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 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);
}
}
private boolean isWholeGenome() {
Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem();
Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem();
return chr1.getName().equals("All") || chr2.getName().equals("All");
}
private boolean isIntraChromosomal() {
Chromosome chr1 = (Chromosome) chrBox1.getSelectedItem();
Chromosome chr2 = (Chromosome) chrBox2.getSelectedItem();
return chr1.getIndex() != chr2.getIndex();
}