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