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));
}
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);
}
}
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);
}
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());
}
}
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());
}
public void setNormalizationBox(int indx) {
normalizationComboBox.setSelectedIndex(indx);
}
public void setDisplayBox(int indx) {
displayOptionComboBox.setSelectedIndex(indx);
}
private void chrBox2ActionPerformed(ActionEvent e) {
if (chrBox2.getSelectedIndex() == 0) {
chrBox1.setSelectedIndex(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);
}