X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=qui%2Fmussa_setup_dialog%2FMussaSetupWidget.cpp;h=c116a9a2e12fc6e9983760a6f80f83906cd69961;hb=4c1d1e263deea85ab00823282c5ca5fc00fa8c26;hp=63e9845274c6ed9c43c8ff9064d662dff27a332c;hpb=3798c713abe45f51c256c2fd47bdbd594662b9cb;p=mussa.git

diff --git a/qui/mussa_setup_dialog/MussaSetupWidget.cpp b/qui/mussa_setup_dialog/MussaSetupWidget.cpp
index 63e9845..c116a9a 100644
--- a/qui/mussa_setup_dialog/MussaSetupWidget.cpp
+++ b/qui/mussa_setup_dialog/MussaSetupWidget.cpp
@@ -22,42 +22,67 @@ namespace fs = boost::filesystem;
 
 MussaSetupWidget::MussaSetupWidget(QWidget *parent)
   : QWidget(parent),
-    createPushButton(tr("Create")),
-    cancelPushButton(tr("Cancel")),
+    analysisNameLineEdit(new QLineEdit),
+    windowEdit(new QSpinBox),
+    thresholdEdit(new QSpinBox),
+    numOfSequencesSpinBox(new QSpinBox),
+    createPushButton(new QPushButton(tr("Create"))),
+    cancelPushButton(new QPushButton(tr("Cancel"))),
     seqSetupFrame(0)
 {
-  
+  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->setBuddy(analysisNameLineEdit);
+  analysisNameLabel->setWhatsThis("Meaningful name for your analysis ");
+  analysisNameLineEdit->setWhatsThis("Meaningful name for your analysis ");
 
   // Window
+  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(&windowLineEdit);
+  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
+  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(&thresholdLineEdit);
+  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
   QLabel *numOfSequencesLabel = new QLabel(tr("Number of sequences"));
-  numOfSequencesLabel->setBuddy(&numOfSequencesSpinBox);
-  numOfSequencesSpinBox.setMinimum(1);
+  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)),
+  connect(numOfSequencesSpinBox, SIGNAL(valueChanged(int)),
 	  seqSetupFrame, SLOT(changeSequenceCount(int)));
 
-  numOfSequencesSpinBox.setValue(2);
+  numOfSequencesSpinBox->setValue(2);
 
   // Create Experiment Button
-  connect(&createPushButton, SIGNAL(pressed()),
+  connect(createPushButton, SIGNAL(pressed()),
 	  this, SLOT(mussaCreatePushed()));
   
   // Cancle Button
-  connect(&cancelPushButton, SIGNAL(pressed()),
+  connect(cancelPushButton, SIGNAL(pressed()),
 	  this, SLOT(mussaCancelPushed()));
 
   // LAYOUT
@@ -67,24 +92,24 @@ MussaSetupWidget::MussaSetupWidget(QWidget *parent)
   QHBoxLayout *buttonLayout = new QHBoxLayout;
 
   row1Layout->addWidget(analysisNameLabel);
-  row1Layout->addWidget(&analysisNameLineEdit);
+  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);
+  row2Layout->addWidget(numOfSequencesSpinBox);
 
-  buttonLayout->addWidget(&createPushButton);
-  buttonLayout->addWidget(&cancelPushButton);
+  buttonLayout->addStretch(1);
+  buttonLayout->addWidget(createPushButton);
+  buttonLayout->addWidget(cancelPushButton);
 
   mainLayout->addLayout(row1Layout);
   mainLayout->addLayout(row2Layout);
   mainLayout->addWidget(seqSetupFrame);
   mainLayout->addLayout(buttonLayout);
   setLayout(mainLayout);
-
 }
 
 void MussaSetupWidget::mussaCreatePushed()
@@ -97,9 +122,14 @@ void MussaSetupWidget::mussaCancelPushed()
   emit cancelButtonPushed();
 }
 
-Mussa* MussaSetupWidget::getMussaObject()
+void MussaSetupWidget::updateThreshold(int new_threshold)
+{
+  thresholdEdit->setMaximum(new_threshold);
+}
+
+MussaRef MussaSetupWidget::getMussaObject()
 {
-  Mussa *mussa = new Mussa;
+  MussaRef mussa = Mussa::init();
 
   int fastaIndex;
   int start;
@@ -124,11 +154,13 @@ Mussa* MussaSetupWidget::getMussaObject()
   }
   setupInfoList.clear();
 
-  int win_size = windowLineEdit.text().toInt();
-  int threshold = thresholdLineEdit.text().toInt();
+  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);
@@ -139,11 +171,3 @@ Mussa* MussaSetupWidget::getMussaObject()
   return mussa;
 }
 
-//MussaSetupWidget::MussaSetupWidget(const MussaSetupWidget& msw)
-//  : analysisNameLineEdit(msw.analysisNameLineEdit),
-//    windowLineEdit(msw.windowLineEdit),
-//    thresholdLineEdit(msw.thresholdLineEdit),
-//    numOfSequencesLineEdit(msw.numOfSequencesLineEdit),
-//    seqSetupFrame(msw.seqSetupFrame)
-//{
-//}