#include <list>
+using namespace std;
+
+#include <boost/filesystem/path.hpp>
+namespace fs = boost::filesystem;
+
//#include "qui/mussa_setup_dialog/SequenceSetupWidget.hpp"
#include "qui/mussa_setup_dialog/SequenceSetupFrame.hpp"
#include "qui/mussa_setup_dialog/MussaSetupWidget.hpp"
#include "qui/mussa_setup_dialog/SetupInfo.hpp"
#include "alg/mussa.hpp"
+#include "mussa_exceptions.hpp"
MussaSetupWidget::MussaSetupWidget(QWidget *parent)
: QWidget(parent),
- analysisNameLineEdit(0),
- windowLineEdit(0),
- thresholdLineEdit(0),
- numOfSequencesSpinBox(0),
- createPushButton(0),
- cancelPushButton(0),
+ analysisNameLineEdit(new QLineEdit),
+ windowEdit(new QSpinBox),
+ thresholdEdit(new QSpinBox),
+ numOfSequencesSpinBox(new QSpinBox),
+ createPushButton(new QPushButton(tr("Create"))),
+ cancelPushButton(new QPushButton(tr("Cancel"))),
seqSetupFrame(0)
{
-
- // Analysis name
analysisNameLineEdit = new QLineEdit;
+ windowEdit = new QSpinBox;
+ thresholdEdit = new QSpinBox;
+ numOfSequencesSpinBox = new QSpinBox;
+ createPushButton = new QPushButton(tr("Create"));
+ cancelPushButton = new QPushButton(tr("Cancel"));
+
+ // Analysis name
QLabel *analysisNameLabel = new QLabel(tr("Analysis Name"));
analysisNameLabel->setBuddy(analysisNameLineEdit);
+ analysisNameLabel->setWhatsThis("Meaningful name for your analysis ");
+ analysisNameLineEdit->setWhatsThis("Meaningful name for your analysis ");
// Window
- windowLineEdit = new QLineEdit;
- QLabel *windowLabel = new QLabel(tr("Window"));
- windowLabel->setBuddy(windowLineEdit);
+ windowEdit->setMinimum(1);
+ windowEdit->setValue(30);
+ windowEdit->setWhatsThis("Sliding window size to use in analysis.\n\nSee Mussagl Manual for more information by selecting the 'Help > Mussagl Manual' menu option. ");
+ QLabel *windowLabel = new QLabel(tr("Window (nt)"));
+ windowLabel->setBuddy(windowEdit);
+ windowLabel->setWhatsThis("Sliding window size to use in analysis.\n\nSee Mussagl Manual for more information by selecting the 'Help > Mussagl Manual' menu option. ");
// Threshold
- thresholdLineEdit = new QLineEdit;
- QLabel *thresholdLabel = new QLabel(tr("Threshold"));
- thresholdLabel->setBuddy(thresholdLineEdit);
+ thresholdEdit->setMinimum(1);
+ thresholdEdit->setMaximum(windowEdit->value());
+ thresholdEdit->setValue(21);
+ thresholdEdit->setWhatsThis("Threshold of minimum number of matches required in a window to be considered a match.\n\nSee Mussagl Manual for more information by selecting the 'Help > Mussagl Manual' menu option. ");
+ QLabel *thresholdLabel = new QLabel(tr("Threshold (nt)"));
+ thresholdLabel->setBuddy(thresholdEdit);
+ thresholdLabel->setWhatsThis("Threshold of minimum number of matches required in a window to be considered a match.\n\nSee Mussagl Manual for more information by selecting the 'Help > Mussagl Manual' menu option. ");
+ connect(windowEdit, SIGNAL(valueChanged(int)),
+ this, SLOT(updateThreshold(int)));
// Number of sequences
- numOfSequencesSpinBox = new QSpinBox;
QLabel *numOfSequencesLabel = new QLabel(tr("Number of sequences"));
numOfSequencesLabel->setBuddy(numOfSequencesSpinBox);
+ numOfSequencesLabel->setWhatsThis("Number of sequences to include in analysis. ");
numOfSequencesSpinBox->setMinimum(1);
-
+ numOfSequencesSpinBox->setWhatsThis("Number of sequences to include in analysis. ");
//Sequence setup frame
seqSetupFrame = new SequenceSetupFrame;
connect(numOfSequencesSpinBox, SIGNAL(valueChanged(int)),
seqSetupFrame, SLOT(changeSequenceCount(int)));
- numOfSequencesSpinBox->setValue(1);
+ numOfSequencesSpinBox->setValue(2);
// Create Experiment Button
- createPushButton = new QPushButton(tr("Create"));
connect(createPushButton, SIGNAL(pressed()),
this, SLOT(mussaCreatePushed()));
// Cancle Button
- cancelPushButton = new QPushButton(tr("Cancel"));
connect(cancelPushButton, SIGNAL(pressed()),
this, SLOT(mussaCancelPushed()));
row1Layout->addWidget(analysisNameLabel);
row1Layout->addWidget(analysisNameLineEdit);
- row2Layout->addWidget(windowLabel);
- row2Layout->addWidget(windowLineEdit);
row2Layout->addWidget(thresholdLabel);
- row2Layout->addWidget(thresholdLineEdit);
+ row2Layout->addWidget(thresholdEdit);
+ row2Layout->addWidget(windowLabel);
+ row2Layout->addWidget(windowEdit);
row2Layout->addWidget(numOfSequencesLabel);
row2Layout->addWidget(numOfSequencesSpinBox);
+ buttonLayout->addStretch(1);
buttonLayout->addWidget(createPushButton);
buttonLayout->addWidget(cancelPushButton);
mainLayout->addWidget(seqSetupFrame);
mainLayout->addLayout(buttonLayout);
setLayout(mainLayout);
-
}
void MussaSetupWidget::mussaCreatePushed()
emit cancelButtonPushed();
}
-Mussa* MussaSetupWidget::getMussaObject()
+void MussaSetupWidget::updateThreshold(int new_threshold)
{
- Mussa *mussa = new Mussa;
-
-
+ thresholdEdit->setMaximum(new_threshold);
+}
+
+MussaRef MussaSetupWidget::getMussaObject()
+{
+ MussaRef mussa = Mussa::init();
- std::string seqFile;
- std::string annotFile;
int fastaIndex;
int start;
int end;
- std::list<SetupInfo *> setupInfoList = seqSetupFrame->getSetupInfo();
-
- const int count = setupInfoList.size();
+ list<SetupInfo *> setupInfoList = seqSetupFrame->getSetupInfo();
- SetupInfo *setupInfo = 0;
- for (int i=0; i < count; i++)
+ for (list<SetupInfo *>::reverse_iterator setup_item = setupInfoList.rbegin();
+ setup_item != setupInfoList.rend();
+ ++setup_item)
{
- setupInfo = setupInfoList.back();
- setupInfoList.pop_back();
-
- seqFile = setupInfo->getSeqFile();
- annotFile = setupInfo->getAnnotFile();
- fastaIndex = setupInfo->getFastaIndex();
- start = setupInfo->getSubSeqStart();
- end = setupInfo->getSubSeqEnd();
-
- mussa->load_sequence(seqFile, annotFile, fastaIndex, start, end);
- delete setupInfo;
+ std::string seqName = (*setup_item)->getName();
+ std::string seqNative = (*setup_item)->getSeqFile();
+ std::string annotNative = (*setup_item)->getAnnotFile();
+ fastaIndex = (*setup_item)->getFastaIndex();
+ start = (*setup_item)->getSubSeqStart();
+ end = (*setup_item)->getSubSeqEnd();
+
+ fs::path seqFile(seqNative, fs::native);
+ fs::path annotFile(annotNative, fs::native);
+ mussa->load_sequence(seqFile, annotFile, fastaIndex, start, end, &seqName);
+ }
+ setupInfoList.clear();
+
+ int win_size = windowEdit->value();
+ int threshold = thresholdEdit->value();
+ std::string name = analysisNameLineEdit->text().toStdString();
+ if (win_size == 0 or threshold == 0) {
+ throw mussa_load_error("must set analysis parameters");
+ } else {
+ mussa->set_name(name);
+ mussa->set_window(win_size);
+ mussa->set_threshold(threshold);
+ mussa->set_analysis_mode(Mussa::TransitiveNway);
+ //mussa->set_entropy(0); // might want to add this at some point
+ mussa->analyze();
}
-
- mussa->analyze(0, 0, Mussa::TransitiveNway, 0.0);
return mussa;
}
-//MussaSetupWidget::MussaSetupWidget(const MussaSetupWidget& msw)
-// : analysisNameLineEdit(msw.analysisNameLineEdit),
-// windowLineEdit(msw.windowLineEdit),
-// thresholdLineEdit(msw.thresholdLineEdit),
-// numOfSequencesLineEdit(msw.numOfSequencesLineEdit),
-// seqSetupFrame(msw.seqSetupFrame)
-//{
-//}
projects / mussa.git / blobdiff