols; ++i ) {
tv->setColumnWidth(i, column_size);
}
}
void PaparaMainWidget::on_scoring_done(QSharedPointer<output_alignment_store> oa, QSharedPointer<papara::scoring_results> res, QString msg ) {
if( progress_dialog_ != 0 ) {
delete progress_dialog_;
}
if( oa.isNull() ) {
QMessageBox::critical(this,"Internal Error", msg );
abort();
}
if( scoring_result_.isNull() ) {
scoring_result_ = res;
}
assert( scoring_result_.data() == res );
output_alignment_ = oa;
// qs_table_model_.set_oas(oa);
// ref_table_model_.set_oas(oa);
// QScopedPointer<TextGridModel> qs_model(new alignment_grid_model(oa, false));
// QScopedPointer<TextGridModel> ref_model(new alignment_grid_model(oa, true));
qs_grid_model_ = QSharedPointer<TextGridModel> (new alignment_grid_model(oa, false, is_protein_));
ref_grid_model_ = QSharedPointer<TextGridModel> (new alignment_grid_model(oa, true, is_protein_));
// float zoom_factor = ui->cbZoom->
{
// int hs = -1;
// int vs = -1;
if( tg_ref_ == 0 ) {
tg_ref_ = new TextGrid(sv_ref_);
sv_ref_->setWidget(tg_ref_);
}
// tg_ref_->setModel(ref_model.data());
tg_ref_->setModel(ref_grid_model_);
tg_ref_->repaint();
// sv_qs_->setLayout(new);
}
{
if( tg_qs_ == 0 ) {
tg_qs_ = new TextGrid(sv_qs_);
sv_qs_->setWidget(tg_qs_);
}
//tg_qs_->setModel(qs_model.data());
tg_qs_->setModel(qs_grid_model_);
tg_qs_->repaint();
}
tg_ref_->setZoom(ui->slZoom->value());
tg_qs_->setZoom(ui->slZoom->value());
connect(tg_ref_, SIGNAL(zoomChanged(int)), tg_qs_, SLOT(setZoom(int)));
connect(tg_qs_, SIGNAL(zoomChanged(int)), tg_ref_, SLOT(setZoom(int)));
connect(tg_ref_, SIGNAL(zoomChanged(int)), ui->slZoom, SLOT(setValue(int)));
connect(tg_qs_, SIGNAL(zoomChanged(int)), ui->slZoom, SLOT(setValue(int)));
connect(ui->slZoom, SIGNAL(valueChanged(int)), tg_ref_, SLOT(setZoom(int)));
connect(ui->slZoom, SIGNAL(valueChanged(int)), tg_qs_, SLOT(setZoom(int)));
int hvalue = -1;
if( sv_qs_->widget() != 0 ) {
// old_num_cols = ui->tv_qs->model()->columnCount();
hvalue = sv_qs_->horizontalScrollBar()->value();
}
// ui->tv_qs->setModel(0);
// ui->tv_qs->setModel(&qs_table_model_);
// ui->tv_qs->horizontalHeader()->hide();
// ui->tv_qs->verticalHeader()->hide();
// ui->tv_qs->resizeColumnsToContents();
// ui->tv_qs->resizeRowsToContents();
//
/*
resize_rows_columns(ui->tv_qs, 12, 12);
if(true) {
int vvalue = -1;
if( ui->tv_alignment->model() != 0 ) {
vvalue = ui->tv_alignment->verticalScrollBar()->value();
}
ui->tv_alignment->setModel(0);
ui->tv_alignment->setModel(&ref_table_model_);
ui->tv_alignment->horizontalHeader()->hide();
ui->tv_alignment->verticalHeader()->hide();
// ui->tv_alignment->resizeColumnsToContents();
// ui->tv_alignment->resizeRowsToContents();
//
resize_rows_columns(ui->tv_alignment, 12, 12);
if( vvalue >= 0 ) {
ui->tv_alignment->horizontalScrollBar()->setValue(vvalue);
}
}*/
// if( hvalue >= 0 ) {
// ui->tv_qs->horizontalScrollBar()->setValue(hvalue);
// }
ui->pte_log->appendPlainText("scoring done\n");
ui->pbRun->setPalette( QPalette() );
ui->pbRun->setAutoFillBackground(false);
ui->frButtons->setEnabled(true);
ui->frRun->setEnabled(true);
ui->pbSaveAs->setEnabled(true);
//ui->pte_log->setVisible(false);
showLog(false);
}
void StateWorker::doWork()
{
try {
std::cout << "doWork\n";
papara_state *ps;
if( is_protein_ ) {
ps = new papara_state_impl<papara::tag_aa>( qpte_, tree_, ref_, qs_, pg_blast_, pg_partitions_);
} else {
ps = new papara_state_impl<papara::tag_dna>( qpte_, tree_, ref_, qs_, pg_blast_, pg_partitions_);
}
ps->do_preprocessing();
emit done(QSharedPointer<papara_state>(ps), QString());
finished_ = true;
} catch( std::runtime_error x ) {
QString error_text(x.what());
QString msg( "Critical error while loading input files:\n" );
msg += error_text;
emit done( QSharedPointer<papara_state>(), msg );
}
}
void ScoringWorker::doWork() {
try {
if( res_.isNull() ) {
res_ = QSharedPointer<papara::scoring_results>(state_->do_scoring_only());
}
assert( res_ != 0 );
output_alignment_store *oa = state_->do_scoring( *res_, ref_gaps_ );
emit done(QSharedPointer<output_alignment_store>(oa), res_, QString());
finished_ = true;
} catch( std::runtime_error x ) {
QString error_text(x.what());
QString msg( "Critical error during alignment:\n" );