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   analysisNameLabel->setWhatsThis("Meaningful name for your analysis ");
  44   analysisNameLineEdit->setWhatsThis("Meaningful name for your analysis ");
  45
  46   // Window
  47   windowEdit->setMinimum(1);
  48   windowEdit->setValue(30);
  49   windowEdit->setWhatsThis("Sliding window size to use in analysis.\n\nSee Mussagl Manual for more information by selecting the 'Help > Mussagl Manual' menu option. ");
  50   QLabel *windowLabel = new QLabel(tr("Window (nt)"));
  51   windowLabel->setBuddy(windowEdit);
  52   windowLabel->setWhatsThis("Sliding window size to use in analysis.\n\nSee Mussagl Manual for more information by selecting the 'Help > Mussagl Manual' menu option. ");
  53
  54   // Threshold
  55   thresholdEdit->setMinimum(1);
  56   thresholdEdit->setMaximum(windowEdit->value());
  57   thresholdEdit->setValue(21);
  58   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. ");
  59   QLabel *thresholdLabel = new QLabel(tr("Threshold (nt)"));
  60   thresholdLabel->setBuddy(thresholdEdit);
  61   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. ");
  62   connect(windowEdit, SIGNAL(valueChanged(int)),
  63           this, SLOT(updateThreshold(int)));
  64
  65   // Number of sequences
  66   QLabel *numOfSequencesLabel = new QLabel(tr("Number of sequences"));
  67   numOfSequencesLabel->setBuddy(numOfSequencesSpinBox);
  68   numOfSequencesLabel->setWhatsThis("Number of sequences to include in analysis. ");
  69   numOfSequencesSpinBox->setMinimum(1);
  70   numOfSequencesSpinBox->setWhatsThis("Number of sequences to include in analysis. ");
  71
  72   //Sequence setup frame
  73   seqSetupFrame = new SequenceSetupFrame;
  74
  75   connect(numOfSequencesSpinBox, SIGNAL(valueChanged(int)),
  76           seqSetupFrame, SLOT(changeSequenceCount(int)));
  77
  78   numOfSequencesSpinBox->setValue(2);
  79
  80   // Create Experiment Button
  81   connect(createPushButton, SIGNAL(pressed()),
  82           this, SLOT(mussaCreatePushed()));
  83
  84   // Cancle Button
  85   connect(cancelPushButton, SIGNAL(pressed()),
  86           this, SLOT(mussaCancelPushed()));
  87
  88   // LAYOUT
  89   QHBoxLayout *row1Layout = new QHBoxLayout;
  90   QHBoxLayout *row2Layout = new QHBoxLayout;
  91   QVBoxLayout *mainLayout = new QVBoxLayout;
  92   QHBoxLayout *buttonLayout = new QHBoxLayout;
  93
  94   row1Layout->addWidget(analysisNameLabel);
  95   row1Layout->addWidget(analysisNameLineEdit);
  96
  97   row2Layout->addWidget(thresholdLabel);
  98   row2Layout->addWidget(thresholdEdit);
  99   row2Layout->addWidget(windowLabel);
 100   row2Layout->addWidget(windowEdit);
 101   row2Layout->addWidget(numOfSequencesLabel);
 102   row2Layout->addWidget(numOfSequencesSpinBox);
 103
 104   buttonLayout->addStretch(1);
 105   buttonLayout->addWidget(createPushButton);
 106   buttonLayout->addWidget(cancelPushButton);
 107
 108   mainLayout->addLayout(row1Layout);
 109   mainLayout->addLayout(row2Layout);
 110   mainLayout->addWidget(seqSetupFrame);
 111   mainLayout->addLayout(buttonLayout);
 112   setLayout(mainLayout);
 113 }
 114
 115 void MussaSetupWidget::mussaCreatePushed()
 116 {
 117   emit createButtonPushed();
 118 }
 119
 120 void MussaSetupWidget::mussaCancelPushed()
 121 {
 122   emit cancelButtonPushed();
 123 }
 124
 125 void MussaSetupWidget::updateThreshold(int new_threshold)
 126 {
 127   thresholdEdit->setMaximum(new_threshold);
 128 }
 129
 130 MussaRef MussaSetupWidget::getMussaObject()
 131 {
 132   MussaRef mussa = Mussa::init();
 133
 134   int fastaIndex;
 135   int start;
 136   int end;
 137
 138   list<SetupInfo *> setupInfoList = seqSetupFrame->getSetupInfo();
 139
 140   for (list<SetupInfo *>::reverse_iterator setup_item = setupInfoList.rbegin();
 141        setup_item != setupInfoList.rend();
 142        ++setup_item)
 143   {
 144     std::string seqName = (*setup_item)->getName();
 145     std::string seqNative = (*setup_item)->getSeqFile();
 146     std::string annotNative = (*setup_item)->getAnnotFile();
 147     fastaIndex = (*setup_item)->getFastaIndex();
 148     start = (*setup_item)->getSubSeqStart();
 149     end = (*setup_item)->getSubSeqEnd();
 150
 151     fs::path seqFile(seqNative, fs::native);
 152     fs::path annotFile(annotNative, fs::native);
 153     mussa->load_sequence(seqFile, annotFile, fastaIndex, start, end, &seqName);
 154   }
 155   setupInfoList.clear();
 156
 157   int win_size = windowEdit->value();
 158   int threshold = thresholdEdit->value();
 159   std::string name = analysisNameLineEdit->text().toStdString();
 160   if (win_size == 0 or threshold == 0) {
 161     throw mussa_load_error("must set analysis parameters");
 162   } else {
 163     mussa->set_name(name);
 164     mussa->set_window(win_size);
 165     mussa->set_threshold(threshold);
 166     mussa->set_analysis_mode(Mussa::TransitiveNway);
 167     //mussa->set_entropy(0); // might want to add this at some point
 168     mussa->analyze();
 169   }
 170
 171   return mussa;
 172 }
 173