/** 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); } } }