develop merge

[jalview.git] / src / jalview / workers / FeatureCounterI.java

diff --git a/src/jalview/workers/FeatureCounterI.java b/src/jalview/workers/FeatureCounterI.java
new file mode 100644 (file)
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--- /dev/null
+++ b/src/jalview/workers/FeatureCounterI.java
@@ -0,0 +1,63 @@
+package jalview.workers;
+
+import jalview.datamodel.SequenceFeature;
+
+import java.util.List;
+
+/**
+ * An interface for a type that returns counts of any value of interest at a
+ * sequence position that can be determined from the sequence character and any
+ * features present at that position
+ * 
+ */
+public interface FeatureCounterI
+{
+  /**
+   * Returns a count of some property of interest, for example
+   * <ul>
+   * <li>the number of variant features at the position</li>
+   * <li>the number of Cath features of status 'True Positive'</li>
+   * <li>1 if the residue is hydrophobic, else 0</li>
+   * <li>etc</li>
+   * </ul>
+   * 
+   * @param residue
+   *          the residue (or gap) at the position
+   * @param a
+   *          list of any sequence features which include the position
+   */
+  int count(String residue, List<SequenceFeature> features);
+
+  /**
+   * Returns a name for the annotation that this is counting, for use as the
+   * displayed label
+   * 
+   * @return
+   */
+  String getName();
+
+  /**
+   * Returns a description for the annotation, for display as a tooltip
+   * 
+   * @return
+   */
+  String getDescription();
+
+  /**
+   * Returns the colour (as [red, green, blue] values in the range 0-255) to use
+   * for the minimum value on histogram bars. If this is different to
+   * getMaxColour(), then bars will have a graduated colour.
+   * 
+   * @return
+   */
+  int[] getMinColour();
+
+  /**
+   * Returns the colour (as [red, green, blue] values in the range 0-255) to use
+   * for the maximum value on histogram bars. If this is the same as
+   * getMinColour(), then bars will have a single colour (not graduated).
+   * 
+   * @return
+   */
+  int[] getMaxColour();
+}