@Override
public void actionPerformed(ActionEvent e) {
// TODO Auto-generated method stub
int l = selectedSets.size();
if (l != 0) {
ArrayList<Protein> temp = new ArrayList<Protein>();
for (Protein p : sortResults.get(curalg)) {
if (p.getSelectGroups() != null && p.getSelectGroups().size() >= l) {
if (p.getSelectGroups().containsAll(selectedSets)) {
temp.add(p);
}
}
}
if (!temp.isEmpty()) {
clearB.doClick();
sproteins.clear();
sproteins.addAll(temp);
pUtil.sortVertex(sproteins, curalg);
pUtil.getResultPanel(id).browserPanel.updateTable(null);
curSetName = "Overlapping Nodes";
} else {
}
} else {
}
}
public void updateNet(String curalg, String curSetName) {
HashSet<CyNode> nodes = new HashSet<CyNode>();
for (Protein p : sproteins) {
nodes.add(p.getN());
}
pg = pUtil.createGraph(network, nodes);
// selectProteins(pg.getSubNetwork());
this.pUtil.setSelected(nodes, network);
this.curalg = curalg;
this.curSetName = curSetName;
}
public void listIt(List<Protein> sproteins) {
this.data = new Object[sproteins.size()][this.columnNames.length];
int i = 0, j;
for (Protein p : sproteins) {
data[i][0] = i + 1;
data[i][1] = p.getName();
j = 0;
for (String s : sortResults.keySet()) {
data[i][2 + j * 5] = p.getPara(s);
j++;
}
i++;
}
j = 0;
for (String s : sortResults.keySet()) {
List<Protein> rankedResult = sortResults.get(s);
int length = rankedResult.size();
DecimalFormat df = new DecimalFormat("#.####");
double max = rankedResult.get(0).getPara(s);
double min = rankedResult.get(length - 1).getPara(s);
double avg = 0;
for (Protein p : rankedResult) {
avg += p.getPara(s);
}
avg = avg / (double) length;
i = 0;
for (Protein p : sproteins) {
data[i][3 + j * 5] = rankedResult.indexOf(p) + 1;
if (s == ParameterSet.IC) df = new DecimalFormat("#.####E0");
data[i][4 + j * 5] = df.format(avg);
data[i][5 + j * 5] = df.format(max);
data[i][6 + j * 5] = df.format(min);
i++;
}
j++;
}
}
@Override
public void actionPerformed(ActionEvent e) {
// TODO Auto-generated method stub
if (pUtil.modifiedNetworkSet != null
&& !pUtil.modifiedNetworkSet.contains(network.getSUID())) {
for (Protein p : sortResults.get(curalg)) {
if (p.getSelectGroups() != null && !p.getSelectGroups().isEmpty()) {
networkView
.getNodeView(p.getN())
.setVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR, p.getOriginColor());
networkView
.getNodeView(p.getN())
.setVisualProperty(BasicVisualLexicon.NODE_TOOLTIP, "");
p.getSelectGroups().clear();
}
}
} else {
for (Protein p : sortResults.get(curalg)) {
if (network.containsNode(p.getN())
&& p.getSelectGroups() != null
&& !p.getSelectGroups().isEmpty()) {
networkView
.getNodeView(p.getN())
.setVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR, p.getOriginColor());
networkView
.getNodeView(p.getN())
.setVisualProperty(BasicVisualLexicon.NODE_TOOLTIP, "");
p.getSelectGroups().clear();
}
}
}
SetColorMap.clear();
selectedSets.clear();
labelPanel.removeAll();
labelPanel.repaint();
networkView.updateView();
SETINDEX = 0;
}
@Override
public void actionPerformed(ActionEvent e) {
// TODO Auto-generated method stub
Color mixc = null, currentc = null;
HashMap<String, Color> mixColors = new HashMap<String, Color>();
JColorChooser jc = new JColorChooser();
currentc = jc.showDialog(null, "Please choose one color", Color.red);
if (currentc != null) {
pUtil.setSelected(null, network);
if (pUtil.modifiedNetworkSet != null
&& !pUtil.modifiedNetworkSet.contains(network.getSUID())) {
for (Protein p : sproteins) {
CyNode n = p.getN();
SetColorMap.put(curSetName, currentc);
if (p.getSelectGroups() == null || p.getSelectGroups().isEmpty()) {
p.setOriginColor(
networkView
.getNodeView(n)
.getVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR));
p.setSelectGroups(new ArrayList<String>());
p.getSelectGroups().add(curSetName);
networkView
.getNodeView(n)
.setVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR, currentc);
networkView
.getNodeView(n)
.setVisualProperty(BasicVisualLexicon.NODE_TOOLTIP, curSetName);
} else {
if (ismixcolor) {
p.getSelectGroups().add(curSetName);
String mixname = "";
double blue = 0, red = 0, green = 0, s = p.getSelectGroups().size();
int r, g, b;
int i = 0;
for (String set : p.getSelectGroups()) {
blue += SetColorMap.get(set).getBlue();
red += SetColorMap.get(set).getRed();
green += SetColorMap.get(set).getGreen();
if (i == 0) mixname += set;
else mixname += " + " + set;
i++;
}
r = (int) Math.round(red / s);
g = (int) Math.round(green / s);
b = (int) Math.round(blue / s);
mixc = new Color(r, g, b);
networkView
.getNodeView(n)
.setVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR, mixc);
networkView
.getNodeView(n)
.setVisualProperty(BasicVisualLexicon.NODE_TOOLTIP, mixname);
mixColors.put(mixname, mixc);
} else {
// p.setOriginColor(networkView.getNodeView(n).getVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR));
p.getSelectGroups().add(curSetName);
networkView
.getNodeView(n)
.setVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR, currentc);
networkView
.getNodeView(n)
.setVisualProperty(BasicVisualLexicon.NODE_TOOLTIP, curSetName);
}
}
}
} else {
for (Protein p : sproteins) {
CyNode n = p.getN();
if (!network.containsNode(n)) {
continue;
}
SetColorMap.put(curSetName, currentc);
if (p.getSelectGroups() == null || p.getSelectGroups().isEmpty()) {
p.setOriginColor(
networkView
.getNodeView(n)
.getVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR));
p.setSelectGroups(new ArrayList<String>());
p.getSelectGroups().add(curSetName);
networkView
.getNodeView(n)
.setVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR, currentc);
networkView
.getNodeView(n)
.setVisualProperty(BasicVisualLexicon.NODE_TOOLTIP, curSetName);
} else {
if (ismixcolor) {
p.getSelectGroups().add(curSetName);
String mixname = "";
double blue = 0, red = 0, green = 0, s = p.getSelectGroups().size();
int r, g, b;
int i = 0;
for (String set : p.getSelectGroups()) {
blue += SetColorMap.get(set).getBlue();
red += SetColorMap.get(set).getRed();
green += SetColorMap.get(set).getGreen();
if (i == 0) mixname += set;
else mixname += " + " + set;
i++;
}
r = (int) Math.round(red / s);
g = (int) Math.round(green / s);
b = (int) Math.round(blue / s);
mixc = new Color(r, g, b);
networkView
.getNodeView(n)
.setVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR, mixc);
networkView
.getNodeView(n)
.setVisualProperty(BasicVisualLexicon.NODE_TOOLTIP, mixname);
mixColors.put(mixname, mixc);
} else {
// p.setOriginColor(networkView.getNodeView(n).getVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR));
p.getSelectGroups().add(curSetName);
networkView
.getNodeView(n)
.setVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR, currentc);
networkView
.getNodeView(n)
.setVisualProperty(BasicVisualLexicon.NODE_TOOLTIP, curSetName);
}
}
}
}
JPanel jp = new JPanel();
jp.setLayout(new BoxLayout(jp, BoxLayout.X_AXIS));
jp.add(new JLabel(curSetName + " ", createColorIcon(currentc), SwingConstants.LEFT));
JCheckBox temp = new JCheckBox();
temp.addActionListener(new ChooseSetsAction());
jp.add(temp);
jp.setBorder(BorderFactory.createTitledBorder(""));
jp.setBounds(10, Ylocation, 300, 25);
Ylocation += 30;
labelPanel.add(jp);
JPanel jj = new JPanel();
jj.setLayout(new BoxLayout(jj, BoxLayout.Y_AXIS));
jj.setAlignmentX(Component.LEFT_ALIGNMENT);
if (!mixColors.isEmpty()) {
for (Entry<String, Color> mix : mixColors.entrySet()) {
jj.add(
new JLabel(mix.getKey(), createColorIcon(mix.getValue()), SwingConstants.LEFT));
jj.setBounds(10, Ylocation, 300, 25);
Ylocation += 30;
labelPanel.add(jj);
}
}
labelPanel.repaint();
}
}
@Override
public void actionPerformed(ActionEvent e) {
// TODO Auto-generated method stub
List<Protein> temp = new ArrayList<Protein>();
int lastLineIndex = namesT.getLineCount() - 1;
int nameNum = lastLineIndex + 1;
int duplicateNum = 0;
try {
for (int i = 0; i < lastLineIndex; i++) {
if (namesT.getLineEndOffset(i) - namesT.getLineStartOffset(i) == 1) {
nameNum--;
continue;
}
String name =
namesT.getText(
namesT.getLineStartOffset(i),
namesT.getLineEndOffset(i) - namesT.getLineStartOffset(i) - 1);
for (Protein p : sortResults.get(curalg)) {
if (p.getName().equals(name)) {
if (temp.contains(p)) {
duplicateNum++;
} else {
temp.add(p);
}
break;
}
}
}
if (namesT.getLineStartOffset(lastLineIndex) == namesT.getLineEndOffset(lastLineIndex)) {
nameNum--;
} else {
String name =
namesT.getText(
namesT.getLineStartOffset(lastLineIndex),
namesT.getLineEndOffset(lastLineIndex)
- namesT.getLineStartOffset(lastLineIndex));
for (Protein p : sortResults.get(curalg)) {
if (p.getName().equals(name)) {
temp.add(p);
break;
}
}
}
} catch (BadLocationException e1) {
// TODO Auto-generated catch block
e1.printStackTrace();
}
if (!temp.isEmpty()) {
sproteins.clear();
sproteins.addAll(temp);
pUtil.sortVertex(sproteins, curalg);
pUtil.getResultPanel(id).browserPanel.updateTable(null);
pUtil.getResultPanel(id).browserPanel.changeSortingRange(false);
curSetName = "Self-select proteins (No. " + ++SETINDEX + ")";
}
JOptionPane.showMessageDialog(
null,
nameNum
+ " node names have been uploaded, "
+ duplicateNum
+ " duplicated values, "
+ temp.size()
+ " nodes have been selected.",
"Result",
JOptionPane.WARNING_MESSAGE);
}