JAL-2228 interface and worker to allow multiple feature types to be counted simultane...

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

diff --git a/src/jalview/workers/FeatureSetCounterI.java b/src/jalview/workers/FeatureSetCounterI.java
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+++ b/src/jalview/workers/FeatureSetCounterI.java
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+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
+package jalview.workers;
+
+import jalview.datamodel.SequenceFeature;
+
+import java.util.List;
+
+/**
+ * Like FeatureCounterI but returns a vector of counts for a set of features
+ * 
+ * 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 FeatureSetCounterI extends ColumnCounterI
+{
+  /**
+   * 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[] getNames();
+
+  /**
+   * Returns a description for the annotation, for display as a tooltip
+   * 
+   * @return
+   */
+  String[] getDescriptions();
+
+  /**
+   * 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();
+}