qui/mussa_setup_dialog/MussaSetupWidget.cpp

   1 #include <QFrame>
   2 #include <QLabel>
   3 #include <QLineEdit>
   4 #include <QSpinBox>
   5 #include <QVBoxLayout>
   6 #include <QHBoxLayout>
   7 #include <QPushButton>
   8
   9 #include <list>
  10
  11 using namespace std;
  12
  13 #include <boost/filesystem/path.hpp>
  14 namespace fs = boost::filesystem;
  15
  16 //#include "qui/mussa_setup_dialog/SequenceSetupWidget.hpp"
  17 #include "qui/mussa_setup_dialog/SequenceSetupFrame.hpp"
  18 #include "qui/mussa_setup_dialog/MussaSetupWidget.hpp"
  19 #include "qui/mussa_setup_dialog/SetupInfo.hpp"
  20 #include "alg/mussa.hpp"
  21 #include "mussa_exceptions.hpp"
  22
  23 MussaSetupWidget::MussaSetupWidget(QWidget *parent)
  24   : QWidget(parent),
  25     analysisNameLineEdit(new QLineEdit),
  26     windowEdit(new QSpinBox),
  27     thresholdEdit(new QSpinBox),
  28     numOfSequencesSpinBox(new QSpinBox),
  29     createPushButton(new QPushButton(tr("Create"))),
  30     cancelPushButton(new QPushButton(tr("Cancel"))),
  31     seqSetupFrame(0)
  32 {
  33   analysisNameLineEdit = new QLineEdit;
  34   windowEdit = new QSpinBox;
  35   thresholdEdit = new QSpinBox;
  36   numOfSequencesSpinBox = new QSpinBox;
  37   createPushButton = new QPushButton(tr("Create"));
  38   cancelPushButton = new QPushButton(tr("Cancel"));
  39
  40   // Analysis name
  41   QLabel *analysisNameLabel = new QLabel(tr("Analysis Name"));
  42   analysisNameLabel->setBuddy(analysisNameLineEdit);
  43
  44   // Window
  45   windowEdit->setMinimum(1);
  46   windowEdit->setValue(30);
  47   QLabel *windowLabel = new QLabel(tr("Window (nt)"));
  48   windowLabel->setBuddy(windowEdit);
  49
  50   // Threshold
  51   thresholdEdit->setMinimum(1);
  52   thresholdEdit->setMaximum(windowEdit->value());
  53   thresholdEdit->setValue(21);
  54   QLabel *thresholdLabel = new QLabel(tr("Threshold (nt)"));
  55   thresholdLabel->setBuddy(thresholdEdit);
  56   connect(windowEdit, SIGNAL(valueChanged(int)),
  57           this, SLOT(updateThreshold(int)));
  58
  59   // Number of sequences
  60   QLabel *numOfSequencesLabel = new QLabel(tr("Number of sequences"));
  61   numOfSequencesLabel->setBuddy(numOfSequencesSpinBox);
  62   numOfSequencesSpinBox->setMinimum(1);
  63
  64   //Sequence setup frame
  65   seqSetupFrame = new SequenceSetupFrame;
  66
  67   connect(numOfSequencesSpinBox, SIGNAL(valueChanged(int)),
  68           seqSetupFrame, SLOT(changeSequenceCount(int)));
  69
  70   numOfSequencesSpinBox->setValue(2);
  71
  72   // Create Experiment Button
  73   connect(createPushButton, SIGNAL(pressed()),
  74           this, SLOT(mussaCreatePushed()));
  75
  76   // Cancle Button
  77   connect(cancelPushButton, SIGNAL(pressed()),
  78           this, SLOT(mussaCancelPushed()));
  79
  80   // LAYOUT
  81   QHBoxLayout *row1Layout = new QHBoxLayout;
  82   QHBoxLayout *row2Layout = new QHBoxLayout;
  83   QVBoxLayout *mainLayout = new QVBoxLayout;
  84   QHBoxLayout *buttonLayout = new QHBoxLayout;
  85
  86   row1Layout->addWidget(analysisNameLabel);
  87   row1Layout->addWidget(analysisNameLineEdit);
  88
  89   row2Layout->addWidget(thresholdLabel);
  90   row2Layout->addWidget(thresholdEdit);
  91   row2Layout->addWidget(windowLabel);
  92   row2Layout->addWidget(windowEdit);
  93   row2Layout->addWidget(numOfSequencesLabel);
  94   row2Layout->addWidget(numOfSequencesSpinBox);
  95
  96   buttonLayout->addStretch(1);
  97   buttonLayout->addWidget(createPushButton);
  98   buttonLayout->addWidget(cancelPushButton);
  99
 100   mainLayout->addLayout(row1Layout);
 101   mainLayout->addLayout(row2Layout);
 102   mainLayout->addWidget(seqSetupFrame);
 103   mainLayout->addLayout(buttonLayout);
 104   setLayout(mainLayout);
 105 }
 106
 107 void MussaSetupWidget::mussaCreatePushed()
 108 {
 109   emit createButtonPushed();
 110 }
 111
 112 void MussaSetupWidget::mussaCancelPushed()
 113 {
 114   emit cancelButtonPushed();
 115 }
 116
 117 void MussaSetupWidget::updateThreshold(int new_threshold)
 118 {
 119   thresholdEdit->setMaximum(new_threshold);
 120 }
 121
 122 MussaRef MussaSetupWidget::getMussaObject()
 123 {
 124   MussaRef mussa = Mussa::init();
 125
 126   int fastaIndex;
 127   int start;
 128   int end;
 129
 130   list<SetupInfo *> setupInfoList = seqSetupFrame->getSetupInfo();
 131
 132   for (list<SetupInfo *>::reverse_iterator setup_item = setupInfoList.rbegin();
 133        setup_item != setupInfoList.rend();
 134        ++setup_item)
 135   {
 136     std::string seqName = (*setup_item)->getName();
 137     std::string seqNative = (*setup_item)->getSeqFile();
 138     std::string annotNative = (*setup_item)->getAnnotFile();
 139     fastaIndex = (*setup_item)->getFastaIndex();
 140     start = (*setup_item)->getSubSeqStart();
 141     end = (*setup_item)->getSubSeqEnd();
 142
 143     fs::path seqFile(seqNative, fs::native);
 144     fs::path annotFile(annotNative, fs::native);
 145     mussa->load_sequence(seqFile, annotFile, fastaIndex, start, end, &seqName);
 146   }
 147   setupInfoList.clear();
 148
 149   int win_size = windowEdit->value();
 150   int threshold = thresholdEdit->value();
 151   std::string name = analysisNameLineEdit->text().toStdString();
 152   if (win_size == 0 or threshold == 0) {
 153     throw mussa_load_error("must set analysis parameters");
 154   } else {
 155     mussa->set_name(name);
 156     mussa->set_window(win_size);
 157     mussa->set_threshold(threshold);
 158     mussa->set_analysis_mode(Mussa::TransitiveNway);
 159     //mussa->set_entropy(0); // might want to add this at some point
 160     mussa->analyze();
 161   }
 162
 163   return mussa;
 164 }
 165