import jalview.datamodel.features.FeatureMatcher;
import jalview.util.ColorUtils;
import jalview.util.Format;
+import jalview.util.MessageManager;
import java.awt.Color;
import java.util.StringTokenizer;
*/
public class FeatureColour implements FeatureColourI
{
+ private static final String I18N_LABEL = MessageManager
+ .getString("label.label");
+
+ private static final String I18N_SCORE = MessageManager
+ .getString("label.score");
+
private static final String ABSOLUTE = "abso";
private static final String ABOVE = "above";
} catch (Exception e)
{
throw new IllegalArgumentException(
- "Couldn't parse the minimum value for graduated colour ("
- + descriptor + ")");
+ "Couldn't parse the minimum value for graduated colour ('"
+ + minval + "')");
}
try
{
/**
* Returns the colour for the given instance of the feature. This may be a
- * simple colour, a colour generated from the feature description (if
- * isColourByLabel()), or a colour derived from the feature score (if
- * isGraduatedColour()).
+ * simple colour, a colour generated from the feature description or other
+ * attribute (if isColourByLabel()), or a colour derived from the feature
+ * score or other attribute (if isGraduatedColour()).
+ * <p>
+ * Answers null if feature score (or attribute) value lies outside a
+ * configured threshold.
*
* @param feature
* @return
attributeName = name;
}
+ @Override
+ public boolean isOutwithThreshold(SequenceFeature feature)
+ {
+ if (!isGraduatedColour())
+ {
+ return false;
+ }
+ float scr = feature.getScore();
+ if (attributeName != null)
+ {
+ try
+ {
+ String attVal = feature.getValueAsString(attributeName);
+ scr = Float.valueOf(attVal);
+ } catch (Throwable e)
+ {
+ scr = Float.NaN;
+ }
+ }
+ if (Float.isNaN(scr))
+ {
+ return false;
+ }
+
+ return ((isAboveThreshold() && scr <= threshold)
+ || (isBelowThreshold() && scr >= threshold));
+ }
+
+ @Override
+ public String getDescription()
+ {
+ if (isSimpleColour())
+ {
+ return "r=" + colour.getRed() + ",g=" + colour.getGreen() + ",b="
+ + colour.getBlue();
+ }
+ StringBuilder tt = new StringBuilder();
+ String by = null;
+
+ if (getAttributeName() != null)
+ {
+ by = FeatureMatcher.toAttributeDisplayName(getAttributeName());
+ }
+ else if (isColourByLabel())
+ {
+ by = I18N_LABEL;
+ }
+ else
+ {
+ by = I18N_SCORE;
+ }
+ tt.append(MessageManager.formatMessage("action.by_title_param", by));
+
+ /*
+ * add threshold if any
+ */
+ if (isAboveThreshold() || isBelowThreshold())
+ {
+ tt.append(" (");
+ if (isColourByLabel())
+ {
+ /*
+ * Jalview features file supports the combination of
+ * colour by label or attribute text with score threshold
+ */
+ tt.append(I18N_SCORE).append(" ");
+ }
+ tt.append(isAboveThreshold() ? "> " : "< ");
+ tt.append(getThreshold()).append(")");
+ }
+
+ return tt.toString();
+ }
+
}