public void setGenome(String key, Genome genome) {
if (!genome.getID().equals(key)) {
throw new IllegalStateException();
}
keyedGenomes_.put(genome.getID(), genome);
return;
}
public void install(DBGenome genome, List<Genome> keyedGenomes) {
rootGenome_ = genome;
keyedGenomes_ = new HashMap<String, Genome>();
if (genome != null) {
keyedGenomes_.put(genome.getID(), genome);
}
if (keyedGenomes != null) {
int numkg = keyedGenomes.size();
for (int i = 0; i < numkg; i++) {
Genome keyedGenome = keyedGenomes.get(i);
keyedGenomes_.put(keyedGenome.getID(), keyedGenome);
}
}
Iterator<Genome> vals = this.keyedGenomes_.values().iterator();
while (vals.hasNext()) {
AbstractGenome keyedCopy = (AbstractGenome) vals.next();
keyedCopy.setGenomeSource(this);
}
return;
}
/**
* ************************************************************************* * * Reduce the genome
* to hold just our results
*/
public LocalGenomeSource reduceToResult(
AllPathsResult apr, String redID, Map<String, String> grpIDMap) {
// Transfer of genome source is occurring here:
LocalGenomeSource retval = new LocalGenomeSource(this, grpIDMap);
Genome reduced = retval.getGenome(redID);
Genome sourceGenome = getGenome(redID);
Set<String> lst = apr.getLinkSet();
Iterator<Linkage> tlit = sourceGenome.getLinkageIterator();
while (tlit.hasNext()) {
Linkage link = tlit.next();
String linkID = link.getID();
if (!lst.contains(linkID)) {
reduced.removeLinkage(linkID);
}
}
Set<String> nst = apr.getNodeSet();
Iterator<Node> nlit = sourceGenome.getAllNodeIterator();
while (nlit.hasNext()) {
Node node = nlit.next();
String nodeID = node.getID();
if (!nst.contains(nodeID)) {
reduced.removeNode(nodeID);
}
}
return (retval);
}
/** ************************************************************************* * * Constructor */
public HaloLayoutSetupPanel(
BTState appState,
Genome genome,
String selectedID,
HaloLayout halo,
HaloLayout.HaloLayoutParams params) {
appState_ = appState;
haveResult_ = false;
params_ = (HaloLayout.HaloLayoutParams) params.clone();
params_.selected = selectedID;
ResourceManager rMan = appState_.getRMan();
setLayout(new GridBagLayout());
GridBagConstraints gbc = new GridBagConstraints();
if ((params_.selected != null) && !halo.selectionIsValid(genome, params_.selected)) {
params_.selected = null;
}
JLabel strategyLabel = new JLabel(rMan.getString("haloLayout.strategyType"));
strategyCombo_ =
new JComboBox(HaloLayout.StartSeed.getChoices(appState_, params_.selected != null));
UiUtil.gbcSet(gbc, 0, 0, 1, 1, UiUtil.HOR, 0, 0, 5, 5, 5, 5, UiUtil.CEN, 1.0, 0.0);
add(strategyLabel, gbc);
UiUtil.gbcSet(gbc, 1, 0, 1, 1, UiUtil.HOR, 0, 0, 5, 5, 5, 5, UiUtil.CEN, 1.0, 0.0);
add(strategyCombo_, gbc);
JLabel overlayLabel = new JLabel(rMan.getString("haloLayout.overlayOptions"));
Vector<ChoiceContent> relayoutChoices = NetOverlayProperties.getRelayoutOptions(appState);
overlayOptionCombo_ = new JComboBox(relayoutChoices);
boolean activate = (genome == null) || (genome.getNetworkOverlayCount() > 0);
if (!activate) {
overlayLabel.setEnabled(false);
overlayOptionCombo_.setEnabled(false);
}
UiUtil.gbcSet(gbc, 0, 1, 1, 1, UiUtil.HOR, 0, 0, 5, 5, 5, 5, UiUtil.CEN, 1.0, 0.0);
add(overlayLabel, gbc);
UiUtil.gbcSet(gbc, 1, 1, 1, 1, UiUtil.HOR, 0, 0, 5, 5, 5, 5, UiUtil.CEN, 1.0, 0.0);
add(overlayOptionCombo_, gbc);
}
public void setGenome(Genome genome) {
rootGenome_ = (DBGenome) genome;
keyedGenomes_.put(genome.getID(), genome);
return;
}
