/*
 * 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.
 */
 
import jalview.workers.FeatureSetCounterI;
import jalview.workers.AlignmentAnnotationFactory;

/*
 * Demonstration of FeatureSetWorker 
 * compute annotation tracks counting number of displayed 
 * features of each type in each column
 */

/*
 * discover features on the current view
 */
 
def featuresVis=jalview.bin.Jalview.currentAlignFrame.getCurrentView().getFeaturesDisplayed().getVisibleFeatures().toList();
assert 'java.util.ArrayList' == featuresVis.class.name

/*
 * A closure that returns a vector for featuresVis of 1 or 0 for any features of type observed
 * Argument should be a list of SequenceFeature 
 */
def hasType = { features -> 
                int[] obs=new int[featuresVis.size()];
                for (sf in features)
                {
                    /*
                     * Here we inspect the type of the sequence feature.
                     * You can also test sf.description, sf.score, sf.featureGroup,
                     * sf.strand, sf.phase, sf.begin, sf.end
                     * or sf.getValue(attributeName) for GFF 'column 9' properties
                     */
                    int pos = 0;
                    for (type in featuresVis) {
                      if (type.equals(sf.type)) {
                      obs[pos]=1;
                      } else {
                      obs[pos]=0;
                      }
                      pos++;
                    }
                }
                obs;
              }
  
/*
 * Closure to generate a counter for feature types in featuresVis 
 * calls hasType to count types in the int[] count(String res, List<SequenceFeature> feats) method  
 */
def getColumnSetCounter = { 
    [
     getNames: { featuresVis as String[] }, 
     getDescriptions:  { featuresVis as String[] },
     getMinColour: { [0, 255, 255] }, // cyan
     getMaxColour: { [0, 0, 255] }, // blue
     count: 
         { res, feats -> 
             hasType.call(feats) 
         }
     ] as FeatureSetCounterI }

/*
 * and register a FeatuerSetCounter instance
 */
AlignmentAnnotationFactory.newCalculator(getColumnSetCounter.call())