@Override
public void actionPerformed(ActionEvent arg0) {
List<Xref> xrefs =
standaloneEngine.getSwingEngine().getEngine().getActivePathway().getDataNodeXrefs();
Set<Xref> setRefs = new HashSet<Xref>(xrefs);
DataInterface gex = standaloneEngine.getGexManager().getCurrentGex();
CachedData cache = standaloneEngine.getGexManager().getCachedData();
Collection<? extends ISample> names = null;
Map<String, List<TissueResult>> data = new TreeMap<String, List<TissueResult>>();
try {
names = gex.getOrderedSamples();
for (ISample is : names) {
if (!is.getName().equals(" Gene Name")) {
data.put(is.getName().trim(), new ArrayList<TissueResult>());
}
}
for (Xref ref : setRefs) {
List<? extends IRow> pwData = cache.syncGet(ref);
if (!pwData.isEmpty()) {
for (ISample is : names) {
for (IRow ir : pwData) {
if (!is.getName().equals(" Gene Name")) {
Double value = (Double) ir.getSampleData(is);
String dd = ir.getXref().getId();
TissueResult tr = new TissueResult(dd, value);
data.get(is.getName().trim()).add(tr);
}
}
}
}
}
} catch (DataException e) {
e.printStackTrace();
} catch (IDMapperException e) {
e.printStackTrace();
}
Vector<Double> vP = new Vector<Double>();
Vector<Double> vM = new Vector<Double>();
for (Entry<String, List<TissueResult>> entry : data.entrySet()) {
int length = entry.getValue().size();
double i = 0;
double tmp = 0;
for (TissueResult tr : entry.getValue()) {
if (tr.getExpression() >= (2 / Math.log10(2))) {
i++;
}
tmp += tr.getExpression();
}
vP.add(i / length * 100);
vM.add(tmp / length);
}
dtm.addCollum(vP, 2);
dtm.addCollum(vM, 3);
}
@Override
public void tableChanged(TableModelEvent arg0) {
VisualizationManager visMgr = standaloneEngine.getVisualizationManager();
ColorSetManager csmgr = visMgr.getColorSetManager();
ColorSet cs = new ColorSet(csmgr);
csmgr.addColorSet(cs);
ColorGradient gradient = new ColorGradient();
cs.setGradient(gradient);
double lowerbound = 3;
double upperbound = 10;
gradient.addColorValuePair(new ColorValuePair(new Color(218, 242, 249), lowerbound));
gradient.addColorValuePair(new ColorValuePair(new Color(0, 0, 255), upperbound));
Visualization v = new Visualization("auto-generated");
ColorByExpression cby =
new ColorByExpression(
standaloneEngine.getGexManager(),
standaloneEngine.getVisualizationManager().getColorSetManager());
DataInterface gex = standaloneEngine.getGexManager().getCurrentGex();
Map<Integer, ? extends ISample> samplesMap = null;
try {
samplesMap = gex.getSamples();
} catch (DataException e1) {
e1.printStackTrace();
}
for (Entry<Integer, ? extends ISample> entry : samplesMap.entrySet()) {
ISample valeur = entry.getValue();
String tissues = valeur.getName().trim();
for (int i = 0; i < vT.size(); i++) {
if (vB.get(i) && vT.get(i).equals(tissues)) {
cby.addUseSample(valeur);
}
}
}
cby.setSingleColorSet(cs);
v.addMethod(cby);
DataNodeLabel dnl = new DataNodeLabel();
v.addMethod(dnl);
visMgr.removeVisualization(v);
visMgr.addVisualization(v);
visMgr.setActiveVisualization(v);
}