Color colour = ColorUtils.parseColourString(descriptor);
if (colour == null)
{
- throw new IllegalArgumentException("Invalid colour descriptor: "
- + descriptor);
+ throw new IllegalArgumentException(
+ "Invalid colour descriptor: " + descriptor);
}
return new FeatureColour(colour);
}
FeatureColour featureColour;
try
{
- featureColour = new FeatureColour(
- new UserColourScheme(mincol).findColour(),
- new UserColourScheme(maxcol).findColour(), min, max);
+ Color minColour = ColorUtils.parseColourString(mincol);
+ Color maxColour = ColorUtils.parseColourString(maxcol);
+ featureColour = new FeatureColour(minColour, maxColour, min, max);
featureColour.setColourByLabel(labelColour);
featureColour.setAutoScaled(autoScaled);
// add in any additional parameters
{
if (!ttype.toLowerCase().startsWith("no"))
{
- System.err.println("Ignoring unrecognised threshold type : "
- + ttype);
+ System.err.println(
+ "Ignoring unrecognised threshold type : " + ttype);
}
}
}
}
if (gcol.hasMoreTokens())
{
- System.err
- .println("Ignoring additional tokens in parameters in graduated colour specification\n");
+ System.err.println(
+ "Ignoring additional tokens in parameters in graduated colour specification\n");
while (gcol.hasMoreTokens())
{
System.err.println("|" + gcol.nextToken());
*/
public FeatureColour(Color low, Color high, float min, float max)
{
+ if (low == null)
+ {
+ low = Color.white;
+ }
+ if (high == null)
+ {
+ high = Color.black;
+ }
graduatedColour = true;
colour = null;
minColour = low;
{
if (isColourByLabel())
{
- return ColorUtils
- .createColourFromName(feature.getDescription());
+ return ColorUtils.createColourFromName(feature.getDescription());
}
if (!isGraduatedColour())
return getColour();
}
- // todo should we check for above/below threshold here?
- if (range == 0.0)
- {
- return getMaxColour();
- }
+ /*
+ * graduated colour case, optionally with threshold
+ * Float.NaN is assigned minimum visible score colour
+ */
float scr = feature.getScore();
if (Float.isNaN(scr))
{
return getMinColour();
}
+ if (isAboveThreshold() && scr <= threshold)
+ {
+ return null;
+ }
+ if (isBelowThreshold() && scr >= threshold)
+ {
+ return null;
+ }
+ if (range == 0.0)
+ {
+ return getMaxColour();
+ }
float scl = (scr - base) / range;
if (isHighToLow)
{
return (isHighToLow) ? (base + range) : base;
}
- /**
- * Answers true if the feature has a simple colour, or is coloured by label,
- * or has a graduated colour and the score of this feature instance is within
- * the range to render (if any), i.e. does not lie below or above any
- * threshold set.
- *
- * @param feature
- * @return
- */
- @Override
- public boolean isColored(SequenceFeature feature)
- {
- if (isColourByLabel() || !isGraduatedColour())
- {
- return true;
- }
-
- float val = feature.getScore();
- if (Float.isNaN(val))
- {
- return true;
- }
- if (Float.isNaN(this.threshold))
- {
- return true;
- }
-
- if (isAboveThreshold() && val <= threshold)
- {
- return false;
- }
- if (isBelowThreshold() && val >= threshold)
- {
- return false;
- }
- return true;
- }
-
@Override
public boolean isSimpleColour()
{