Esempio n. 1
0
 public void setSelectedChromosomesNoRefresh(
     Chromosome xChrom, Chromosome yChrom, Context xContext, Context yContext) {
   chrBox1.setSelectedIndex(yChrom.getIndex());
   chrBox2.setSelectedIndex(xChrom.getIndex());
   rulerPanelX.setContext(xContext, HiCRulerPanel.Orientation.HORIZONTAL);
   rulerPanelY.setContext(yContext, HiCRulerPanel.Orientation.VERTICAL);
   resolutionSlider.setEnabled(!xChrom.getName().equals(Globals.CHR_ALL));
 }
Esempio n. 2
0
 public void setSelectedDisplayOption(MatrixType[] options, boolean control) {
   if (control) {
     MatrixType originalMatrixType = (MatrixType) displayOptionComboBox.getSelectedItem();
     displayOptionComboBox.setModel(new DefaultComboBoxModel<MatrixType>(options));
     int indx = 0;
     for (int i = 0; i < displayOptionComboBox.getItemCount(); i++) {
       if (originalMatrixType.equals(displayOptionComboBox.getItemAt(i))) {
         indx = i;
         break;
       }
     }
     displayOptionComboBox.setSelectedIndex(indx);
   } else {
     displayOptionComboBox.setModel(new DefaultComboBoxModel<MatrixType>(options));
     displayOptionComboBox.setSelectedIndex(0);
   }
 }
Esempio n. 3
0
  public void setNormalizationDisplayState(HiC hic) {

    // Test for new dataset ("All"),  or change in chromosome
    if (isWholeGenome()) { // for now only allow observed
      hic.setDisplayOption(MatrixType.OBSERVED);
      displayOptionComboBox.setSelectedIndex(0);
      normalizationComboBox.setSelectedIndex(0);
    } else if (isIntraChromosomal()) {
      if (hic.getDisplayOption() == MatrixType.PEARSON) {
        hic.setDisplayOption(MatrixType.OBSERVED);
        displayOptionComboBox.setSelectedIndex(0);
      }
    }

    normalizationComboBox.setEnabled(!isWholeGenome());
    displayOptionComboBox.setEnabled(true);
  }
Esempio n. 4
0
 public void setEnabledForNormalization(String[] normalizationOptions, boolean status) {
   if (normalizationOptions.length == 1) {
     normalizationComboBox.setEnabled(false);
   } else {
     normalizationComboBox.setModel(new DefaultComboBoxModel<String>(normalizationOptions));
     normalizationComboBox.setSelectedIndex(0);
     normalizationComboBox.setEnabled(status && !isWholeGenome());
   }
 }
Esempio n. 5
0
  public void unsafeRefreshChromosomes(SuperAdapter superAdapter) {

    if (chrBox1.getSelectedIndex() == 0 || chrBox2.getSelectedIndex() == 0) {
      chrBox1.setSelectedIndex(0);
      chrBox2.setSelectedIndex(0);
    }

    Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem();
    Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem();

    Chromosome chrX = chr1.getIndex() < chr2.getIndex() ? chr1 : chr2;
    Chromosome chrY = chr1.getIndex() < chr2.getIndex() ? chr2 : chr1;

    setNormalizationDisplayState(superAdapter.getHiC());

    superAdapter.unsafeUpdateHiCChromosomes(chrX, chrY);

    updateThumbnail(superAdapter.getHiC());
  }
Esempio n. 6
0
 public void setNormalizationBox(int indx) {
   normalizationComboBox.setSelectedIndex(indx);
 }
Esempio n. 7
0
 public void setDisplayBox(int indx) {
   displayOptionComboBox.setSelectedIndex(indx);
 }
Esempio n. 8
0
 private void chrBox2ActionPerformed(ActionEvent e) {
   if (chrBox2.getSelectedIndex() == 0) {
     chrBox1.setSelectedIndex(0);
   }
 }
Esempio n. 9
0
 /*
  * Only accessed from within another unsafe method in Heatmap Panel class,
  * which in turn is encapsulated (i.e. made safe)
  */
 public void unsafeSetSelectedChromosomes(
     SuperAdapter superAdapter, Chromosome xChrom, Chromosome yChrom) {
   chrBox1.setSelectedIndex(yChrom.getIndex());
   chrBox2.setSelectedIndex(xChrom.getIndex());
   unsafeRefreshChromosomes(superAdapter);
 }