1 package jalview.workers;
3 import jalview.datamodel.SequenceFeature;
8 * An interface for a type that returns counts of any value of interest at a
9 * sequence position that can be determined from the sequence character and any
10 * features present at that position
13 public interface FeatureCounterI
16 * Returns a count of some property of interest, for example
18 * <li>the number of variant features at the position</li>
19 * <li>the number of Cath features of status 'True Positive'</li>
20 * <li>1 if the residue is hydrophobic, else 0</li>
25 * the residue (or gap) at the position
27 * list of any sequence features which include the position
29 int count(String residue, List<SequenceFeature> features);
32 * Returns a name for the annotation that this is counting, for use as the
40 * Returns a description for the annotation, for display as a tooltip
44 String getDescription();
47 * Returns the colour (as [red, green, blue] values in the range 0-255) to use
48 * for the minimum value on histogram bars. If this is different to
49 * getMaxColour(), then bars will have a graduated colour.
56 * Returns the colour (as [red, green, blue] values in the range 0-255) to use
57 * for the maximum value on histogram bars. If this is the same as
58 * getMinColour(), then bars will have a single colour (not graduated).