/** After clicking execute button, all data in dialog is saved to GoIOptionsPack */
public void storeValuesToOptionsPack(QueryOptionsPack opt) {
// store Length Limit
opt.setLengthLimit(Integer.parseInt(lengthLimit.getText()));
// if currentView is selected
if (currentViewButton.getSelection()) {
opt.setCurrentView(true);
}
// if newView is selected
else {
opt.setCurrentView(false);
}
if (downstreamButton != null) {
// if downstream is selected
if (downstreamButton.getSelection()) {
opt.setDownstream(true);
opt.setUpstream(false);
}
// if upstream is selected
else if (upstreamButton.getSelection()) {
opt.setDownstream(false);
opt.setUpstream(true);
}
// if both is selected
else {
opt.setDownstream(true);
opt.setUpstream(true);
}
}
// store stop distance according to user's selection
if (shortestPlusKButton != null) {
opt.setLimitType(!shortestPlusKButton.getSelection());
opt.setShortestPlusKLimit(Integer.parseInt(shortestPlusK.getText()));
}
// if strict is selected.
if (strictButton != null && strictButton.getSelection()) {
opt.setStrict(true);
} else {
opt.setStrict(false);
}
if (sourceST != null) opt.setSourceList(sourceST.getSymbols());
if (targetST != null) opt.setTargetList(targetST.getSymbols());
if (forSIF) {
opt.setSifTypes(selectedTypes);
}
}
private void collectUnknownSymbols(SymbolText st, java.util.List<String> unkwn) {
if (st != null) {
for (String s : st.getSymbols()) {
if (HGNC.getSymbol(s) == null && !unkwn.contains(s)) unkwn.add(s);
}
}
}
