public CachedProbe(AffyProbe ap, Vector<AffyExperiment> expts) {
probe = ap;
min = max = 0.0;
color = Color.lightGray;
stroke = new BasicStroke((float) 2.0);
values = new Vector<Double>();
for (AffyExperiment e : expts) {
AffyMeasurement am = e.getMeasurement(probe);
if (am != null) {
values.add(am.getValue());
min = Math.min(am.getValue(), min);
max = Math.max(am.getValue(), max);
} else {
values.add(null);
}
}
}
public void paintProbe(Graphics2D g2, int x1, int y1, int x2, int y2, double tmin, double tmax) {
g2.setStroke(stroke);
g2.setColor(color);
int ppx = -1, ppy = -1;
for (int i = 0; i < values.size(); i++) {
Double v = values.get(i);
if (v != null && tmax - tmin > 0.0) {
double frac = (v - tmin) / (tmax - tmin);
int pixY = y2 - (int) Math.round(frac * (y2 - y1));
int pixX = x1 + (int) Math.floor((double) (i + 1) / (double) (values.size() + 2));
if (ppx != -1) {
g2.drawLine(ppx, ppy, pixX, pixY);
}
ppx = pixX;
ppy = pixY;
} else {
ppx = ppy = -1;
}
}
}
public Collection<Experiment> findExpts(CellLine cells, ExptCondition cond) throws SQLException {
LinkedList<Integer> dbids = new LinkedList<Integer>();
String tables = "experiment e";
if (genome != null) {
tables += ", probe_platform_to_genome p2g";
}
String query = "select e.id from " + tables;
Vector<String> conds = new Vector<String>();
if (genome != null) {
int gid = genome.getDBID();
conds.add("e.platform=p2g.platform and p2g.genome=" + gid);
}
if (cells != null) {
conds.add("e.cells=" + cells.getDBID());
}
if (cond != null) {
conds.add("e.condition=" + cond.getDBID());
}
for (int i = 0; i < conds.size(); i++) {
if (i == 0) {
query += " where ";
} else {
query += " and ";
}
query += conds.get(i);
}
System.out.println("Final Query: \"" + query + "\"");
java.sql.Connection cxn = loader.getConnection();
Statement s = cxn.createStatement();
ResultSet rs = s.executeQuery(query);
while (rs.next()) {
int dbid = rs.getInt(1);
dbids.addLast(dbid);
}
rs.close();
s.close();
Collection<Experiment> expts = loader.loadExperiments(dbids);
return expts;
}
public void addAffyProbe(AffyProbe ap) {
if (!probes.contains(ap)) {
probes.add(ap);
}
}