// Walks the tree, checking to make sure that we haven't violated any
// logical constraints. This is a method for debugging.
public boolean check() {
String path = pathLabel();
if (suffixLink != null) {
String suffixPath = suffixLink.pathLabel();
if (!path.substring(1, path.length()).equals(suffixPath)) {
logger.log(
Level.SEVERE,
String.format("Suffix Link for node (%s) didn't match: %s", path, suffixPath));
return false;
}
}
for (char c : childEdges.keySet()) {
TreeEdge e = childEdges.get(c);
if (!e.check()) {
return false;
}
}
for (int k : terminalEdges.keySet()) {
TreeEdge e = terminalEdges.get(k);
if (!e.check()) {
return false;
}
}
return true;
}
public void collectSuffixes(Set<StringSuffix> suffices) {
suffices.addAll(suffixes);
for (char key : childEdges.keySet()) {
childEdges.get(key).tailNode.collectSuffixes(suffices);
}
for (int key : terminalEdges.keySet()) {
terminalEdges.get(key).tailNode.collectSuffixes(suffices);
}
}
/** @param aProperties the updated properties. */
@SuppressWarnings("rawtypes")
final void setProperties(final Dictionary aProperties) {
final Map<String, String> newProps = new HashMap<String, String>();
Enumeration keys = aProperties.keys();
while (keys.hasMoreElements()) {
final String key = (String) keys.nextElement();
if (!KNOWN_KEYS.contains(key) && !IGNORED_KEYS.contains(key)) {
LOG.log(Level.WARNING, "Unknown/unsupported profile key: " + key);
continue;
}
final String value = aProperties.get(key).toString();
newProps.put(key, value.trim());
}
// Verify whether all known keys are defined...
final List<String> checkedKeys = new ArrayList<String>(KNOWN_KEYS);
checkedKeys.removeAll(newProps.keySet());
if (!checkedKeys.isEmpty()) {
throw new IllegalArgumentException(
"Profile settings not complete! Missing keys are: " + checkedKeys.toString());
}
this.properties.putAll(newProps);
LOG.log(
Level.INFO,
"New device profile settings applied for {1} ({0}) ...", //
new Object[] {getType(), getDescription()});
}
public void addSelection(Point p) {
ExprPoint ep = null;
int minDist = -1;
for (ExprPoint ex : points) {
int sd = ex.screenDist(p);
if (ep == null || sd < minDist) {
ep = ex;
minDist = sd;
}
}
if (ep != null) {
Set<Point> remove = new HashSet<Point>();
for (Point rp : selections.keySet()) {
if (selections.get(rp).equals(ep)) {
remove.add(rp);
}
}
selections.put(p, ep);
for (Point rp : remove) {
selections.remove(rp);
}
}
}
public void print(int indent, PrintStream ps) {
if (isLeaf()) {
printSuffixes(ps);
ps.println();
} else {
int i = 0;
for (char c : childEdges.keySet()) {
TreeEdge edge = childEdges.get(c);
edge.print(indent, i != 0, ps);
i++;
}
for (int k : terminalEdges.keySet()) {
TreeEdge edge = terminalEdges.get(k);
edge.print(indent, i != 0, ps);
i++;
}
}
}
public Map<String, Rxn> getReactions(String compartment) {
TreeMap<String, Rxn> crxns = new TreeMap<String, Rxn>();
for (String rn : reactions.keySet()) {
Rxn r = reactions.get(rn);
if (r.getLocation().equals(compartment)) {
crxns.put(rn, r);
}
}
return crxns;
}
public Set<String> getOutputReactions(Rxn r) {
TreeSet<String> rxns = new TreeSet<String>();
for (String rn : reactions.keySet()) {
Rxn rxn = reactions.get(rn);
if (r.connects(rxn)) {
rxns.add(rn);
}
}
return rxns;
}
public void paintRegion(Graphics2D g, int x1, int y1, int w, int h) {
int h2 = h / 2;
int rad = 3;
int diam = rad * 2;
Color lg = Color.cyan;
Color dg = Color.orange;
lg = new Color(lg.getRed(), lg.getGreen(), lg.getBlue(), 75);
dg = new Color(dg.getRed(), dg.getGreen(), dg.getBlue(), 75);
/*
* Draw the Baseline
*/
g.setColor(Color.black);
g.drawLine(x1, y1 + h, x1 + w, y1 + h);
Stroke oldStroke = g.getStroke();
g.setStroke(new BasicStroke((float) 2.0));
/*
* Draw the datapoints
*/
for (ExprPoint ep : points) {
if (ep.strand == '+') {
g.setColor(lg);
} else {
g.setColor(dg);
}
g.drawOval(x1 + ep.x - rad, y1 + ep.y - rad, diam, diam);
}
g.setStroke(oldStroke);
/*
* Paint the hash marks...
*/
if (!displayOppositeChannel) {
g.setColor(Color.black);
boolean flipper = true;
for (int value = 100;
value <= scale.getMax();
value *= (flipper ? 5 : 2), flipper = !flipper) {
int yoff = getYOffset((double) value);
String line = String.format("%d", value);
int uy = y1 + h2 - yoff, ly = y1 + h2 + yoff;
g.drawLine(x1, uy, x1 + 10, uy);
g.drawString(line, x1 + 12, uy + 5);
g.drawLine(x1, ly, x1 + 10, ly);
g.drawString(line, x1 + 12, ly + 5);
}
}
/*
* Draw any selections.
*/
g.setColor(Color.black);
for (Point p : selections.keySet()) {
ExprPoint ep = selections.get(p);
g.drawLine(p.x, p.y, ep.x, ep.y);
g.drawString(ep.getLabel(), p.x, p.y);
}
/*
* Draw the label in the upper-right hand corner.
*/
g.setColor(Color.black);
Font oldFont = g.getFont();
Font newFont = new Font("Arial", Font.BOLD, 24);
g.setFont(newFont);
FontMetrics fm = g.getFontMetrics();
int lblHeight = fm.getAscent() + fm.getDescent();
int lblWidth = fm.charsWidth(label.toCharArray(), 0, label.length());
int padding = 5;
int lblx = x1 + w - lblWidth - padding;
int lbly = y1 + lblHeight + padding;
g.drawString(label, lblx, lbly);
g.setFont(oldFont);
}
public Set<String> getReactionAbbreviations() {
return reactions.keySet();
}