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     createPushButton(tr("Create")),
  26     cancelPushButton(tr("Cancel")),
  27     seqSetupFrame(0)
  28 {
  29
  30   // Analysis name
  31   QLabel *analysisNameLabel = new QLabel(tr("Analysis Name"));
  32   analysisNameLabel->setBuddy(&analysisNameLineEdit);
  33
  34   // Window
  35   QLabel *windowLabel = new QLabel(tr("Window"));
  36   windowLabel->setBuddy(&windowLineEdit);
  37
  38   // Threshold
  39   QLabel *thresholdLabel = new QLabel(tr("Threshold"));
  40   thresholdLabel->setBuddy(&thresholdLineEdit);
  41
  42   // Number of sequences
  43   QLabel *numOfSequencesLabel = new QLabel(tr("Number of sequences"));
  44   numOfSequencesLabel->setBuddy(&numOfSequencesSpinBox);
  45   numOfSequencesSpinBox.setMinimum(1);
  46
  47   //Sequence setup frame
  48   seqSetupFrame = new SequenceSetupFrame;
  49
  50   connect(&numOfSequencesSpinBox, SIGNAL(valueChanged(int)),
  51           seqSetupFrame, SLOT(changeSequenceCount(int)));
  52
  53   numOfSequencesSpinBox.setValue(2);
  54
  55   // Create Experiment Button
  56   connect(&createPushButton, SIGNAL(pressed()),
  57           this, SLOT(mussaCreatePushed()));
  58
  59   // Cancle Button
  60   connect(&cancelPushButton, SIGNAL(pressed()),
  61           this, SLOT(mussaCancelPushed()));
  62
  63   // LAYOUT
  64   QHBoxLayout *row1Layout = new QHBoxLayout;
  65   QHBoxLayout *row2Layout = new QHBoxLayout;
  66   QVBoxLayout *mainLayout = new QVBoxLayout;
  67   QHBoxLayout *buttonLayout = new QHBoxLayout;
  68
  69   row1Layout->addWidget(analysisNameLabel);
  70   row1Layout->addWidget(&analysisNameLineEdit);
  71
  72   row2Layout->addWidget(windowLabel);
  73   row2Layout->addWidget(&windowLineEdit);
  74   row2Layout->addWidget(thresholdLabel);
  75   row2Layout->addWidget(&thresholdLineEdit);
  76   row2Layout->addWidget(numOfSequencesLabel);
  77   row2Layout->addWidget(&numOfSequencesSpinBox);
  78
  79   buttonLayout->addWidget(&createPushButton);
  80   buttonLayout->addWidget(&cancelPushButton);
  81
  82   mainLayout->addLayout(row1Layout);
  83   mainLayout->addLayout(row2Layout);
  84   mainLayout->addWidget(seqSetupFrame);
  85   mainLayout->addLayout(buttonLayout);
  86   setLayout(mainLayout);
  87
  88 }
  89
  90 void MussaSetupWidget::mussaCreatePushed()
  91 {
  92   emit createButtonPushed();
  93 }
  94
  95 void MussaSetupWidget::mussaCancelPushed()
  96 {
  97   emit cancelButtonPushed();
  98 }
  99
 100 Mussa* MussaSetupWidget::getMussaObject()
 101 {
 102   Mussa *mussa = new Mussa;
 103
 104   int fastaIndex;
 105   int start;
 106   int end;
 107
 108   list<SetupInfo *> setupInfoList = seqSetupFrame->getSetupInfo();
 109
 110   for (list<SetupInfo *>::iterator setup_item = setupInfoList.begin();
 111        setup_item != setupInfoList.end();
 112        ++setup_item)
 113   {
 114     std::string seqNative = (*setup_item)->getSeqFile();
 115     std::string annotNative = (*setup_item)->getAnnotFile();
 116     fastaIndex = (*setup_item)->getFastaIndex();
 117     start = (*setup_item)->getSubSeqStart();
 118     end = (*setup_item)->getSubSeqEnd();
 119
 120     fs::path seqFile(seqNative, fs::native);
 121     fs::path annotFile(annotNative, fs::native);
 122     mussa->load_sequence(seqFile, annotFile, fastaIndex, start, end);
 123   }
 124   setupInfoList.clear();
 125
 126   int win_size = windowLineEdit.text().toInt();
 127   int threshold = thresholdLineEdit.text().toInt();
 128   if (win_size == 0 or threshold == 0) {
 129     throw mussa_load_error("must set analysis parameters");
 130   } else {
 131     mussa->set_window(win_size);
 132     mussa->set_threshold(threshold);
 133     mussa->set_analysis_mode(Mussa::TransitiveNway);
 134     //mussa->set_entropy(0); // might want to add this at some point
 135     mussa->analyze();
 136   }
 137
 138   return mussa;
 139 }
 140
 141 //MussaSetupWidget::MussaSetupWidget(const MussaSetupWidget& msw)
 142 //  : analysisNameLineEdit(msw.analysisNameLineEdit),
 143 //    windowLineEdit(msw.windowLineEdit),
 144 //    thresholdLineEdit(msw.thresholdLineEdit),
 145 //    numOfSequencesLineEdit(msw.numOfSequencesLineEdit),
 146 //    seqSetupFrame(msw.seqSetupFrame)
 147 //{
 148 //}